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https://en.wikipedia.org/wiki/FKBP8 | FK506-binding protein 8 is a protein that in humans is encoded by the FKBP8 gene.
The protein encoded by this gene is a member of the immunophilin protein family, which play a role in immunoregulation and basic cellular processes involving protein folding and trafficking. Unlike the other members of the family, this encoded protein does not seem to have PPIase/rotamase activity. It may have a role in neurons associated with memory function.
References
Further reading
EC 5.2.1 |
https://en.wikipedia.org/wiki/Kallikrein-5 | Kallikrein-5, formerly known as stratum corneum tryptic enzyme (SCTE), is a serine protease expressed in the epidermis. In humans it is encoded by the KLK5 gene. This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. Its expression is up-regulated by estrogens and progestins. Alternative splicing results in multiple transcript variants encoding the same protein.
KLK5 has been suggested to regulate cell shedding (desquamation) in conjunction with KLK7 and KLK14, given its ability to degrade proteins which form the extracellular component of cell junctions in the stratum corneum. It is proposed that KLK5 regulates this process since it is able to self-activate in addition to activating KLK7 and KLK14.
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: S01.017 |
https://en.wikipedia.org/wiki/ATP5F1A | ATP synthase F1 subunit alpha, mitochondrial is an enzyme that in humans is encoded by the ATP5F1A gene.
Function
This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, using an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel consists of three main subunits (a, b, c). This gene encodes the alpha subunit of the catalytic core. Alternatively spliced transcript variants encoding the same protein have been identified. Pseudogenes of this gene are located on chromosomes 9, 2, and 16.
Structure
The ATP5F1A gene, located on the q arm of chromosome 18 in position 21, is made up of 13 exons and is 20,090 base pairs in length. The ATP5F1A protein weighs 59.7 kDa and is composed of 553 amino acids. The protein is a subunit of the catalytic portion of the F1Fo ATPase, also known as Complex V, which consists of 14 nuclear and 2 mitochondrial -encoded subunits. As an alpha subunit, ATP5F1A is contained within the catalytic F1 portion of the complex. The nomenclature of the enzyme has |
https://en.wikipedia.org/wiki/BACH1 | Transcription regulator protein BACH1 is a protein that in humans is encoded by the BACH1 gene.
Function
This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. The C-terminus of the protein is a leucine zipper of the bzip_maf family. When this protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. Some exons of this gene overlap with some exons from the C21orf41 gene, which is transcribed in an opposite orientation to this gene but does not seem to encode a protein.
See also
Small Maf
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/NFATC3 | Nuclear factor of activated T-cells, cytoplasmic 3 is a protein that in humans is encoded by the NFATC3 gene.
Function
The product of this gene is a member of the nuclear factors of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation and an inducible nuclear component. Other members of this family participate to form this complex also. The product of this gene plays a role in the regulation of gene expression in T cells and immature thymocytes. Four transcript variants encoding distinct isoforms have been identified for this gene.
See also
NFAT
References
Further reading
External links
Transcription factors
Human proteins |
https://en.wikipedia.org/wiki/PCBD1 | Pterin-4-alpha-carbinolamine dehydratase is an enzyme that in humans is encoded by the PCBD1 gene.
Function
This gene encodes pterin-4 alpha-carbinolamine dehydratase, an enzyme involved in phenylalanine hydroxylation. The enzyme regulates the homodimerization of the transcription factor hepatocyte nuclear factor 1 (HNF1).
Clinical significance
Mutations of the PCBD1 gene cause pterin-4 alpha-carbinolamine dehydratase deficiency, one of the forms of tetrahydrobiopterin deficiency.
Interactions
PCBD1 has been shown to interact with DYRK1B and HNF1A.
References
Further reading |
https://en.wikipedia.org/wiki/POU2AF1 | POU domain class 2-associating factor 1 is a protein that in humans is encoded by the POU2AF1 gene. The protein is also termed Oct coactivator from B cells (i.e. OCAB), Oct binding factor 1 (OBF1 or OBF-1), and, as commonly found in the literature, BOB1. BOB1 is a transcriptional coactivator (i.e. a protein that controls the activity of transcription factors) which is expressed principally by B-cell lymphocytes and controls immunoglobulin and other genes critical for these cells expression of CD20, CRISP-3, and CD36. The expression of BOB1 has proven useful for identifying certain lymphomas as being B-cell lymphomas, as exemplified in studies which use BAB1 expression to help identify lymphomas as being diffuse large B-cell lymphomas, not otherwise specified.
Interactions
POU2AF1 has been shown to interact with:
POU2F1 and
SIAH1.
See also
POU domain
POU domain class 2 transcription factors:
POU2F1, POU2F2, POU2F3
References
Further reading |
https://en.wikipedia.org/wiki/PRKCSH | Glucosidase 2 subunit beta is an enzyme that in humans is encoded by the PRKCSH gene.
This gene encodes the beta-subunit of glucosidase II, an N-linked glycan-processing enzyme in the endoplasmic reticulum (ER). This protein is an acidic phospho-protein known to be a substrate for protein kinase C. Mutations in this gene have been associated with the autosomal dominant polycystic liver disease (PCLD). Alternatively spliced transcript variants encoding distinct isoforms have been observed.
References
Further reading
EF-hand-containing proteins |
https://en.wikipedia.org/wiki/HTRA1 | Serine protease HTRA1 is an enzyme that in humans is encoded by the HTRA1 gene. The HTRA1 protein is composed of four distinct protein domains. They are from amino-terminus to carboxyl-terminus an Insulin-like growth factor binding domain, a kazal domain, a trypsin-like peptidase domain and a PDZ domain.
This gene encodes a member of the trypsin family of serine proteases. This protein is a secreted enzyme that is proposed to regulate the availability of insulin-like growth factors (IGFs) by cleaving IGF-binding proteins. It has also been suggested to be a regulator of cell growth.
Mutations of this gene are responsible for the development of CARASIL, a genetic form of cerebral vasculopathy.
References
External links
GeneReviews/NCBI/NIH/UW entry on CARASIL Cerebral Autosomal Recessive Arteriopathy with Subcortical Infarcts and Leukoencephalopathy, Maeda Syndrome
OMIM entries on CARASIL
Further reading |
https://en.wikipedia.org/wiki/PTPRJ | Receptor-type tyrosine-protein phosphatase eta is an enzyme that in humans is encoded by the PTPRJ gene.
Function
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region containing five fibronectin type III repeats, a single transmembrane region, and a single intracytoplasmic catalytic domain, and thus represents a receptor-type PTP. This PTP is present in all hematopoietic lineages, and was shown to negatively regulate T cell receptor signaling possibly through interfering with the phosphorylation of Phospholipase C Gamma 1 (PLCG1) and Linker for Activation of T Cells (LAT). This PTP was also found to dephosphorylate PDGF beta receptor, and may be involved in UV-induced signal transduction.
Interactions
PTPRJ has been shown to interact with CTNND1.
References
Further reading |
https://en.wikipedia.org/wiki/RAD21 | Double-strand-break repair protein rad21 homolog is a protein that in humans is encoded by the RAD21 gene. RAD21 (also known as Mcd1, Scc1, KIAA0078, NXP1, HR21), an essential gene, encodes a DNA double-strand break (DSB) repair protein that is evolutionarily conserved in all eukaryotes from budding yeast to humans. RAD21 protein is a structural component of the highly conserved cohesin complex consisting of RAD21, SMC1A, SMC3, and SCC3 [ STAG1 (SA1) and STAG2 (SA2) in multicellular organisms] proteins, involved in sister chromatid cohesion.
Discovery
rad21 was first cloned by Birkenbihl and Subramani in 1992 by complementing the radiation sensitivity of the rad21-45 mutant fission yeast, Schizosaccharomyces pombe, and the murine and human homologs of S. pombe rad21 were cloned by McKay, Troelstra, van der Spek, Kanaar, Smit, Hagemeijer, Bootsma and Hoeijmakers. The human RAD21 (hRAD21) gene is located on the long (q) arm of chromosome 8 at position 24.11 (8q24.11). In 1997, RAD21 was independently discovered by two groups to be a major component of the chromosomal cohesin complex, and its dissolution by the cysteine protease Separase at the metaphase to anaphase transition results in the separation of sister chromatids and chromosomal segregation.
Structure
RAD21, belongs to a superfamily of eukaryotic and prokaryotic proteins called a-Kleisins, is a nuclear phospho-protein, ranges in size from 278aa in the house lizard (Gekko Japonicus) to 746aa in the killer whale |
https://en.wikipedia.org/wiki/RAD51C | RAD51 homolog C (S. cerevisiae), also known as RAD51C, is a protein which in humans is encoded by the RAD51C gene.
Function
The RAD51C protein is one of five paralogs of RAD51, including RAD51B (RAD51L1), RAD51C (RAD51L2), RAD51D (RAD51L3), XRCC2 and XRCC3. They each share about 25% amino acid sequence identity with RAD51 and each other.
The RAD51 paralogs are all required for efficient DNA double-strand break repair by homologous recombination and depletion of any paralog results in significant decreases in homologous recombination frequency.
RAD51C forms two distinct complexes with other related paralogs: BCDX2 (RAD51B-RAD51C-RAD51D-XRCC2) and CX3 (RAD51C-XRCC3). These two complexes act at two different stages of homologous recombinational DNA repair. The BCDX2 complex is responsible for RAD51 recruitment or stabilization at damage sites. The BCDX2 complex appears to act by facilitating the assembly or stability of the RAD51 nucleoprotein filament.
The CX3 complex acts downstream of RAD51 recruitment to damage sites. The CX3 complex was shown to associate with Holliday junction resolvase activity, probably in a role of stabilizing gene conversion tracts.
The RAD51C gene is one of genes four localized to a region of chromosome 17q23 where amplification occurs frequently in breast tumors. Overexpression of the four genes during amplification has been observed and suggests a possible role in tumor progression. Alternative splicing has been observed for this gene and |
https://en.wikipedia.org/wiki/RBP1 | Retinol binding protein 1, cellular, also known as RBP1, is a protein that in humans is encoded by the RBP1 gene.
Function
RBP1 is the carrier protein involved in the transport of retinol (vitamin A alcohol) from the liver storage site to peripheral tissue. Vitamin A is a fat-soluble vitamin necessary for growth, reproduction, differentiation of epithelial tissues, and vision. The gene harbors four exons encoding 24, 59, 33, and 16 amino acid residues, respectively. The second intervening sequence alone occupies 19 kb of the 21 kb of the gene.
Clinical significance
Cellular retinol-binding protein-1 (CRBP-1) contributes to the maintenance of the differentiative state of endometrial cells through the regulation of bioavailability of retinol. On the converse, loss of CRBP-1 is associated with development of endometrial cancer.
References
Further reading
Lipocalins |
https://en.wikipedia.org/wiki/REG1B | Lithostathine-1-beta is a protein that in humans is encoded by the REG1B gene.
Function
This gene is a type I subclass member of the Reg gene family. The Reg gene family is a multigene family grouped into four subclasses, types I, II, III and IV based on the primary structures of the encoded proteins. This gene encodes a protein that is secreted by the exocrine pancreas. It is associated with islet cell regeneration and diabetogenesis and may be involved in pancreatic lithogenesis. Reg family members REG1A, REGL, PAP and this gene are tandemly clustered on chromosome 2p12 and may have arisen from the same ancestral gene by gene duplication.
References
Further reading |
https://en.wikipedia.org/wiki/RFC2 | Replication factor C subunit 2 is a protein that in humans is encoded by the RFC2 gene.
Function
The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins, proliferating cell nuclear antigen (PCNA) and replication factor C (RFC). RFC, also called activator 1, is a protein complex consisting of five distinct subunits of 145, 40, 38, 37, and 36.5 kD. This gene encodes the 40 kD subunit, which has been shown to be responsible for binding ATP. Deletion of this gene has been associated with Williams syndrome. Alternatively spliced transcript variants encoding distinct isoforms have been described.
Interactions
RFC2 has been shown to interact with BRD4, CHTF18, PCNA, RFC4 and RFC5.
References
Further reading |
https://en.wikipedia.org/wiki/RFX1 | MHC class II regulatory factor RFX1 is a protein that, in humans, is encoded by the RFX1 gene located on the short arm of chromosome 19.
Structure
The RFX1 gene is a member of the regulatory factor X (RFX) gene family, which encodes transcription factors that contain five conserved domains including a highly conserved, centrally located, winged helix DNA binding domain as well as a dimerization domain located in the C-terminal region of the sequence. Apart from the five conserved domains, the RFX proteins diverge significantly. The DNA binding and dimerization domains of the RFX family proteins show no similarities to the other domains with the same functions in other proteins.
Species distribution
The RFX protein family is conserved in S. pombe, S. cerevisiae, C. elegans, mice and humans. There are seven known RFX proteins in humans, five in mice, and one in C. elegans as well as one in each of the two species of yeast.
Function
The protein encoded by this gene is structurally related to regulatory factors X2, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with RFX family members X2, X3, and X5, but not with X4. This protein binds to the Xboxes of MHC class II genes and is essential for their expression. Also, it can bind to an inverted repeat that is required for expression of hepatitis B virus genes. The RFX proteins were originally cloned and characterized due to their high affinity for a cis-acting promoter |
https://en.wikipedia.org/wiki/BRD2 | Bromodomain-containing protein 2 is a protein that in humans is encoded by the BRD2 gene. BRD2 is part of the Bromodomain and Extra-Terminal motif (BET) protein family that also contains BRD3, BRD4, and BRDT in mammals
Early descriptions demonstrated that BRD2 gene product is a mitogen-activated kinase which localizes to the nucleus. The gene maps to the major histocompatibility complex (MHC) class II region on chromosome 6p21.3 but sequence comparison suggests that the protein is not involved in the immune response. Homology to the Drosophila gene female sterile homeotic suggests that this human gene may be part of a signal transduction pathway involved in growth control.
Functions
BRD2 has been implicated in cancer.
BRD2 loss in mice causes obesity without diabetes for unknown reasons.
BRD2 may have functional overlap with close homolog BRD3.
BRD2 function is blocked by BET inhibitors.
Interactions
BRD2 has been shown to interact with E2F2, and many transcription factors including GATA1.
References
External links
Further reading |
https://en.wikipedia.org/wiki/RP2%20%28gene%29 | Protein XRP2 is a protein that in humans is encoded by the RP2 gene.
Function
The RP2 locus has been implicated as one cause of X-linked retinitis pigmentosa. The predicted gene product shows homology with human cofactor C, a protein involved in the ultimate step of beta-tubulin folding. Progressive retinal degeneration may therefore be due to the accumulation of incorrectly folded photoreceptor or neuron-specific tubulin isoforms, followed by progressive cell death. The RP2 protein is also involved in regulating the function and extension of the outer segment of cone photoreceptors in mice.
References
Further reading |
https://en.wikipedia.org/wiki/S100P | S100 calcium-binding protein P (S100P) is a protein that in humans is encoded by the S100P gene.
Function
The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21; however, this gene is located at 4p16. This protein, in addition to binding Ca2+, also binds Zn2+ and Mg2+. This protein may play a role in the etiology of prostate cancer.
Interactions
S100P has been shown to interact with EZR and RAGE. The interactions between S100P and RAGE are disrupted by cromolyn and pentamidine.
References
Further reading
S100 proteins |
https://en.wikipedia.org/wiki/PARD6A | Partitioning defective 6 homolog alpha is a protein that in humans is encoded by the PARD6A gene.
Function
This gene is a member of the PAR6 family and encodes a protein with a PSD95/Discs-large/ZO1 (PDZ) domain and a semi-Cdc42/Rac interactive binding (CRIB) domain. This cell membrane protein is involved in asymmetrical cell division and cell polarization processes as a member of a multi-protein complex. The protein also has a role in the epithelial-to-mesenchymal transition (EMT) that characterizes the invasive phenotype associated with metastatic carcinomas. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.
A recent study shows that Par6 associates with PKC-ι but not with PKC-zeta in melanoma. Oncogenic PKC-iota can promote melanoma cell invasion by up-regulating PKC-ι/Par6 pathway during EMT. PKC-ι inhibition or knockdown resulted an increase E-cadherin and RhoA levels while decreasing total Vimentin, phophorylated Vimentin (S39) and Par6 in metastatic melanoma cells. These results suggested that PKC-ι is involved in signaling pathways which upregulate EMT in melanoma.
Interactions
PARD6A has been shown to interact with:
CDC42,
ECT2
Protein kinase Mζ, and
RAC1.
Protein kinase C-ι.
References
Further reading |
https://en.wikipedia.org/wiki/HDAC7 | Histone deacetylase 7 is an enzyme that in humans is encoded by the HDAC7 gene.
Function
Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene has sequence homology to members of the histone deacetylase family. This gene is orthologous to mouse HDAC7 gene whose protein promotes repression mediated via transcriptional corepressor SMRT. Multiple alternatively spliced transcript variants encoding several isoforms have been found for this gene. HDAC7 has both structural and functional similarity to HDACs 4, 5, and 9, as these four HDACs make up the Class IIa of HDACs in higher eukaryotes. Class IIa HDACs are phosphorylated by calcium/calmodulin dependent-kindase (CaMK) and protein kinase D (PKD) in response to kinase-dependent signaling. HDAC7 possesses little intrinsic deacetylase activity and therefore requires association with the class I HDAC, HDAC3 in order to suppress gene expression. It has been demonstrated through crystal structures of the human HDAC7 that the catalytic domain of HDAC7 has an additional class IIa HDAC-specific zinc binding motif adjacent to the active site. This is most likely to allow for substrate recognition and protein-protein interactions that are necessary for class IIa HDAC enzymes.
Alternative functions
Although HDAC7 has shown to have little i |
https://en.wikipedia.org/wiki/ERAP1 | Type 1 tumor necrosis factor receptor shedding aminopeptidase regulator, also known as endoplasmic reticulum aminopeptidase 1 (ARTS-1), is a protein which in humans is encoded by the ARTS-1 gene.
Endoplasmic reticulum amino peptidase 1 is active in the endoplasmic reticulum, which is involved in protein processing and transport. This protein is an aminopeptidase, which is an enzyme that cleaves peptides at the N-terminal into smaller fragments called amino acids.
Nomenclature
ARTS1 is also known as:
ER aminopeptidase 1 (ERAP1) the name accepted by the Hugo Gene Nomenclature Committee
ER aminopeptidase associated with antigen processing (ERAAP) in mice
Adipocyte-derived leucine aminopeptidase (ALAP)
Puromycin-insensitive leucine aminopeptidase (PILS-AP)
Function
ERAP1 has two major functions in the immune system:
First, ERAP1 cleaves several proteins called cytokine receptors on the surface of cells. Cleaving these receptors reduces their ability to transmit chemical signals into the cell, which affects the process of inflammation.
Second, ERAP1 trims peptides within the endoplasmic reticulum so that they can be loaded onto major histocompatibility complex (MHC) class I. These peptides are attached to MHC class I in the endoplasmic reticulum and exported to the cell surface, where they are displayed to the immune system. If the immune system recognizes the peptides as foreign (such as viral or bacterial peptides), it responds by triggering the infected cell to sel |
https://en.wikipedia.org/wiki/PRPF40A | Pre-mRNA-processing factor 40 homolog A is a protein that in humans is encoded by the PRPF40A gene.
Interactions
PRPF40A has been shown to interact with Huntingtin.
References
Further reading |
https://en.wikipedia.org/wiki/MMP26 | Matrix metalloproteinase-26 also known as matrilysin-2 and endometase is an enzyme that in humans is encoded by the MMP26 gene.
Function
Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. The encoded protein degrades type IV collagen, fibronectin, fibrinogen, casein, vitronectin, alpha 1-antitrypsin (A1AT), alpha 2-macroglobulin (A2M), and insulin-like growth factor-binding protein 1 (IGFBP), and activates MMP9 by cleavage. The protein differs from most MMP family members in that it lacks a conserved C-terminal protein domain.
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: M10.029
Matrix metalloproteinases |
https://en.wikipedia.org/wiki/DAZ3 | Deleted in azoospermia protein 3 is a protein that in humans is encoded by the DAZ3 gene.
This gene is a member of the DAZ gene family and is a candidate for the human Y-chromosomal azoospermia factor (AZF). Its expression is restricted to premeiotic germ cells, particularly in spermatogonia. It encodes an RNA-binding protein that is important for spermatogenesis. Four copies of this gene are found on chromosome Y within palindromic duplications; one pair of genes is part of the P2 palindrome and the second pair is part of the P1 palindrome. Each gene contains a 2.4 kb repeat including a 72-bp exon, called the DAZ repeat; the number of DAZ repeats is variable and there are several variations in the sequence of the DAZ repeat. Each copy of the gene also contains a 10.8 kb region that may be amplified; this region includes five exons that encode an RNA recognition motif (RRM) domain. This gene contains one copy of the 10.8 kb repeat.
References
Further reading |
https://en.wikipedia.org/wiki/GOPC | Golgi-associated PDZ and coiled-coil motif-containing protein is a protein that in humans is encoded by the GOPC gene.
PIST is a PDZ domain-containing Golgi protein. PDZ domains contain approximately 90 amino acids and bind the extreme C terminus of proteins in a sequence-specific manner.[supplied by OMIM]
Interactions
GOPC has been shown to interact with GRID2, BECN1, RHOQ, ACCN3, Cystic fibrosis transmembrane conductance regulator and CSPG5.
References
Further reading |
https://en.wikipedia.org/wiki/Calpain%20small%20subunit%201 | Calpain small subunit 1 (CSS1) is a protein that in humans is encoded by the CAPNS1 gene.
Function
Calpains are a ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. Calpain families have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. Calpain I and II are heterodimeric with distinct large subunits associated with common small subunits, all of which are encoded by different genes. The small regulatory subunit consists of an N-terminal domain, containing about 30% glycine residues and a C-terminal Ca-binding domain. Two transcript variants encoding the same protein have been identified for this gene.
Functions
Myotonic dystrophy
This gene encodes a small subunit common to both calpain I and II and is associated with myotonic dystrophy.
Biomarker
'Elevated expression of CAPNS1 has been found to be associated with progression of various cancers such as hepatocellular and renal carcinoma.
References
External links
Further reading
EF-hand-containing proteins |
https://en.wikipedia.org/wiki/SHB%20%28gene%29 | SH2 domain-containing adapter protein B is a protein that in humans is encoded by the SHB gene.
Interactions
SHB (gene) has been shown to interact with:
EPS8,
Fibroblast growth factor receptor 1,
Linker of activated T cells,
Lymphocyte cytosolic protein 2,
PIK3R1,
Src,
VAV1, and
ZAP-70.
References
Further reading |
https://en.wikipedia.org/wiki/SIAH2 | E3 ubiquitin-protein ligase SIAH2 is an enzyme that in humans is encoded by the SIAH2 gene.
Function
This gene encodes a protein that is a member of the seven in absentia homolog (SIAH) family. The protein is an E3 ligase and is involved in ubiquitination and proteasome-mediated degradation of specific proteins. The activity of this ubiquitin ligase has been implicated in regulating cellular response to hypoxia.
Interactions
SIAH2 has been shown to interact with PEG10, Synaptophysin, PEG3 and VAV1.
References
Further reading |
https://en.wikipedia.org/wiki/Excitatory%20amino%20acid%20transporter%203 | Excitatory amino acid transporter 3 (EAAT3), is a protein that in humans is encoded by the SLC1A1 gene.
Tissue distribution
EAAT3 is expressed on the plasma membrane of neurons, specifically on the dendrites and axon terminals.
Function
Excitatory amino acid transporter 3 is a member of the high-affinity glutamate transporters which plays an essential role in transporting glutamate across plasma membranes in neurons. In the brain, excitatory amino acid transporters are crucial in terminating the postsynaptic action of the neurotransmitter glutamate, and in maintaining extracellular glutamate concentrations below neurotoxic levels. EAAT3 also transports aspartate, and mutations in this gene are thought to cause dicarboxylic aminoaciduria, also known as glutamate-aspartate transport defect. EAAT3 is also the major route of neuronal cysteine uptake. Cysteine is a component of the major antioxidant glutathione, and mice lacking EAAT3 exhibit reduced levels of glutathione in neurons, increased oxidative stress, and age-dependent loss of neurons, especially neurons of the substantia nigra. A meta-analysis identified a small but significant association between a polymorphism of the gene SLC1A1 and Obsessive-Compulsive Disorder.
Interactions
SLC1A1 has been shown to interact with ARL6IP5.
See also
Excitatory amino acid transporter
Glutamate transporter
Solute carrier family
References
Further reading
Amphetamine
Solute carrier famil |
https://en.wikipedia.org/wiki/SLC22A1 | Solute carrier family 22 member 1 is a protein that in humans is encoded by the gene SLC22A1.
Function
Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. Two transcript variants encoding two different isoforms have been found for this gene, but only the longer variant encodes a functional transporter.
It is also required for the uptake of metformin by cells.
See also
Solute carrier family
Organic cation transport proteins
References
Further reading
Solute carrier family |
https://en.wikipedia.org/wiki/SMARCE1 | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 is a protein that in humans is encoded by the SMARCE1 gene.
Function
The protein encoded by this gene is part of the large ATP-dependent chromatin remodeling complex SWI/SNF, which is required for transcriptional activation of genes normally repressed by chromatin. The encoded protein, either alone or when in the SWI/SNF complex, can bind to 4-way junction DNA, which is thought to mimic the topology of DNA as it enters or exits the nucleosome. The protein contains a DNA-binding HMG domain, but disruption of this domain does not abolish the DNA-binding or nucleosome-displacement activities of the SWI/SNF complex. Unlike most of the SWI/SNF complex proteins, this protein has no yeast counterpart.
Interactions
SMARCE1 has been shown to interact with Estrogen receptor alpha, SMARCB1 and SMARCA4.
References
Further reading |
https://en.wikipedia.org/wiki/SOX4 | Transcription factor SOX-4 is a protein that in humans is encoded by the SOX4 gene.
Function
This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins, such as syndecan binding protein (syntenin). The protein may function in the apoptosis pathway leading to cell death as well as to tumorigenesis and may mediate downstream effects of parathyroid hormone (PTH) and PTH-related protein (PTHrP) in bone development. The solution structure has been resolved for the HMG-box of a similar mouse protein.
Sox4 is expressed in lymphocytes (B and T) and is required for B lymphocyte development.
Clinical significance
A genomic region close to the SOX4 gene has been associated with endometrial cancer development.
Interactions
SOX4 has been shown to interact with SDCBP.
See also
SOX gene family
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/SRI%20%28gene%29 | Sorcin is a protein that in humans is encoded by the SRI gene.
Interactions
SRI (gene) has been shown to interact with Ryanodine receptor 2, ANXA7 and GCA.
References
Further reading
Penta-EF-hand proteins |
https://en.wikipedia.org/wiki/Vesicle-associated%20membrane%20protein%207 | Vesicle-associated membrane protein 7 (VAMP-7), is a protein that in humans is encoded by the VAMP7 gene also known as the or SYBL1 gene.
Function
VAMP-7 is a transmembrane protein that is a member of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) family. VAMP-7 localizes to late endosomes and lysosomes and is involved in the fusion of transport vesicles to their target membranes.
Interactions
VAMP-7 has been shown to interact with SNAP23 and AP3D1.
References
Further reading
External links |
https://en.wikipedia.org/wiki/TAF5 | Transcription initiation factor TFIID subunit 5 is a protein that in humans is encoded by the TAF5 gene.
Function
Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes an integral subunit of TFIID associated with all transcriptionally competent forms of that complex. This subunit interacts strongly with two TFIID subunits that show similarity to histones H3 and H4, and it may participate in forming a nucleosome-like core in the TFIID complex.
Interactions
TAF5 has been shown to interact with:
TAF6,
TAF9, and
TAF15,
TATA binding protein.
References
Further reading
External links |
https://en.wikipedia.org/wiki/TFAM | Mitochondrial transcription factor A, abbreviated as TFAM or mtTFA, is a protein that in humans is encoded by the TFAM gene.
Function
This gene encodes a mitochondrial transcription factor that is a key activator of mitochondrial transcription as well as a participant in mitochondrial genome replication. TFAM binds mitochondrial promoter DNA to aid transcription of the mitochondrial genome. Studies in mice have demonstrated that this gene product is required to regulate the mitochondrial genome copy number and is essential for embryonic development. A mouse model for Kearns–Sayre syndrome was produced when expression of this gene was eliminated by targeted disruption in heart and muscle cells.
TFAM is a double box High-mobility group DNA-binding and bending protein. This bending action is important for mitochondrial transcription initiation in mammals, but not in yeasts with the homolog Abf2. TFAM may also participate in the packaging of the mitochondrial genome, as its binding activity is non-sequence-specific.
Interactions
TFAM has been shown to interact with TFB1M and TFB2M.
References
Further reading
External links |
https://en.wikipedia.org/wiki/Thrombospondin-2 | Thrombospondin-2 is a protein that in humans is encoded by the THBS2 gene.
The protein encoded by this gene belongs to the thrombospondin family. It is a disulfide-linked homotrimeric glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. The role of the protein in cancer is controversial, contrasting studies show positive and negative roles for cancer development. Studies of the mouse counterpart suggest that this protein may modulate the cell surface properties of mesenchymal cells and be involved in cell adhesion and migration.
Interactions
THBS2 has been shown to interact with MMP2.
References
Further reading
Thrombospondins |
https://en.wikipedia.org/wiki/TIAL1 | Nucleolysin TIAR is a protein that in humans is encoded by the TIAL1 gene.
The protein encoded by this gene is a member of a family of RNA-binding proteins, has three RNA recognition motifs (RRMs), and binds adenine and uridine-rich elements in mRNA and pre-mRNAs of a wide range of genes. It regulates various activities including translational control, splicing and apoptosis. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. The different isoforms have been shown to function differently with respect to post-transcriptional silencing.
References
Further reading
External links |
https://en.wikipedia.org/wiki/UBE2N | Ubiquitin-conjugating enzyme E2 N is a protein that in humans is encoded by the UBE2N gene.
Function
The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Studies in mouse suggest that this protein plays a role in DNA postreplication repair.
Interactions
UBE2N has been shown to interact with:
AURKA,
HLTF,
TRAF2,
TRAF6, and
UBE2V1.
References
Further reading |
https://en.wikipedia.org/wiki/VAV2 | Guanine nucleotide exchange factor VAV2 is a protein that in humans is encoded by the VAV2 gene.
VAV2 is the second member of the VAV oncogene family. Unlike VAV1, which is expressed exclusively in hematopoietic cells, VAV2 transcripts were found in most tissues.
Interactions
VAV2 has been shown to interact with CD19 and Grb2.
References
Further reading
External links |
https://en.wikipedia.org/wiki/SF1%20%28gene%29 | Splicing factor 1 also known as zinc finger protein 162 (ZFM162) is a protein that in humans is encoded by the SF1 gene.
Splicing factor SF1 is involved in the ATP-dependent formation of the spliceosome complex. SF1 gene is necessary to make the bipotential gonad ; but while SF1 levels decline in the genital ridge of XX mouse embryos, the SF1 gene stays on the developing testes. SF 1 (transcription factor) appears to be active in masculining both the Leydig cells and Sertoli cells. In Sertoli cells with the SOX9 protein it elevates the level of AMH transcription. In Leydig cells it activates the gene encoding the enzyme that make testosterone hormone.
Interactions
SF1 (gene) has been shown to interact with Ewing sarcoma breakpoint region 1, U2AF2, Testis determining factor, and Transcription elongation regulator 1.
References
Further reading |
https://en.wikipedia.org/wiki/ZMYM2 | Zinc finger MYM-type protein 2 is a protein that in humans is encoded by the ZMYM2 gene.
See also
Chromosome 13 (human)
Myeloproliferative neoplasm
Zinc finger protein
References
Further reading |
https://en.wikipedia.org/wiki/HIST2H4A | Histone H4 is a protein that in humans is encoded by the HIST2H4A gene.
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a member of the histone H4 family. Transcripts from this gene lack polyA tails; instead, they contain a palindromic termination element. This gene is found in a histone cluster on chromosome 1. This gene is one of four histone genes in the cluster that are duplicated; this record represents the centromeric copy.
References
Further reading |
https://en.wikipedia.org/wiki/CUL2 | Cullin-2 is a protein that in humans is encoded by the CUL2 gene.
Interactions
CUL2 has been shown to interact with:
CAND1,
DCUN1D1,
RBX1,
SAP130,
TCEB2 and
Von Hippel-Lindau tumor suppressor.
References
External links
Further reading |
https://en.wikipedia.org/wiki/PPM1D | Protein phosphatase 1D is an enzyme that in humans is encoded by the PPM1D gene.
The protein encoded by this gene is a member of the PP2C family of Ser/Thr protein phosphatases. PP2C family members are known to be negative regulators of cell stress response pathways. The expression of this gene is induced in a p53-dependent manner in response to various environmental stresses. While being induced by tumor suppressor protein TP53/p53, this phosphatase negatively regulates the activity of p38 MAP kinase (MAPK/p38) through which it reduces the phosphorylation of p53, and in turn suppresses p53-mediated transcription and apoptosis. This phosphatase thus mediates a feedback regulation of p38-p53 signaling that contributes to growth inhibition and the suppression of stress induced apoptosis. This gene is located in a chromosomal region known to be amplified in breast cancer. The amplification of this gene has been detected in both breast cancer cell line and primary breast tumors, which suggests a role of this gene in cancer development.
Interactions
PPM1D has been shown to interact with CDC5L.
References
Further reading |
https://en.wikipedia.org/wiki/EIF2B2 | Translation initiation factor eIF-2B subunit beta is a protein that in humans is encoded by the EIF2B2 gene.
Function
Eukaryotic initiation factor-2B (EIF2B) is a GTP exchange protein essential for protein synthesis. It consists of alpha (EIF2B1; MIM 606686), beta (EIF2B2), gamma (EIF2B3; MIM 606273), delta (EIF2B4; MIM 606687), and epsilon (EIF2B5; MIM 603945) subunits. EIF2B activates its EIF2 (see MIM 603907) substrate by exchanging EIF2-bound GDP for GTP.
Interactions
EIF2B2 has been shown to interact with EIF2B5 and NCK1.
References
Further reading |
https://en.wikipedia.org/wiki/HIST1H2BJ | Histone H2B type 1-J is a protein that in humans is encoded by the HIST1H2BJ gene.
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the histone microcluster on chromosome 6p21.33.
References
Further reading |
https://en.wikipedia.org/wiki/ADAM33 | Disintegrin and metalloproteinase domain-containing protein 33 is an enzyme that in humans is encoded by the ADAM33 gene.
Function
This gene encodes a member of the ADAM (a disintegrin and metalloprotease domain) family. Members of this family are membrane-anchored proteins structurally related to snake venom disintegrins, and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. This protein is a type I transmembrane protein implicated in asthma and bronchial hyperresponsiveness. Alternative splicing of this gene results in two transcript variants encoding different isoforms.
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: M12.244 |
https://en.wikipedia.org/wiki/RASSF5 | Ras association domain-containing protein 5 is a protein that in humans is encoded by the RASSF5 or F5 gene.
Function
This gene is a member of the Ras association domain family. It functions as a tumor suppressor, and is inactivated in a variety of cancers. The encoded protein localizes to centrosomes and microtubules, and associates with the GTP-activated forms of Ras, Rap1, and several other Ras-like small GTPases. The protein regulates lymphocyte adhesion and suppresses cell growth in response to activated Rap1 or Ras. Multiple transcript variants encoding different isoforms have been found for this gene.
Interactions
RASSF5 has been shown to interact with RRAS, RAP2A, MRAS and RASSF1.
References
Further reading |
https://en.wikipedia.org/wiki/HIST1H2BK | Histone H2B type 1-K is a protein that in humans is encoded by the HIST1H2BK gene.
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene encodes a member of the histone H2B family. This gene is found in the histone microcluster on chromosome 6p21.33.
Interactions
HIST1H2BK has been shown to interact with HIRA.
References
Further reading |
https://en.wikipedia.org/wiki/ADD2 | Beta-adducin is a protein that in humans is encoded by the ADD2 gene.
Function
Adducins are heteromeric proteins composed of different subunits referred to as adducin alpha, beta, and gamma. The three subunits are encoded by distinct genes and belong to a family of membrane skeletal proteins involved in the assembly of spectrin-actin network in erythrocytes and at sites of cell-cell contact in epithelial tissues.
While adducins alpha and gamma are ubiquitously expressed, the expression of adducin beta is restricted to brain and hematopoietic tissues. Adducin, originally purified from human erythrocytes, was found to be a heterodimer of adducins alpha and beta. Polymorphisms resulting in amino acid substitutions in these two subunits have been associated with the regulation of blood pressure in an animal model of hypertension. Heterodimers consisting of alpha and gamma subunits have also been described. Structurally, each subunit is composed of two distinct domains.
The amino-terminal region is protease resistant and globular in shape, while the carboxy-terminal region is protease sensitive. The latter contains multiple phosphorylation sites for protein kinase C, the binding site for calmodulin, and is required for association with spectrin and actin. Various adducin beta mRNAs, alternatively spliced at 3' end and/or internally spliced and encoding different isoforms, have been described. The functions of all the different isoforms are not known.
Interactions
A |
https://en.wikipedia.org/wiki/CDKN2C | Cyclin-dependent kinase 4 inhibitor C is an enzyme that in humans is encoded by the CDKN2C gene.
Function
The protein encoded by this gene is a member of the INK4 family of cyclin-dependent kinase inhibitors. This protein has been shown to interact with CDK4 or CDK6, and prevent the activation of the CDK kinases, thus function as a cell growth regulator that controls cell cycle G1 progression. Ectopic expression of this gene was shown to suppress the growth of human cells in a manner that appears to correlate with the presence of a wild-type RB1 function. Studies in the knockout mice suggested the roles of this gene in regulating spermatogenesis, as well as in suppressing tumorigenesis. Two alternatively spliced transcript variants of this gene, which encode an identical protein, have been reported.
Interactions
CDKN2C has been shown to interact with Cyclin-dependent kinase 4 and Cyclin-dependent kinase 6.
References
Further reading
External links
Cell cycle regulators |
https://en.wikipedia.org/wiki/Collagen%2C%20type%20VI%2C%20alpha%203 | Collagen alpha-3(VI) chain is a protein that in humans is encoded by the COL6A3 gene. This protein is an alpha chain of type VI collagen that aids in microfibril formation. As part of type VI collagen, this protein has been implicated in Bethlem myopathy, Ullrich congenital muscular dystrophy (UCMD), and other diseases related to muscle and connective tissue.
Structure
This gene encodes the alpha 3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha 3 chain of type VI collagen is much larger than the alpha 1 and 2 chains. This difference in size is largely due to an increase in the number of subdomains, similar to von Willebrand Factor type A domains, found in the amino terminal globular domain of all the alpha chains. In addition to the full length transcript, four transcript variants have been identified that encode proteins with N-terminal globular domains of varying sizes.
Function
The alpha 3 type VI chain has been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Microfibril formation has been traced to interactions between its N-terminal subdomain N5 and its C-terminal C5 domain in adjacent type VI collagen monomers.
Clinical significance
Mutations in the type VI collagen genes are associated with Bethlem myopathy and Ullrich congenital muscular dystrophy (UCMD). Typically, both Bethlem myopathy |
https://en.wikipedia.org/wiki/Collagen%2C%20type%20IX%2C%20alpha%201 | Collagen alpha-1(IX) chain is a protein that in humans is encoded by the COL9A1 gene.
This gene encodes one of the three alpha chains of type IX collagen, a collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene may be associated with multiple epiphyseal dysplasia. Two transcript variants have been identified for this gene.
References
External links
GeneReviews/NCBI/NIH/UW entry on Multiple Epiphyseal Dysplasia, Dominant
GeneReviews/NCBI/NIH/UW entry on Stickler Syndrome
Further reading
Collagens |
https://en.wikipedia.org/wiki/CRYGC | Crystallin, gamma C, also known as CRYGC, is a protein which in humans is encoded by the CRYGC gene.
Function
Crystallins are separated into two classes: taxon-specific, or enzyme, and ubiquitous. The latter class constitutes the major proteins of vertebrate eye lens and maintains the transparency and refractive index of the lens. Since lens central fiber cells lose their nuclei during development, these crystallins are made and then retained throughout life, making them extremely stable proteins. Mammalian lens crystallins are divided into alpha, beta, and gamma families; beta and gamma crystallins are also considered as a superfamily. Alpha and beta families are further divided into acidic and basic groups. Seven protein regions exist in crystallins: four homologous motifs, a connecting peptide, and N- and C-terminal extensions. Gamma-crystallins are a homogeneous group of highly symmetrical, monomeric proteins typically lacking connecting peptides and terminal extensions. They are differentially regulated after early development. Four gamma-crystallin genes (gamma-A through gamma-D) and three pseudogenes (gamma-E, gamma-F, gamma-G) are organized in a genomic segment as a gene cluster. Whether due to aging or mutations in specific genes, gamma-crystallins have been involved in cataract formation.
Interactions
CRYGC has been shown to interact with CRYBB2, CRYAA and CRYAB.
References
External links
Further reading |
https://en.wikipedia.org/wiki/CSPG4 | Chondroitin sulfate proteoglycan 4, also known as melanoma-associated chondroitin sulfate proteoglycan (MCSP) or neuron-glial antigen 2 (NG2), is a chondroitin sulfate proteoglycan that in humans is encoded by the CSPG4 gene.
Function
CSPG4 plays a role in stabilizing cell-substratum interactions during early events of melanoma cell spreading on endothelial basement membranes. It represents an integral membrane chondroitin sulfate proteoglycan expressed by human malignant melanoma cells.
Implications in disease
CSPG4/NG2 is also a hallmark protein of oligodendrocyte progenitor cells (OPCs) and OPC dysfunction has been implicated as a candidate pathophysiological mechanism of familial schizophrenia. A research group investigating the role of genetics in schizophrenia, reported, two rare missense mutations in CSPG4 gene, segregating within families (CSPG4A131T and CSPG4V901G mutations). The researchers also demonstrate that the induced pluripotent stem cells (iPSCs)-derived OPCs from CSPG4A131T mutation carriers exhibited abnormal post-translational processing, subcellular localization of the mutant NG2 protein, aberrant cellular morphology, and a decreased cell viability and myelination potential. In vivo diffusion tensor imaging of the brain of CSPG4A131T mutation carriers demonstrated a reduced white matter integrity compared to the unaffected sibling and matched general population controls.
See also
NG2-glia
References
Further reading
External links |
https://en.wikipedia.org/wiki/Cochlin | Cochlin is a protein that in humans is encoded by the COCH gene. It is an extracellular matrix (ECM) protein highly abundant in the cochlea and vestibule of the inner ear, constituting the major non-collagen component of the ECM of the inner ear. The protein is highly conserved in human, mouse, and chicken, showing 94% and 79% amino acid identity of human to mouse and chicken sequences, respectively.
Structure
Cochlin contains three protein domains: an N-terminal LCCL domain, and two copies of Von Willebrand factor type A domains.
Function
The gene is expressed in spindle-shaped cells located along nerve fibers between the auditory ganglion and sensory epithelium. These cells accompany neurites at the habenula perforata, the opening through which neurites extend to innervate hair cells. This and the pattern of expression of this gene in chicken inner ear paralleled the histologic findings of acidophilic deposits, consistent with mucopolysaccharide ground substance, in temporal bones from DFNA9 (autosomal dominant nonsyndromic sensorineural deafness 9) patients. Mutations that cause DFNA9 have been reported in this gene.
Cochlin has been identified in the trabecular meshwork (TM) of glaucoma patients, but not in healthy controls. The TM is a filter like area of tissue in the eye; cochlin may have a role in cell adhesion, mechanosensation, and modulation of the TM filter.
It is also expressed in follicular dendritic cells in spleen and lymph nodes. Here, cochlin is cleave |
https://en.wikipedia.org/wiki/CYTH1 | Cytohesin-1 formerly known as Pleckstrin homology, Sec7 and coiled/coil domains 1 (PSCD1) is a protein that in humans is encoded by the CYTH1 gene.
Function
Cytohesin-1 (CYTH1) is a member of the cytohesin family. Members of this family have identical structural organization that consists of an N-terminal coiled-coil motif, a central Sec7 domain, and a C-terminal pleckstrin homology (PH) domain. The coiled-coil motif is involved in homodimerization, the Sec7 domain contains guanine-nucleotide exchange protein (GEP) activity, and the PH domain interacts with phospholipids and is responsible for association of CYTHs with membranes. Members of this family appear to mediate the regulation of protein sorting and membrane trafficking. The CYTH1 is highly expressed in natural killer and peripheral T cells, and regulates the adhesiveness of integrins at the plasma membrane of lymphocytes. CYTH1 protein is 83% homologous to CYTH2.
Interactions
CYTH1 has been shown to interact with:
ARFRP1,
CD18, and
TRIM23.
References
Further reading |
https://en.wikipedia.org/wiki/TRIP10 | Cdc42-interacting protein 4 is a protein that in humans is encoded by the TRIP10 gene.
Interactions
TRIP10 has been shown to interact with STAT3, Wiskott-Aldrich syndrome protein, Huntingtin, CDC42, AKAP9 and RHOQ.
References
Further reading |
https://en.wikipedia.org/wiki/KIF23 | Kinesin-like protein KIF23 is a protein that in humans is encoded by the KIF23 gene.
Function
In cell division
KIF23 (also known as Kinesin-6, CHO1/MKLP1, C. elegans ZEN-4 and Drosophila Pavarotti) is a member of kinesin-like protein family. This family includes microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. This protein has been shown to cross-bridge antiparallel microtubules and drive microtubule movement in vitro. Alternate splicing of this gene results in two transcript variants encoding two different isoforms, better known as CHO1, the larger isoform and MKLP1, the smaller isoform. KIF23 is a plus-end directed motor protein expressed in mitosis, involved in the formation of the cleavage furrow in late anaphase and in cytokinesis. KIF23 is part of the centralspindlin complex that includes PRC1, Aurora B and 14-3-3 which cluster together at the spindle midzone to enable anaphase in dividing cells.
In neurons
In neuronal development KIF23 is involved in the transport of minus-end distal microtubules into dendrites and is expressed exclusively in cell bodies and dendrites. Knockdown of KIF23 by antisense oligonucleotides and by siRNA both cause a significant increase in axon length and a decrease in dendritic phenotype in neuroblastoma cells and in rat neurons. In differentiating neurons, KIF23 restricts the movement of short microtubules into axons by acting as a "brake" against the driving |
https://en.wikipedia.org/wiki/KLK4 | Kallikrein-related peptidase 4 is a protein which in humans is encoded by the KLK4 gene.
Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. In particular, they may serve as biomarkers for both prostate cancer and breast cancer.
This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. In some tissues its expression is hormonally regulated. The expression pattern of a similar mouse protein in murine developing teeth supports a role for the protein in the degradation of enamel proteins. Alternate splice variants for this gene have been described, but their biological validity has not been determined.
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: S01.251 |
https://en.wikipedia.org/wiki/GIT2 | ARF GTPase-activating protein GIT2 is an enzyme that in humans is encoded by the GIT2 gene.
Function
This gene encodes a member of the GIT protein family. GIT proteins interact with G protein-coupled receptor kinases and possess ADP-ribosylation factor (ARF) GTPase-activating protein (GAP) activity. This gene undergoes extensive alternative splicing; although ten transcript variants have been described, the full length sequence has been determined for only four variants. The various isoforms have functional differences, with respect to ARF GAP activity and to G protein-coupled receptor kinase 2 binding.
Model organisms
Model organisms have been used in the study of GIT2 function. A conditional knockout mouse line, called Git2Gt(XG510)Byg was generated as part of the International Knockout Mouse Consortium program — a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists — at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Mice lacking Git2 had no significant defects in viability or fertility, so further tests were carried out and four significant phenotypes were reported:
Mutant mice had differences in their clinical blood chemistry compared to wildtype control mice.
Mutant male mice had a decrease in white blood cell count.
An increased thickness in hippocampus was observed.
Mutant female mice were slower to r |
https://en.wikipedia.org/wiki/SETDB1 | Histone-lysine N-methyltransferase SETDB1 is an enzyme that in humans is encoded by the SETDB1 gene. SETDB1 is also known as KMT1E or H3K9 methyltransferase ESET.
Function
The SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure. It was originally identified as part of a larger conserved region present in the Drosophila Trithorax protein and was subsequently identified in the Drosophila Su(var)3-9 and 'Enhancer of zeste' proteins, from which the acronym SET is derived. Studies have suggested that the SET domain may be a signature of proteins that modulate transcriptionally active or repressed chromatin states through chromatin remodeling activities.
Model organisms
Model organisms have been used in the study of SETDB1 function. A conditional knockout mouse line, called Setdb1tm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium program — a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty seven tests were carried out on mutant mice and four significant abnormalities were observed. No homozygous mutant embryos were identified during gestation, and therefore none survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice and two significant abnormalities were |
https://en.wikipedia.org/wiki/PAK4 | Serine/threonine-protein kinase PAK 4 is an enzyme that in humans is encoded by the PAK4 gene.
PAK4 is one of six members of the PAK family of serine/threonine kinases which are divided into group I (PAK1, PAK2 and PAK3) and group II (PAK4, PAK6 and PAK5/7). PAK4 localizes in sub-cellular domains of the cytoplasm and nucleus. PAK4 regulates cytoskeleton remodeling, phenotypic signaling and gene expression, and affects directional motility, invasion, metastasis, and growth. Similar to PAK1, PAK4-signaling-dependent cellular functions also regulate both physiologic and disease processes such as cancer, as PAK4 is overexpressed and/or hyperstimulated in human cancer, at-large.
Discovery
PAK4, the founding member of Group II PAK member, was cloned and identified by Minden A. and colleagues in 1998 using a PCR-based strategy from a cDNA library prepared from Jurkett cells.
Gene and spliced variants
The group II PAKs have less coding exons compared with group I PAKs, highlights the potential structural and functional differences between two group of PAKs. The human PAK4 is about 57-kb in length with 13 exons. The PAK4 generates 12 transcripts of which 10 coding transcripts are predicted to code proteins of about 438 to 591 amino acids long, while remaining two transcripts are non-coding in nature. In contrast to human PAK4, murine PAK4 contains four transcripts - two coding for 593 amino acids long polypeptides and two are non-coding RNA transcripts.
Protein domains
The core |
https://en.wikipedia.org/wiki/TCIRG1 | The TCIRG1 (T cell immune regulator 1) gene encodes for the V-type proton ATPase (V-ATPase) 116 kDa subunit a isoform 3 enzyme.
Gene
TCIRG1 (T cell immune regulator 1) is a gene that encodes the V-type proton ATPase (V-ATPase) 116 kDa subunit a isoform 3 enzyme.
Function
Through alternate splicing, the TCIRG1 gene encodes two protein isoforms with similarity to subunits of the vacuolar ATPase (V-ATPase) but the encoded proteins seem to have different functions. V-ATPase is a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, and receptor-mediated endocytosis. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain.
The two isoforms are:
long isoform a, also named OC116
short isoform b, also named TIRC7 (N-terminus truncated, lacks amino acid residues 1-216 of the long isoform)
TIRC7 is expressed in T lymphocytes and is essential for normal T cell activation. This variant uses a transcription start site that is within exon 5 of variant 1 followed by an intron as part of its 5' UTR.
TIRC7
TIRC7 is a 75 kDa membrane protein, first described in 1998, that plays a central role in T cell activation.
Expression
TIRC7 is induced after immune activation on the cell surface of certain peripheral human T and B cells as well as monocytes and IL-10 expressing regulatory T cells. During imm |
https://en.wikipedia.org/wiki/TFG%20%28gene%29 | Protein TFG is a protein that in humans is encoded by the TFG gene.
Interactions
TFG (gene) has been shown to interact with PLSCR1.
References
Further reading
External links |
https://en.wikipedia.org/wiki/FBLN5 | Fibulin-5 (also known as DANCE (developmental arteries and neural crest epidermal growth factor (EGF)-like)) is a protein that in humans is encoded by the FBLN5 gene.
Function
The protein encoded by this gene is a secreted, extracellular matrix protein containing an Arg-Gly-Asp (RGD) motif and calcium-binding EGF-like domains. It promotes adhesion of endothelial cells through interaction of integrins and the RGD motif. It is prominently expressed in developing arteries but less so in adult vessels. However, its expression is reinduced in balloon-injured vessels and atherosclerotic lesions, notably in intimal vascular smooth muscle cells and endothelial cells. Therefore, the protein encoded by this gene may play a role in vascular development and remodeling.
Interactions
FBLN5 has been shown to interact with LOXL1 and apolipoprotein(a).
Clinical relevance
FBLN5 mutations have been described in patients with age-related macular degeneration, as well as being involved in Charcot-Marie-Tooth neuropathies.
References
Further reading
External links
GeneReview/NIH/UW entry on FBLN5-Related Cutis Laxa |
https://en.wikipedia.org/wiki/Solute%20carrier%20organic%20anion%20transporter%20family%20member%201B1 | Solute carrier organic anion transporter family member 1B1 is a protein that in humans is encoded by the SLCO1B1 gene. Pharmacogenomic research indicates that genetic variations in this gene are associated with response to simvastatin. Clinical guidelines exist that can guide dosing of simvastatin based on SLCO1B1 gene variant using genotyping or whole exome sequencing.
See also
Solute carrier family
References
Further reading
Solute carrier family |
https://en.wikipedia.org/wiki/PDLIM5 | PDZ and LIM domain protein 5 is a protein that in humans is encoded by the PDLIM5 gene.
The protein encoded by this gene is a LIM domain protein. LIM domains are cysteine-rich double zinc fingers composed of 50 to 60 amino acids that are involved in protein-protein interactions. LIM domain-containing proteins are scaffolds for the formation of multiprotein complexes. The proteins are involved in cytoskeleton organization, cell lineage specification, organ development, and oncogenesis. The encoded protein is also a member of the Enigma class of proteins, a family of proteins that possess a 100-amino acid PDZ domain in the N-terminus and 1 to 3 LIM domains in the C terminus. Multiple transcript variants encoding different isoforms have been found for this gene, although not all of them have been fully characterized.
Interactions
PDLIM5 has been shown to interact with PRKCB1.
References
Further reading
Biology of bipolar disorder |
https://en.wikipedia.org/wiki/PDPN | Podoplanin is a protein that in humans is encoded by the PDPN gene.
Structure and function
Podoplanin is a mucin-type protein with a mass of 36- to 43-kDa. It is relatively well conserved between species, with homologues in humans, mice, rats, dogs and hamsters.
This gene encodes a type-I, integral membrane, heavily O-glycosylated glycoprotein with diverse distribution in human tissues. The physiological function of this protein may be related to its mucin-type character. The homologous protein in other species has been described as a differentiation antigen and influenza-virus receptor. The specific function of this protein has not been determined but it has been proposed as a marker of lung injury. Alternatively spliced transcript variants encoding different isoforms have been identified.
This protein has been found to have functions in lung alveolar cells, kidney podocytes, and lymphatic endothelial cells. More recently, this protein has been found in neural tissue in both mouse and human samples.
In lymphatic endothelial cells, experimentation has indicated that podoplanin plays a role in proper formation of linkages between the cardiovascular system and the lymphatic systems, typically causing fatty liver disease in these mice.
Although the exact function is unknown in many tissues, podoplanin is generally receptive to detection via immunofluorescent staining and has been shown to co-localize with the protein nestin, a type VI intermediate filament protein expresse |
https://en.wikipedia.org/wiki/CUGBP1 | CUG triplet repeat, RNA binding protein 1, also known as CUGBP1, is a protein which in humans is encoded by the CUGBP1 gene.
Function
Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. This gene may play a role in myotonic dystrophy type 1 (DM1) via interactions with the dystrophia myotonica-protein kinase (DMPK) gene. Alternative splicing results in multiple transcript variants encoding different isoforms.
mRNA degradation factor
It is estimated that 5 to 8% of human mRNAs are unstable because of mRNA instability elements in their 3' untranslated regions (3'UTR). A number of such elements have been called AU-rich elements (AREs). It is now known that AREs are binding sites for RNA-binding proteins that target mRNAs to rapid degradation. However, only few of the proteins reported to bind AREs were demonstrated to play a role in mRNA degradation. A shared feature of these proteins is to bind only to a subclass of the known AREs that contain the pentamer AUUUA. A convergent effort of several research teams now adds CUGBP1 (CUG binding protein 1) to the short list of ARE-Binding proteins that control mRNA stability, with the peculiarity that it binds to non-AUUUA AREs. CUGBP1 has been involved |
https://en.wikipedia.org/wiki/SEPT9 | Septin-9 is a protein that in humans is encoded by the SEPT9 gene.
Interactions
SEPT9 has been shown to interact with SEPT2 and SEPT7.
Function
Along with AHNAK, eIF4E and S100A11, SEPT9 has been shown to be essential for pseudopod protrusion, tumor cell migration and invasion.
Clinical significance
The v2 region of the SEPT9 promoter has been shown to be methylated in colorectal cancer tissue compared with normal colonic mucosa. Using highly sensitive real time PCR assays, methylated SEPT9 was detected in the blood of colorectal cancer patients. This alternate methylation pattern in cancer samples is suggestive of an aberrant activation or repression of the gene compared to normal tissue samples.
Testing to detect methylated SEPT9 is not indicated as a first option for colorectal cancer screening. It is similar in specificity and sensitivity to the stool guaiac test or fecal immune tests, and those tests should be used in preference. In cases when the physician aggressively has recommended a colonoscopy and the patient has declined that and these other tests, then this test has advantages over patients having no screening at all.
See also
Hereditary neuralgic amyotrophy
References
Further reading |
https://en.wikipedia.org/wiki/FAF1 | FAS-associated factor 1 is a protein that in humans is encoded by the FAF1 gene.
Interaction of Fas ligand (TNFSF6) with the FAS antigen (TNFRSF6) mediates programmed cell death, also called apoptosis, in a number of organ systems. The protein encoded by this gene binds to FAS antigen and can initiate apoptosis or enhance apoptosis initiated through FAS antigen. Initiation of apoptosis by the protein encoded by this gene requires a ubiquitin-like domain but not the FAS-binding domain.
References
Further reading |
https://en.wikipedia.org/wiki/DDX20 | Probable ATP-dependent RNA helicase DDX20, also known as DEAD-box helicase 20 and gem-associated protein 3 (GEMIN3), is an enzyme that in humans is encoded by the DDX20 gene.
Function
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which has an ATPase activity and is a component of the survival of motor neuron (SMN) complex.
SMN is the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on RNPs.
Clinical significance
Previous research has revealed that DDX20 may act as a tumor suppressor in hepatocellular carcinoma and as a tumor promoter in breast cancer. DDX20 deficiency enhances NF-κB activity by impairing the NF-κB-suppressive action of microRNAs, and suggest that dysregulation of the microRNA machinery components may also be involved in pathogenesis in various human diseases. Such as miRNA-140 which acts as a liver tumor suppressor, and due to a deficiency of DDX20, miRNA-140 function gets impair, this subsequent functional impairment of miRNAs could lea |
https://en.wikipedia.org/wiki/Aldehyde%20dehydrogenase%203%20family%2C%20member%20A1 | Aldehyde dehydrogenase, dimeric NADP-preferring is an enzyme that in humans is encoded by the ALDH3A1 gene.
Aldehyde dehydrogenases oxidize various aldehydes to the corresponding acids. They are involved in the detoxification of alcohol-derived acetaldehyde and in the metabolism of corticosteroids, biogenic amines, neurotransmitters, and lipid peroxidation. The enzyme encoded by this gene forms a cytoplasmic homodimer that preferentially oxidizes aromatic aldehyde substrates. The gene is located within the Smith–Magenis syndrome region on chromosome 17.
ALDH3A1 expression is notably high in the cornea of mammalian species, comprising from 5 to 50% of soluble protein content, but is almost absent from the cornea of other vertebrates.
Structure and mechanism
ALDH3A1 is a homodimer consisting of alpha helices (43.8%), beta sheets (4.2%), p-loop turns (28.2%) and random coils (23.8%). The catalytic residue–Cys244—is located on an active site that contains a Rossmann fold that binds the enzyme's cofactor, NAD(P)+.
ALDH3A1's catalytic mechanism mirrors that of other enzymes of the aldehyde dehydrogenase family. The sulfur atom of Cys244 attacks the carbonyl of the aldehyde substrate in a nucleophilic attack that releases a hydride ion. The hydride ion is accepted by the NAD(P)+ bound to the Rossmann fold. Unique interactions between the cofactor and the Rossmann fold facilitate an isomerization of the enzyme that releases the cofactor while maintaining the integrity of the ac |
https://en.wikipedia.org/wiki/ARF3 | ADP-ribosylation factor 3 is a protein that in humans is encoded by the ARF3 gene.
Function
ADP-ribosylation factor 3 (ARF3) is a member of the human ARF gene family. These genes encode small guanine nucleotide-binding proteins that stimulate the ADP-ribosyltransferase activity of cholera toxin and play a role in vesicular trafficking and as activators of phospholipase D. The gene products include 6 ARF proteins and 11 ARF-like proteins and constitute 1 family of the RAS superfamily. The ARF proteins are categorized as class I (ARF1, ARF2, and ARF3), class II (ARF4 and ARF5) and class III (ARF6) and members of each class share a common gene organization. The ARF3 gene contains five exons and four introns.
Interactions
ARF3 has been shown to interact with:
ARFIP1,
ARFIP2,
GGA1,
GGA3, and
KIF23.
References
External links
Further reading |
https://en.wikipedia.org/wiki/DUSP6 | Dual specificity phosphatase 6 (DUSP6) is an enzyme that in humans is encoded by the DUSP6 gene.
Function
The protein encoded by this gene is a member of the dual specificity protein phosphatase subfamily. These phosphatases inactivate their target kinases by dephosphorylating both the phosphoserine/threonine and phosphotyrosine residues. They negatively regulate members of the mitogen-activated protein (MAP) kinase superfamily (MAPK/ERK, SAPK/JNK, p38), which are associated with cellular proliferation and differentiation. Different members of the family of dual specificity phosphatases show distinct substrate specificities for various MAP kinases, different tissue distribution and subcellular localization, and different modes of inducibility of their expression by extracellular stimuli. This gene product inactivates ERK2, is expressed in a variety of tissues with the highest levels in heart and pancreas and, unlike most other members of this family, is localized in the cytoplasm. Two transcript variants encoding different isoforms have been found for this gene. Upregulation of MKP-3 has been shown to alleviate chronic postoperative pain.
Interactions
DUSP6 has been shown to interact with MAPK3.
References
Further reading
External links
EC 3.1.3 |
https://en.wikipedia.org/wiki/ECT2 | Protein ECT2 is a protein that in humans is encoded by the ECT2 gene.
Function
The protein encoded by this gene is a transforming protein that is related to Rho-specific exchange factors and yeast cell cycle regulators. The expression of this gene is elevated with the onset of DNA synthesis and remains elevated during G2 and M phases. In situ hybridization analysis showed that expression is at a high level in cells undergoing mitosis in regenerating liver. Thus, this protein is expressed in a cell cycle-dependent manner during liver regeneration, and is thought to have an important role in the regulation of cytokinesis.
Interactions
ECT2 has been shown to interact with PARD6A.
References
Further reading |
https://en.wikipedia.org/wiki/EPHB6 | Ephrin type-B receptor 6 is a protein that in humans is encoded by the EPHB6 gene.
Ephrin receptors and their ligands, the ephrins, mediate numerous developmental processes, particularly in the nervous system. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. The Eph family of receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Ephrin receptors make up the largest subgroup of the receptor tyrosine kinase (RTK) family. The ephrin receptor encoded by this gene lacks the kinase activity of most receptor tyrosine kinases and binds to ephrin-B ligands.
References
Further reading
Tyrosine kinase receptors |
https://en.wikipedia.org/wiki/EPS8 | Epidermal growth factor receptor kinase substrate 8 is an enzyme that in humans is encoded by the EPS8 gene.
Function
This gene encodes a member of the EPS8 family. This protein contains one PH domain and one SH3 domain. It functions as part of the EGFR pathway, though its exact role has not been determined. Highly similar proteins in other organisms are involved in the transduction of signals from Ras to Rac and growth factor-mediated actin remodeling. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized.
Clinical significance
Mutations in EPS8 cause congenital deafness.
Interactions
EPS8 has been shown to interact with:
ABI1,
BAIAP2,
DVL1,
SHB,
SHC1
SOS1, and
Src.
References
Further reading |
https://en.wikipedia.org/wiki/GJB3 | Gap junction beta-3 protein (GJB3), also known as connexin 31 (Cx31) — is a protein that in humans is encoded by the GJB3 gene.
Function
This gene is a member of the connexin gene family. The encoded protein is a component of gap junctions, which are composed of arrays of intercellular channels that provide a route for the diffusion of low molecular weight materials from cell to cell. Mutations in this gene can cause non-syndromic deafness or erythrokeratodermia variabilis, a skin disorder. Alternative splicing results in multiple transcript variants encoding the same protein.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Deafness and Hereditary Hearing Loss Overview
Connexins |
https://en.wikipedia.org/wiki/HHEX | Hematopoietically-expressed homeobox protein HHEX is a protein that in humans is encoded by the HHEX gene and also known as Proline Rich Homeodomain protein PRH.
This gene encodes a member of the homeobox family of transcription factors, many of which are involved in developmental processes. Expression in specific hematopoietic lineages suggests that this protein may play a role in hematopoietic differentiation but the expression of this protein is not limited to hematopoietic cells.
Function
The HHEX transcription factor acts as a activator of transcription in some instances and a repressor of transcription others. It interacts with a number of other signaling molecules to play an important role in the development of multiple organs, such as the liver, thyroid and forebrain. HHEX serves to repress VEGFA, another protein which is important in endothelial cell development. SCL, a significant transcription factor for blood and endothelial cell differentiation, is shown to interact with HHEX to promote the correct development of the hematopoiesis process. HHEX appears to work together with another molecule, β-catenin, for the development of the anterior organizer. It also contributes to developmental remodeling and stabilization of endothelial cells in an unborn organism. The importance of this transcription factor is illustrated by the inability of HHEX knockout mice embryos to survive gestation. Without the expression of HHEX, these mice embryos die in utero between Day 13 |
https://en.wikipedia.org/wiki/HMGN1 | Non-histone chromosomal protein HMG-14 is a protein that in humans is encoded by the HMGN1 gene.
Function
Chromosomal protein HMG14 and its close analog HMG17 (MIM 163910) bind to the inner side of the nucleosomal DNA, potentially altering the interaction between the DNA and the histone octamer. The 2 proteins may be involved in the process that maintains transcribable genes in a unique chromatin conformation. Their ubiquitous distribution and relative abundance, as well as the high evolutionary conservation of the DNA-binding domain of the HMG14 family of proteins, suggest that they may be involved in an important cellular function.
Interactions
HMGN1 has been shown to interact with YWHAZ.
See also
HMGN2
High mobility group protein HMG14 and HMG17
References
Further reading |
https://en.wikipedia.org/wiki/IGLL1 | Immunoglobulin lambda-like polypeptide 1 is a protein that in humans is encoded by the IGLL1 gene. IGLL1 has also recently been designated CD179B (cluster of differentiation 179B).
It is associated with agammaglobulinemia-2.
The preB cell receptor is found on the surface of proB and preB cells, where it is involved in transduction of signals for cellular proliferation, differentiation from the proB cell to the preB cell stage, allelic exclusion at the Ig heavy chain gene locus, and promotion of Ig light chain gene rearrangements. The preB cell receptor is composed of a membrane-bound Ig mu heavy chain in association with a heterodimeric surrogate light chain. This gene encodes one of the surrogate light chain subunits and is a member of the immunoglobulin gene superfamily. This gene does not undergo rearrangement. Mutations in this gene can result in B cell deficiency and agammaglobulinemia, an autosomal recessive disease in which few or no gamma globulins or antibodies are made. Two transcript variants encoding different isoforms have been found for this gene.
References
Further reading
Clusters of differentiation |
https://en.wikipedia.org/wiki/Insulin-induced%20gene%201%20protein | Insulin induced gene 1, also known as INSIG1, is a protein which in humans is encoded by the INSIG1 gene.
INSIG1 is short for insulin-induced gene 1; it is located on chromosome 7 (7q36). This human gene encodes for a transmembrane protein of 277 amino acids with probably 6 transmembrane domains. It is localized in the endoplasmic reticulum (ER) and seems to be expressed in all tissues, especially in liver. This gene is called an insulin-induced gene because the molecule insulin can regulate it. Importantly, the protein encoded by this gene plays a critical role in regulating cholesterol concentrations in cells.
Function
INSIG1 plays an important role in the SREBP-mediated regulation of cholesterol biosynthesis: by binding to the sterol-sensing domain of SCAP (SREBP cleavage activating protein) it makes the SCAP/SREBP complex stay longer in the ER, thus prohibiting SCAP from carrying activated SREBP to the golgi complex. This ultimately blocks SREBP from acting as a transcription factor for the SRE in the promoter region of the HMG-CoA-reductase gene and results in a decreased expression of HMG-CoA-reductase.
INSIG1 also binds to the sterol-sensing domain of HMG-CoA-reductase, resulting in the enzyme's increased degradation.
Both functions require the binding of INSIG1 protein via the same site.
There are two other proteins whose sterol-binding sites show a great similarity to the ones of SCAP and HMG-CoA-reductase and who might thus be regulated by INSIG1 as well:
Niem |
https://en.wikipedia.org/wiki/Regular%20modal%20logic | In modal logic, a regular modal logic is a modal logic containing (as axiom or theorem) the duality of the modal operators:
and closed under the rule
Every normal modal logic is regular, and every regular modal logic is classical.
References
Chellas, Brian. Modal Logic: An Introduction. Cambridge University Press, 1980.
Logic
Modal logic |
https://en.wikipedia.org/wiki/EIF6 | Eukaryotic translation initiation factor 6 (EIF6), also known as Integrin beta 4 binding protein (ITGB4BP), is a human gene.
Hemidesmosomes are structures which link the basal lamina to the intermediate filament cytoskeleton. An important functional component of hemidesmosomes is the integrin beta-4 subunit (ITGB4), a protein containing two fibronectin type III domains. The protein encoded by this gene binds to the fibronectin type III domains of ITGB4 and may help link ITGB4 to the intermediate filament cytoskeleton. The encoded protein, which is insoluble and found both in the nucleus and in the cytoplasm, can function as a translation initiation factor and catalyzes the association of the 40S and 60S ribosomal subunits along with eIF5 bound to GTP. Multiple transcript variants encoding several different isoforms have been found for this gene.
EIF6 plays important roles in Eukaryotic 80S ribosome formation, cell growth and gene expression. The 80S ribosome, which can separate into 40S and 60S subunits. EIF6 helps to protect mature 60s subunit and then EIF6 should disassociate with 60s subunit so that it can binds to 40s subunit to form ribosome. Keeping in balance of EIF6 is essential for the body: few EIF6 helps synthesis of normal ribosome, while large amount of EIF6 inhibited 60s subunits bind to 40s subunits.
Function
EIF6 exists both in nucleolus and cytoplasm. In the eukaryotic nucleolus, a 90S pre-ribosomal complex separate to a 60S pre-ribosomal complex and a 40 |
https://en.wikipedia.org/wiki/Laminin%2C%20alpha%204 | Laminin subunit alpha-4 is a protein that in humans is encoded by the LAMA4 gene.
Function
Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis.
Laminins are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. Several isoforms of each chain have been described. Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms which are designated by Arabic numerals in the order of their discovery, i.e. alpha1beta1gamma1 heterotrimer is laminin 1. The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo.
This gene encodes the alpha chain isoform laminin, alpha 4. The domain structure of alpha 4 is similar to that of alpha 3, both of which resemble truncated versions of alpha 1 and alpha 2, in that approximately 1,200 residues at the N-terminus (domains IV, V and |
https://en.wikipedia.org/wiki/MAPRE1 | Microtubule-associated protein RP/EB family member 1 is a protein that in humans is encoded by the MAPRE1 gene.
Function
The protein encoded by this gene was first identified by its binding to the APC (Adenomatous polyposis coli) protein which is often mutated in familial and sporadic forms of colorectal cancer.
Immunofluorescence has demonstrated that EB1 localizes to the centrosome, mitotic spindle, and distal tips of cytoplasmic microtubules. Throughout the cell cycle, EB1 proteins situate on the microtubule plus ends, which is why EB1 is categorized as a microtubule plus end tracking protein(+TIP protein).
The protein also associates with components of the dynactin complex and the intermediate chain of cytoplasmic dynein. Because of these associations, it is thought that this protein is involved in the regulation of microtubule structures and chromosome stability. This gene is a member of the RP/EB family.
Interactions
MAPRE1 has been shown to interact with TERF1.
References
Further reading |
https://en.wikipedia.org/wiki/KIF1B | Kinesin-like protein KIF1B is a protein that in humans is encoded by the KIF1B gene.
Clinical significance
It is associated with Charcot–Marie–Tooth disease, type 2A1.
Interactions
KIF1B has been shown to interact with GIPC1.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Charcot-Marie-Tooth Neuropathy Type 2 |
https://en.wikipedia.org/wiki/ICOSLG | ICOS ligand is a protein that in humans is encoded by the ICOSLG gene located at chromosome 21. ICOSLG has also been designated as CD275 (cluster of differentiation 275).
ICOSLG is glycosylated transmembrane structure, which is classified as a member of the B7 family due to the significant homology with B7 family members. The B7/CD28 superfamily provides both positive and negative co-signals to immunocytes in immune responses.
The interaction of ICOSLG with ICOS, the specific receptor for ICOSLG, is critically involved in the activation, proliferation, differentiation and cytokine production of T cells as well as in the antibody secretion from B cells during secondary immune responses.
ICOSLG, which is extensively expressed in both non-lymphatic and lymphatic tissues, is an important molecule in upregulating and promoting T cell immune responses. Expression of ICOSLG in naive B cells and monocytes in PBMCs is at a low level. After stimulation by IFN-γ, TNF-α, or LPS, it can be quickly up-regulated. The induced expression of ICOS on activated T cells mainly regulates the secretion of Th2 cytokines and thus shifts the immune response to the Th2 type. It has been reported that the ICOS/ICOSLG pathway is involved in immunopathogenesis such as infection, hypersensitivity, autoimmune diseases, transplantation immunity and tumor immunity.
ICOSLG is also a major costimulator in endothelial cell-mediated T cell activation. It has an important physiological role of ICOSLG in the re |
https://en.wikipedia.org/wiki/PPP1R15A | Protein phosphatase 1 regulatory subunit 15A, also known as growth arrest and DNA damage-inducible protein (GADD34), is a protein that in humans is encoded by the PPP1R15A gene.
The Gadd34/MyD116 gene was originally discovered as a member in a set of gadd and MyD mammalian genes encoding acidic proteins that synergistically suppress cell growth. Later on it has been characterized as a gene playing a role in ER stress-induced cell death, being a target of ATF4 that plays a role in ER-mediated cell death via promoting protein dephosphorylation of eIF2α and reversing translational inhibition.
Function
This gene is a member of a group of genes whose transcript levels are increased following stressful growth arrest conditions and treatment with DNA-damaging agents. The induction of this gene by ionizing radiation occurs in certain cell lines regardless of p53 status, and its protein response is correlated with apoptosis following ionizing radiation.
Interactions
PPP1R15A has been shown to interact with:
BAG1
LYN,
MLL,
PPP1CA,
PPP1CB,
PPP1CC,
SMARCB1, and
TSN.
References
Further reading |
https://en.wikipedia.org/wiki/PRDX5 | Peroxiredoxin-5 (PRDX5), mitochondrial is a protein that in humans is encoded by the PRDX5 gene, located on chromosome 11.
This gene encodes a member of the six-member peroxiredoxin family of antioxidant enzymes. Like the other five members, PRDX5 is widely expressed in tissues but differs by its large subcellular distribution. In human cells, it has been shown that PRDX5 can be localized to mitochondria, peroxisomes, the cytosol, and the nucleus. Human PRDX5 is identified by virtue of the sequence homologies to yeast peroxisomal antioxidant enzyme PMP20.
Biochemically, PRDX5 is a peroxidase that can use cytosolic or mitochondrial thioredoxins to reduce alkyl hydroperoxides or peroxynitrite with high rate constants in the 106 to 107 M−1s−1 range, whereas its reaction with hydrogen peroxide is more modest, in the 105 M−1s−1 range. So far, PRDX5 has been shown to be a cytoprotective antioxidant enzyme that inhibits endogenous or exogenous peroxide accumulation.
Structure
According to its amino acid sequence, this 2-Cys peroxiredoxin, PRDX5, is the most divergent isoform among mammalian peroxiredoxins, processing only 28% to 30% sequence identity with typical 2-Cys and 1-Cys peroxiredoxins. The divergent amino acid sequence of this atypical peroxiredoxin is reflected in its unique crystal structure. The typical peroxiredoxin is composed of a thioredoxin domain and a C-terminal, whereas PRDX5 has an N-terminal domain and a unique alpha helix replaces a loop structure in the t |
https://en.wikipedia.org/wiki/CHMP2B | Charged multivesicular body protein 2b is a protein that in humans is encoded by the CHMP2B gene. It forms part of one of the endosomal sorting complexes required for transport (ESCRT) - specifically ESCRT-III - which are a series of complexes involved in cell membrane remodelling. CHMP2B forms long chains that spiral around the neck of a budding vesicle. Along with the other components of ESCRT-III, CHMP2B constricts the neck of the vesicle just before it is cleaved away from the membrane.
Mutations of this gene cause chromosome 3-linked frontotemporal dementia (FTD3), which has been described in several members of one Danish family . In a study of French families with several forms of frontotemporal dementia, it was found to be a relatively rare cause.
References
External links
GeneReviews/NCBI/NIH/UW entry on CHMP2B-Related Frontotemporal Dementia
Further reading |
https://en.wikipedia.org/wiki/EIF2C2 | Protein argonaute-2 is a protein that in humans is encoded by the EIF2C2 gene.
This gene encodes a member of the Argonaute family of proteins which play a role in RNA interference. The encoded protein is highly basic, and contains a PAZ domain and a PIWI domain. It may interact with Dicer1 and play a role in short-interfering-RNA-mediated gene silencing.
Interactions
EIF2C2 has been shown to interact with
DDX20,
DICER1,
FMRP, FXR1P, FXR2P, and
TNRC6B.
References
Further reading
RNA interference |
https://en.wikipedia.org/wiki/HTATSF1 | HIV Tat-specific factor 1 is a protein that in humans is encoded by the HTATSF1 gene.
Function
Whereas most DNA sequence-specific transcription factors increase the rate of initiation and interact with enhancer or promoter DNA, human immunodeficiency virus-1 (HIV-1) Tat predominantly stimulates elongation and interacts with the trans-acting responsive (TAR) RNA element. Tat is essential for HIV replication.
HTATSF1 has also been shown to be involved in intron retention, and is associated with splicing of mRNAs that encode ribosomal proteins. It is also associated with a naïve pluripotent state, although the relationship is complex and is strongly affected by other pluripotency factors such as Nanog and KLF2.
Interactions
HTATSF1 has been shown to interact with SUPT5H and GTF2F2.
References
Further reading |
https://en.wikipedia.org/wiki/Drebrin-like | Drebrin-like protein is a protein that in humans is encoded by the DBNL gene.
Interactions
Drebrin-like has been shown to interact with Cyclin-dependent kinase 4, MAP4K1 and ZAP-70.
References
Further reading |
https://en.wikipedia.org/wiki/H19%20%28gene%29 | H19 is a gene for a long noncoding RNA, found in humans and elsewhere. H19 has a role in the negative regulation (or limiting) of body weight and cell proliferation. This gene also has a role in the formation of some cancers and in the regulation of gene expression.
.
The H19 gene is expressed exclusively on one parental allele in a phenomenon known as imprinting. H19 is only transcribed from the maternally inherited allele; the paternal H19 allele is not expressed. H19 was first named ASM (for Adult Skeletal Muscle) because of its expression in adult skeletal muscle ("ASM") in rats. H19 is also known as BWS because aberrant H19 expression can be involved in Beckwith-Wiedemann Syndrome ("BWS"), as well as Silver-Russell syndrome. Epigenetics deregulations at H19 imprinted gene in sperm have been observed associated with male infertility.
Gene characterization
The H19 gene contains 3 Sp1 binding sites, however these 3 sites are present in a part of the sequence that has shown no transcriptional activity in deletion assays. As a result, these Sp1 binding sites are not expected to contribute much to the regulation of H19 gene transcription. The H19 gene sequence also contains binding sites for the C/EBP family of transcription factors. One of these C/EBP transcription factor binding sites also contains a CpG site. In vitro methylation of this CpG site on a DNA construct strongly inhibited transcription of the H19 gene.
In cell lines derived from human choriocarcinomas, Kopf |
https://en.wikipedia.org/wiki/ASIC1 | Acid-sensing ion channel 1 (ASIC1) also known as amiloride-sensitive cation channel 2, neuronal (ACCN2) or brain sodium channel 2 (BNaC2) is a protein that in humans is encoded by the ASIC1 gene. The ASIC1 gene is one of the five paralogous genes that encode proteins that form trimeric acid-sensing ion channels (ASICs) in mammals. The cDNA of this gene was first cloned in 1996. The ASIC genes have splicing variants that encode different proteins that are called isoforms.
These genes are mainly expressed in the central and peripheral nervous system.
ASICs can form both homotrimeric (meaning composed of three identical subunits) and heterotrimeric channels.
Structure and function
This gene encodes a member of the ASIC/ENaC superfamily of proteins. The members of this family are amiloride-sensitive sodium channels that contain intracellular N and C termini, 2 hydrophobic transmembrane (TM) regions, and a large extracellular loop, which has many cysteine residues with conserved spacing. The TM regions are generally symbolized as TM1 (clone to N-terminus) and TM2 (close to C-terminus).
The pore of the channel through which ions selectively flow from the extracellular side into the cytoplasm is formed by the three TM2 regions of the trimer.
Interactions
ASIC1 has been shown to interact with PICK1.
References
Further reading
External links
Sodium channels |
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