source stringlengths 32 209 | text stringlengths 18 1.5k |
|---|---|
https://en.wikipedia.org/wiki/HOXB4 | Homeobox protein Hox-B4 is a protein that in humans is encoded by the HOXB4 gene.
Function
This gene is a member of the Antp homeobox family and encodes a nuclear protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox B genes located on chromosome 17. The encoded protein functions as a sequence-specific transcription factor that is involved in development. Intracellular or ectopic expression of this protein expands hematopoietic stem and progenitor cells in vivo and in vitro, making it a potential candidate for therapeutic stem cell expansion.
See also
Homeobox
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/HOXC8 | Homeobox protein Hox-C8 is a protein that in humans is encoded by the HOXC8 gene.
Function
This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. The product of this gene may play a role in the regulation of cartilage differentiation. It could also be involved in chondrodysplasias or other cartilage disorders. HOXC8 was found to have activity in promoting nerve growth and its expression is dysregulated in patients with neurofibromatosis type 1.
See also
Homeobox
Interactions
HOXC8 has been shown to interact with Mothers against decapentaplegic homolog 6 and Mothers against decapentaplegic homolog 1.
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/HOXD13 | Homeobox protein Hox-D13 is a protein that in humans is encoded by the HOXD13 gene. This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms.
Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9–11 genes arranged in tandem. HOXD13 is the first of several HOXD genes located in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. The product of the mouse Hoxd13 gene plays a role in axial skeleton development and forelimb morphogenesis.
Changes in the expression of the Hoxd13 gene in early lobe-finned fish may have also contributed to the evolution of the tetrapod limb. Experiments investigating the impact of 5′ Hoxd overexpression in zebrafish embryos observed modified development of distal fin structures, resulting in increased proliferation, distal expansion of cartilage tissue and fin fold reduction. A number of similar studies conducted with a range of animals, including catsharks and marsupials, lend further credibility to the role of the Hoxd13 gene in the fin-to-limb transition.
Clinical significance
Mutations in HOXD13 can cause several types of autosomal dominant syndactyly and brachydactyly, including brachydactyly type D ("cl |
https://en.wikipedia.org/wiki/HSD17B2 | 17β-Hydroxysteroid dehydrogenase 2 (17β-HSD2) is an enzyme of the 17β-hydroxysteroid dehydrogenase (17β-HSD) family that in humans is encoded by the HSD17B2 gene.
Function
17β-HSD2 is involved in inactivation of androgens and estrogens, being accurately describable as "antiandrogenic" and "antiestrogenic", and is the key 17β-HSD isozyme in androgen and estrogen inactivation. Specific reactions catalyzed by 17β-HSD2 include estradiol to estrone, testosterone to androstenedione, and androstenediol to . In addition to 17β-HSD activity, this enzyme also shows high 20α-hydroxysteroid dehydrogenase activity and can activate the weak progestogen 20α-hydroxyprogesterone into the potent progestogen progesterone.
Expression
17β-HSD2 is widely expressed throughout the body including in the placenta, liver, intestines, endometrium, kidney, pancreas, breast, prostate, bone, and many other tissues.
Clinical significance
Polymorphisms in HSD17B2 have been associated with breast cancer and prostate cancer. 17β-HSD2 activity has also been associated with endometriosis and osteoporosis, and inhibitors of the enzyme are of potential interest in the treatment of the latter condition. Inactivating mutations resulting in a syndrome of congenital deficiency of 17β-HSD2 have not been reported to date.
References
Further reading |
https://en.wikipedia.org/wiki/HSPA1L | Heat shock 70 kDa protein 1L is a protein that in humans is encoded by the HSPA1L gene on chromosome 6. As a member of the heat shock protein 70 (Hsp70) family and a chaperone protein, it facilitates the proper folding of newly translated and misfolded proteins, as well as stabilize or degrade mutant proteins. Its functions contribute to biological processes including signal transduction, apoptosis, protein homeostasis, and cell growth and differentiation. It has been associated with an extensive number of cancers, neurodegenerative diseases, cell senescence and aging, and Graft-versus-host disease.
Structure
This gene encodes a 70kDa heat shock protein and is located in the major histocompatibility complex class III region, in a cluster with two closely related genes which also encode isoforms of the 70kDa heat shock protein. The amino acid sequence of the encoded protein shares a 90% homology to the isoforms HSPA1A and HSPA1B. As a Hsp70 protein, it has a C-terminal protein substrate-binding domain and an N-terminal ATP-binding domain. The substrate-binding domain consists of two subdomains, a two-layered β-sandwich subdomain (SBDβ) and an α-helical subdomain (SBDα), which are connected by the loop Lα,β. SBDβ contains the peptide binding pocket while SBDα serves as a lid to cover the substrate binding cleft. The ATP binding domain consists of four subdomains split into two lobes by a central ATP/ADP binding pocket. The two terminal domains are linked together by a con |
https://en.wikipedia.org/wiki/ISL1 | Insulin gene enhancer protein ISL-1 is a protein that in humans is encoded by the ISL1 gene.
Function
This gene encodes a transcription factor containing two N-terminal LIM domains and one C-terminal homeodomain. The encoded protein plays an important role in the embryogenesis of pancreatic islets of Langerhans. In mouse embryos, a deficiency of this gene results in failure to undergo neural tube motor neuron differentiation.
Interactions
ISL1 has been shown to interact with Estrogen receptor alpha.
Role in cardiac development
ISL1 is a marker for cardiac progenitors of the secondary heart field (SHF) which includes the right ventricle and the outflow tract. The biological function of ISL1 is demonstrated through ISL1 mutant mice and chick embryos that have altered cell proliferation, survival, and migration of cardiogenic precursors and severe cardiac defects. More recently it has been defined as a marker for a cardiac progenitor cell lineage that is capable of differentiating into all 3 major cell types of the heart: cardiomyocytes, smooth muscle and endothelial cell lineages. Research has shown that ISL1 promotes differentiation of cardiac cells and a depletion of ISL1 can respecify the cell fate of nascent cardiomyocytes, such as from ventricular to an atrial identity.
The validity of ISL1 as a marker for cardiac progenitor cells has been questioned since some groups have found no evidence that ISL1 cells serve as cardiac progenitors. Furthermore, ISL1 is not r |
https://en.wikipedia.org/wiki/ITIH3 | Inter-alpha-trypsin inhibitor heavy chain H3 is a protein that in humans is encoded by the ITIH3 gene.
See also
Inter-alpha-trypsin inhibitor
ITIH1
ITIH2
ITIH4
References
Further reading |
https://en.wikipedia.org/wiki/KCNA3 | Potassium voltage-gated channel, shaker-related subfamily, member 3, also known as KCNA3 or Kv1.3, is a protein that in humans is encoded by the KCNA3 gene.
Potassium channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. Four sequence-related potassium channel genes – shaker, shaw, shab, and shal – have been identified in Drosophila, and each has been shown to have human homolog(s).
This gene encodes a member of the potassium channel, voltage-gated, shaker-related subfamily. This member contains six membrane-spanning domains with a shaker-type repeat in the fourth segment. It belongs to the delayed rectifier class, members of which allow nerve cells to efficiently repolarize following an action potential. It plays an essential role in T cell proliferation and activation. This gene appears to be intronless and is clustered together with KCNA2 and KCNA10 genes on chromosome 1.
Function
KCNA3 encodes the voltage-gated Kv1.3 channel, which is expressed in T and B lymphocytes. All human T cells express roughly 300 Kv1.3 channels per cell along with 10-20 calcium-activated KCa3.1 channels. Upon activation, naive and central memory T cells increase expression of the KCa3.1 channel to approximately 500 channels per |
https://en.wikipedia.org/wiki/KIF5B | Kinesin family member 5B (KIF5B) is a protein that in humans is encoded by the KIF5B gene. It is part of the kinesin family of motor proteins.
Interactions
KIF5B has been shown to interact with:
KLC1,
KLC2,
SNAP-25,
SNAP23, and
YWHAH.
References
Further reading
External links
Human proteins
Motor proteins |
https://en.wikipedia.org/wiki/Lipocalin%201 | Lipocalin-1 is a protein that in humans is encoded by the LCN1 gene.
The protein encoded by this gene belongs to the lipocalin family. Lipocalins are a group of extracellular proteins that are able to bind lipophiles by enclosure within their structures to minimize solvent contact. This protein may bind hydrophobic ligands and inhibit cysteine proteinases. It may also play a role in taste reception.
Structure
Proteins are classified into the lipocalin family by their 8 antiparallel beta-sheets that form a barrel structure which acts as the binding site for ligands.
Function
Lipocalin-1 (LCN1) is capable of binding a wide variety of lipophilic molecules along with zinc and chloride ions. Because of this feature, LCN1’s main function is thought to be the removal of potentially harmful lipids and lipophilic molecules from the body by binding them. The LCN1-Ligand complex is then imported via Lipocalin-1-Interacting Membrane Receptor (LIMR) so the bound molecule can be broken down safely within the cell. This process of retrieving molecules may impact several processes including pheromone signaling, immunodulation, inflammation, detoxification, tissue development, apoptosis and more.
LCN1 shares three sequence motifs with cystatins which enables LCN1 to act in a similar manner to cystatins as a cysteine proteinase inhibitor. These domains have specifically been shown to bind Papain.
LCN1 also plays a role in stabilizing the lipid layer of the tear film, though the details |
https://en.wikipedia.org/wiki/LSP1 | Lymphocyte-specific protein 1 is a protein that in humans is encoded by the LSP1 gene.
This gene encodes an intracellular F-actin binding protein. The protein is expressed in lymphocytes, neutrophils, macrophages, and endothelium and may regulate neutrophil motility, adhesion to fibrinogen matrix proteins, and transendothelial migration. Alternative splicing results in multiple transcript variants encoding different isoforms.
References
Further reading |
https://en.wikipedia.org/wiki/CRB1 | Crumbs homolog 1 is a protein that in humans is encoded by the CRB1 gene.
This gene encodes a protein which is similar to the Drosophila crumbs protein and localizes to the inner segment of mammalian photoreceptors. In Drosophila, crumbs localizes to the stalk of the fly photoreceptor and may be a component of the molecular scaffold that controls proper development of polarity in the eye. Mutations in this gene are associated with a severe form of retinitis pigmentosa, RP12, and with Leber congenital amaurosis. Alternatively spliced transcript variants have been observed but their full-length nature has yet to be determined. One small study suggests that mutations in this gene are associated with keratoconus in patients that already have Leber's congenital amaurosis.
References
External links
GeneReviews/NIH/NCBI/UW entry on Retinitis Pigmentosa Overview
Further reading |
https://en.wikipedia.org/wiki/SEC14L2 | SEC14L2 is a gene that, in humans, encodes the protein SEC14-like protein 2.
Function
This gene encodes a cytosolic protein which belongs to a family of lipid-binding proteins including Sec14p, alpha-tocopherol transfer protein, and cellular retinol-binding protein. The encoded protein stimulates squalene monooxygenase which is a downstream enzyme in metabolism of cholesterol.
References
Further reading |
https://en.wikipedia.org/wiki/TMEFF2 | The Transmembrane protein with an EGF-like and two follistatin-like domains 2 (TMEFF2) gene is located on chromosome 2q32-q33 and encodes a 374-residue long single polypeptide, type-I transmembrane proteoglycan. According to the HUGO gene nomenclature committee, the aliases of TMEFF2 include,HPP1, Tomoregulin (TR), Transmembrane protein TENB2 (TENB2), Cancer/testis antigen family 120, member 2 (CT120.2) and Transmembrane protein containing EGF and follistatin domains (TPEF). TMEFF2 was identified and characterized by at least five independent groups within the time span of approximately a year.
TMEFF2 is proteolytically shed from the cell surface. The reported functions of TMEFF2 span across a wide range of physiological and pathological spectra including metabolism, neuroprotection, apoptosis, embryonic development, onco-suppression and endocrine function. TMEFF2 promoter and its 5′-upstream CpG island are methylated in a number of cancers. An inverse correlation between TMEFF2 methylation and the stage, response to therapy and survival outcome has been observed. The detection of methylated free-circulating TMEFF2 DNA has been suggested as a potential diagnostic tool for colorectal cancer. The TMEFF2 downregulation signature equals and sometimes outperforms the Gleason and pathological scores in prostate cancer. TMEFF2 is downregulated in glioma and cotricotropinomas, and it impairs the production of adrenocorticotropic hormone in glioma cells. Through binding the amyloid β |
https://en.wikipedia.org/wiki/CLIC4 | Chloride intracellular channel 4, also known as CLIC4,p644H1,HuH1, is a eukaryotic gene.
Chloride channels are a diverse group of proteins that regulate fundamental cellular processes including stabilization of cell membrane potential, transepithelial transport, maintenance of intracellular pH, and regulation of cell volume. Chloride intracellular channel 4 (CLIC4) protein, encoded by the clic4 gene, is a member of the p64 family; the gene is expressed in many tissues. These channels are implicated in angiogenesis, pulmonary hypertension, cancer, and cardioprotection from ischemia-reperfusion injury. They exhibit an intracellular vesicular pattern in PANC-1 cells (pancreatic cancer cells).
Binding partners
CLIC4 binds to dynamin I, α-tubulin, β-actin, creatine kinase and two 14-3-3 isoforms.
See also
Chloride channel
References
Further reading
External links
Ion channels |
https://en.wikipedia.org/wiki/Low-density%20lipoprotein%20receptor%20adapter%20protein%201 | Low-density lipoprotein receptor adapter protein 1 is a protein that in humans is encoded by the LDLRAP1 gene.
The protein encoded by this gene is a cytosolic protein which contains a phosphotyrosine binding (PTB) domain. The PTB domain has been found to interact with the cytoplasmic tail of the LDL receptor. Mutations in this gene lead to LDL receptor malfunction and cause the disorder autosomal recessive hypercholesterolaemia.
Interactions
LDLRAP1 has been shown to interact with AP2B1 and LRP2.
References
Further reading |
https://en.wikipedia.org/wiki/TINF2 | TERF1-interacting nuclear factor 2 is a protein that in humans is encoded by the TINF2 gene. TINF2 is a component of the shelterin protein complex found at the end of telomeres.
Interactions
TINF2 has been shown to interact with ACD, POT1 and TERF1.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Dyskeratosis Congenita
PDBe-KB provides an overview of all the structure information available in the PDB for Human TERF1-interacting nuclear factor 2 (TINF2)
Telomere-related proteins |
https://en.wikipedia.org/wiki/Sialin | Sialin, also known as H(+)/nitrate cotransporter and H(+)/sialic acid cotransporter, is a protein which in humans is encoded by the SLC17A5 gene.
Clinical significance
A deficiency of this protein causes Salla disease. and Infantile Sialic Acid Storage Disease (ISSD).
The gene for HP59 contains, entirely within its coding region, the Sialin Gene SLC17A5. Member 5, also known as SLC17A5 or sialin is a lysosomal membrane sialic acid transport protein which in humans is encoded by the SLC17A5 gene on Chromosome 6
See also
Solute carrier family
References
Further reading
Solute carrier family |
https://en.wikipedia.org/wiki/ACOX1 | Peroxisomal acyl-coenzyme A oxidase 1 is an enzyme that in humans is encoded by the ACOX1 gene.
The protein encoded by this gene is the first enzyme of the fatty acid beta-oxidation pathway, which catalyzes the desaturation of acyl-CoAs to 2-trans-enoyl-CoAs. It donates electrons directly to molecular oxygen, thereby producing hydrogen peroxide. Defects in this gene result in pseudoneonatal adrenoleukodystrophy, a disease that is characterized by accumulation of very long chain fatty acids. Alternatively spliced transcript variants encoding different isoforms have been identified.
See also
ACOX3
Acyl-CoA oxidase
References
External links
Further reading
Human proteins |
https://en.wikipedia.org/wiki/ASCL1 | Achaete-scute homolog 1 is a protein that in humans is encoded by the ASCL1 gene. Because it was discovered subsequent to studies on its homolog in Drosophila, the Achaete-scute complex, it was originally named MASH-1 for mammalian achaete scute homolog-1.
Function
This gene encodes a member of the basic helix-loop-helix (BHLH) family of transcription factors. The protein activates transcription by binding to the E box (5'-CANNTG-3'). Dimerization with other BHLH proteins is required for efficient DNA binding. This protein plays a role in the neuronal commitment and differentiation and in the generation of olfactory and autonomic neurons. It is highly expressed in medullary thyroid cancer and small cell lung cancer and may be a useful marker for these cancers. The presence of a CAG repeat in the gene suggests that it may also play a role in tumor formation.
Role in neuronal commitment
Development of the vertebrate nervous system begins when the neural tube forms in the early embryo. The neural tube eventually gives rise to the entire nervous system, but first neuroblasts must differentiate from the neuroepithelium of the tube. The neuroblasts are the cells that undergo mitotic division and produce neurons. Asc is central to the differentiation of the neuroblasts and the lateral inhibition mechanism which inherently creates a safety net in the event of damage or death in these incredibly important cells.
Differentiation of the neuroblast begins when the cells of the neura |
https://en.wikipedia.org/wiki/LTBP1%20%28gene%29 | Latent-transforming growth factor beta-binding protein 1 is a protein that in humans is encoded by the LTBP1 gene.
The protein encoded by this gene belongs to the family of latent TGF-beta binding proteins (LTBPs). The secretion and activation of TGF-betas is regulated by their association with latency-associated proteins and with latent TGF-beta binding proteins. The product of this gene targets latent complexes of transforming growth factor beta to the extracellular matrix, where the latent cytokine is subsequently activated by several different mechanisms. Alternatively spliced transcript variants encoding different isoforms have been identified.
Interactions
LTBP1 (gene) has been shown to interact with TGF beta 1.
References
Further reading |
https://en.wikipedia.org/wiki/MAF%20%28gene%29 | Transcription factor Maf also known as proto-oncogene c-Maf or V-maf musculoaponeurotic fibrosarcoma oncogene homolog is a transcription factor that in humans is encoded by the MAF gene.
Types
One type, MafA, also known as RIPE3b1, promotes pancreatic development, as well as insulin gene transcription.
Interactions
MAF has been shown to interact with:
CREBBP
EP300
MYB
SOX9.
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/MARK1 | Serine/threonine-protein kinase MARK1 is an enzyme that in humans is encoded by the MARK1 gene.
References
Further reading
EC 2.7.11 |
https://en.wikipedia.org/wiki/RAB8A | Ras-related protein Rab-8A is a protein that in humans is encoded by the RAB8A gene.
Function
The protein encoded by this gene is a member of the RAS superfamily which are small GTP/GDP-binding proteins with an average size of 200 amino acids. The RAS-related proteins of the RAB/YPT family may play a role in the transport of proteins from the endoplasmic reticulum to the Golgi and the plasma membrane. This protein shares 97%, 96%, and 51% similarity with the dog RAB8, mouse MEL, and mouse YPT1 proteins, respectively and contains the 4 GTP/GDP-binding sites that are present in all the RAS proteins. The putative effector-binding site of this protein is similar to that of the RAB/YPT proteins. However, this protein contains a C-terminal CAAX motif that is characteristic of many RAS superfamily members but which is not found in YPT1 and the majority of RAB proteins. Although this gene was isolated as a transforming gene from a melanoma cell line, no linkage between MEL and malignant melanoma has been demonstrated. This oncogene is located 800 kb distal to MY09B on chromosome 19p13.1.
Interactions
RAB8A has been shown to interact with Optineurin and MAP4K2.
References
Further reading |
https://en.wikipedia.org/wiki/Mesoderm-specific%20transcript%20homolog%20protein | Mesoderm-specific transcript homolog protein is a protein that in humans is encoded by the MEST gene.
This gene encodes a member of the Alpha/beta hydrolase superfamily and has isoform-specific imprinting. The loss of imprinting of this gene has been linked to certain types of cancer and may be due to promoter switching. The encoded protein may play a role in development. Three transcript variants encoding two distinct isoforms have been identified for this gene. A pseudogene for this locus is located on chromosome 6.
References
Further reading |
https://en.wikipedia.org/wiki/AFF1 | AF4/FMR2 family member 1 is a protein that in humans is encoded by the AFF1 gene. At its same location was a record for a separate PBM1 gene, which has since been withdrawn and considered an alias. It was previously known as AF4 (ALL1-fused gene from chromosome 4).
The gene is a member of the AF4/FMR2 (AFF) family, a group of nuclear transcriptional activators which encourage RNA elongation. It is a component of the super elongation complex. It is recognized as a proto-oncogene: chromosomal translocations associated with leukemia can fuse this gene with others like KMT2A, producing an uncontrolled activator protein.
References
External links
Further reading |
https://en.wikipedia.org/wiki/MMP11 | Stromelysin-3 (SL-3) also known as matrix metalloproteinase-11 (MMP-11) is an enzyme that in humans is encoded by the MMP11 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. However, the enzyme encoded by this gene is activated intracellularly by furin within the constitutive secretory pathway. Also in contrast to other MMP's, this enzyme cleaves alpha 1-proteinase inhibitor but weakly degrades structural proteins of the extracellular matrix.
References
Further reading
Matrix metalloproteinases
EC 3.4.24 |
https://en.wikipedia.org/wiki/MYL2 | Myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC-2) also known as the regulatory light chain of myosin (RLC) is a protein that in humans is encoded by the MYL2 gene. This cardiac ventricular RLC isoform is distinct from that expressed in skeletal muscle (MYLPF), smooth muscle (MYL12B) and cardiac atrial muscle (MYL7).
Ventricular myosin light chain-2 (MLC-2v) refers to the ventricular cardiac muscle form of myosin light chain 2 (Myl2). MLC-2v is a 19-KDa protein composed of 166 amino acids, that belongs to the EF-hand Ca2+ binding superfamily. MLC-2v interacts with the neck/tail region of the muscle thick filament protein myosin to regulate myosin motility and function.
Structure
Cardiac, ventricular RLC is an 18.8 kDa protein composed of 166 amino acids. RLC and the second ventricular light chain, essential light chain (ELC, MYL3), are non-covalently bound to IQXXXRGXXXR motifs in the 9 nm S1-S2 lever arm of the myosin head, both alpha (MYH6) and beta (MYH7) isoforms. Both light chains are members of the EF-hand superfamily of proteins, which possess two helix-loop-helix motifs in two globular domains connected by an alpha-helical linker.
Function
The N-terminal EF-hand domain of RLC binds calcium/magnesium at activating concentrations, however the dissociation rate is too slow to modulate cardiac contractility on a beat-by-beat basis. Perturbing the calcium binding region of RLC through site-directed mutagenesis (D47A) decreased tension and st |
https://en.wikipedia.org/wiki/PAX7 | Paired box protein Pax-7 is a protein that in humans is encoded by the PAX7 gene.
Function
Pax-7 plays a role in neural crest development and gastrulation, and it is an important factor in the expression of neural crest markers such as Slug, Sox9, Sox10 and HNK-1. PAX7 is expressed in the palatal shelf of the maxilla, Meckel's cartilage, mesencephalon, nasal cavity, nasal epithelium, nasal capsule and pons.
Pax7 is a transcription factor that plays a role in myogenesis through regulation of muscle precursor cells proliferation. It can bind to DNA as an heterodimer with PAX3. Also interacts with PAXBP1; the interaction links PAX7 to a WDR5-containing histone methyltransferase complex By similarity. Interacts with DAXX too.
PAX7 functions as a marker for a rare subset of spermatogonial stem cells, specifically a sub set of Asingle spermatogonia. These PAX7+ spermatogonia are rare in adult testis but are much more prevalent in newborns, making up 28% of germ cells in neonate testis. Unlike PAX7+ muscle satellite cells, PAX7+ spermatogonia rapidly proliferate and are not quiescent. PAX7+ spermatogonia are able to give rise to all stages of spermatogenesis and produce motile sperm. However, PAX7 is not required for spermatogenesis, as mice without PAX7+ spermatogonia show no deficits in fertility.
PAX7 may also function in the recovery in spermatogenesis. Unlike other spermatogonia, PAX7+ spermatogonia are resistant to radiation and chemotherapy. The surviving PAX7+ spermatog |
https://en.wikipedia.org/wiki/PAX9 | Paired box gene 9, also known as PAX9, is a protein which in humans is encoded by the PAX9 gene. It is also found in other mammals.
Expression and function
This gene is a member of the paired box (PAX) family of transcription factors. During mouse embryogenesis Pax9 expression starts from embryonic day 8.5 and becomes more evident by E9.5; at this stage its expression is restricted to the pharyngeal endoderm. Later on, Pax9 is also expressed in the axial skeleton. Pax9 is required for craniofacial, tooth and limb development, and may more generally involve development of stratified squamous epithelia as well as various organs and skeletal elements. PAX9 plays a role in the absence of wisdom teeth in some human populations (possibly along with the less well studied AXIN2 and MSX1).
Clinical significance
This gene was found amplified in lung cancer. The amplification covers three tissue developmental genes - TTF1, NKX2-8, and PAX9. It appears that certain lung cancer cells select for DNA copy number amplification and increased RNA/protein expression of these three coamplified genes for functional advantages.
Oligodontia
Oligodontia is a genetic disorder caused by the mutation of the PAX9 gene. This disorder results in the congenital absence of 6 or more permanent teeth, with the exception of the third molar. Also known as selective tooth agenesis (STHAG), it is the most common disorder in regard to human dentition, affecting a little less than one fourth of the popu |
https://en.wikipedia.org/wiki/PDK2 | Pyruvate dehydrogenase kinase isoform 2 (PDK2) also known as pyruvate dehydrogenase lipoamide kinase isozyme 2, mitochondrial is an enzyme that in humans is encoded by the PDK2 gene. PDK2 is an isozyme of pyruvate dehydrogenase kinase.
Structure
The protein encoded by the PDK2 gene has two sites, an active site and an allosteric site that allow for the activity and regulation of this enzyme. There are many structural motifs that are important to the regulation of this enzyme. Nov3r and AZ12 inhibitors bind at the lipoamide binding site that is located at one end of the R domain. Pfz3 binds in an extended site at the other end of the R domain. One inhibitor, dicholoroacetate (DCA), binds at the center of the R domain. Within the active site, there are three amino acid residues, R250, T302, and Y320, that make the kinase resistant to the inhibitor dichloroacetate, which uncouples the active site from the allosteric site. This supports the theory that R250, T302, and Y320 stabilize the "open" and "closed" conformations of the built-in lid that controls the access of a nucleotide into the nucleotide-binding cavity. This strongly suggests that the mobility of ATP lid is central to the allosteric regulation of PDHK2 activity serving as a conformational switch required for communication between the active site and allosteric sites in the kinase molecule. There is also a DW-motif that is crucial in mediating DCA, nucleotide, and lipoyl domain binding site communication. This netwo |
https://en.wikipedia.org/wiki/PFKFB3 | PFKFB3 is a gene that encodes the 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 enzyme in humans. It is one of 4 tissue-specific PFKFB isoenzymes identified currently (PFKFB1-4).
Gene
The PFKFB3 gene is mapped to single locus on chromosome 10 (10p15-p14). It spans a region of 32.5kb with an open reading frame that is 5,675bp long. It is estimated to consist of 19 exons, of which 15 are regularly expressed. Alternative splicing of the variable, COOH-terminal domain has been observed, leading to 6 different isoforms termed UBI2K1 to UBI2K6 in humans. Different nomenclature also recognizes two broad categories of PFKFB3 isoforms, termed ‘inducible’ and ‘ubiquitous’. The inducible protein isoform, iPFK2, is named as such because its expression has been shown to be induced by hypoxic conditions.
The PFKFB3 promoter is predicted to contain multiple binding sites, including Sp-1 and AP-2 binding sites. It also contains motifs for the binding of E-box, nuclear factor-1 (NF-1), and progesterone response element. Expression of the promoter is shown to be induce by phorbol esters and cyclic-AMP-dependent protein kinase signaling.
Structure
The four PFKFB isoforms share high (85%) ‘2-Kase/2-Pase core’ sequence homology, but have different properties based on variable N- and C- terminal regulatory domains and variation in residues surrounding the active sites. The PFKFB3 inducible isoform has higher ‘2-Kase’ (kinase) activity than other isoforms, due to phosphorylation of Se |
https://en.wikipedia.org/wiki/PFKL | 6-phosphofructokinase, liver type (PFKL) is an enzyme that in humans is encoded by the PFKL gene on chromosome 21. This gene encodes the liver (L) subunit of an enzyme that catalyzes the conversion of D-fructose 6-phosphate to D-fructose 1,6-bisphosphate, which is a key step in glucose metabolism (glycolysis). This enzyme is a tetramer that may be composed of different subunits encoded by distinct genes in different tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
Structure
Gene
The PFKL mRNA sequence includes 55 nucleotides at the 5' and 515 nucleotides at the 3' noncoding regions, as well as 2,337 nucleotides in the coding region, encoding 779 amino acids. This coding region only shares a 68% similarity between PFKL and the muscle-type PFKM.
Protein
This 80-kDa protein is one of three subunit types that comprise the five tetrameric PFK isozymes. The liver PFK (PFK-5) contains solely PFKL, while the erythrocyte PFK includes five isozymes composed of different combinations of PFKL and the second subunit type, PFKM. The muscle isozyme (PFK-1) is composed solely of PFKM. These subunits evolved from a common prokaryotic ancestor via gene duplication and mutation events. Generally, the N-terminal of the subunits carries out their catalytic activity while the C-terminal contains allosteric ligand binding sites
Function
This gene encodes one of three protein subunits of PFK, which are expressed and combined to form the te |
https://en.wikipedia.org/wiki/PHKG1 | Phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform is an enzyme that in humans is encoded by the PHKG1 gene.
This gene is a member of the Ser/Thr protein kinase family and encodes a protein with one protein kinase domain and two calmodulin-binding domains. This protein is the catalytic member of a 16 subunit protein kinase complex which contains equimolar ratios of 4 subunit types. The complex is a crucial glycogenolytic regulatory enzyme. This gene has two pseudogenes at chromosome 7q11.21 and one at chromosome 11p11.12.
References
Further reading
EC 2.7.11 |
https://en.wikipedia.org/wiki/SERPINE2 | Glia-derived nexin is a protein that in humans is encoded by the SERPINE2 gene.
See also
Serpin
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: I04.021
Serine protease inhibitors |
https://en.wikipedia.org/wiki/PI4KB | Phosphatidylinositol 4-kinase beta is an enzyme that in humans is encoded by the PI4KB gene.
Classification
This gene encodes a phosphatidylinositol 4-kinase which catalyzes phosphorylation of phosphatidylinositol at the D-4 position, yielding phosphatidylinositol 4-phosphate (PI4P). Besides the fact, that PI4P serves as a precursor for other important phosphoinositides, such as phosphatidylinositol 4,5-bisphosphate, PI4P is an essential molecule in the cellular signaling and trafficking especially in the Golgi apparatus and the trans Golgi network.
Phosphatidylinositol 4-kinases are evolutionary conserved among eukaryotes and include four human isoforms
phosphatidylinositol 4-kinase alpha (PI4KA)
phosphatidylinositol 4-kinase beta (PI4KB)
phosphatidylinositol 4-kinase 2-alpha (PI4K2A)
phosphatidylinositol 4-kinase 2-beta (PI4K2B)
Function
Phosphatidylinositol 4-kinase beta (PI4KB) is a soluble protein shuttling between the cytoplasm and the nucleus, and can be recruited to the membranes of the Golgi system via protein-protein interactions, e.g. with small GTP binding proteins Arf1 and Rab11, or a Golgi adaptor protein ACBD3. PI4KB can be phosphorylated by the protein kinase D, which promotes the interaction with 14-3-3 proteins and stabilization of the protein in its active conformation. In cytoplasm PI4KB regulates the trafficking from the Golgi system to the plasma membrane, nevertheless, its nuclear function remains to be determined.
Clinical significance
A |
https://en.wikipedia.org/wiki/PKNOX1 | PBX/Knotted 1 Homeobox 1 (PKNOX1) is a protein that in humans is encoded by the PKNOX1 gene.
An important paralog of this gene is PKNOX2.
Function
PKNOX1 belongs to the three amino acid loop extension (TALE) class of homeodomain transcription factors that form transcriptionally active complexes involved in development and organogenesis. PKNOX1 is essential for embryogenesis, but it can also act as a tumor suppressor in adulthood.
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/PPM1A | Protein phosphatase 1A is an enzyme that in humans is encoded by the PPM1A 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. This phosphatase dephosphorylates, and negatively regulates the activities of, MAP kinases and MAP kinase kinases. It has been shown to inhibit the activation of p38 and JNK kinase cascades induced by environmental stresses. This phosphatase can also dephosphorylate cyclin-dependent kinases, and thus may be involved in cell cycle control. Overexpression of this phosphatase is reported to activate the expression of the tumor suppressor gene TP53/p53, which leads to G2/M cell cycle arrest and apoptosis. Three alternatively spliced transcript variants encoding two distinct isoforms have been described.
Interactions
PPM1A has been shown to interact with Metabotropic glutamate receptor 3.
In 2006, Dr. Feng found that PPM1A can terminate TGF-beta signaling by inactivating Smad3 via dephosphorylation. Smad3 is an essential component of the TGF-beta signalling pathway.
References
Further reading |
https://en.wikipedia.org/wiki/TREM1 | Triggering receptor expressed on myeloid cells 1 (TREM1) an immunoglobulin (Ig) superfamily transmembrane protein that, in humans, is encoded by the TREM1 gene. TREM1 is constitutively expressed on the surface of peripheral blood monocytes and neutrophils, and upregulated by toll-like receptor (TLR) ligands; activation of TREM1 amplifies immune responses.
Function
Monocyte-, macrophage- and neutrophil-mediated inflammatory responses can be stimulated via receptors such as G protein-linked 7-transmembrane receptors (such as FPR1), Fc receptors, CD14, TLRs (such as TLR4), and cytokine receptors. TREM1 amplifies TLR-induced inflammation by increasing production of inflammatory cytokines. The ligand of TREM1 is unknown, however, bacterial infection, ischemic stroke and challenge with lipopolysaccharide or lipoteichoic acid were observed to increase TREM1 expression. In granulocytes, C/EBPε induces TREM1 expression independently from inflammatory response.
TREM1 forms a complex with transmembrane adaptor DAP12 and, upon TREM1 engagement, a protein tyrosine kinase Syk-mediated cascade of tyrosine phosphorylation is initiated, activating downstream mediators such as PLCγ, PI3K, and MAPK. This cascade promotes the release of inflammatory cytokines and/or chemokines by neutrophils and macrophages, as well as their migration.
Based on laboratory studies, TREM1 might be involved in development of atherosclerosis, non-alcoholic fatty liver disease (NAFLD), and ischemic stroke.
Can |
https://en.wikipedia.org/wiki/ARFGAP1 | ADP-ribosylation factor GTPase-activating protein 1 is an enzyme that in humans is encoded by the ARFGAP1 gene. Two transcript variants encoding different isoforms have been found for this gene.
Function
The protein encoded by this gene is a GTPase-activating protein (GAP) which associates with the Golgi apparatus and which interacts with ADP-ribosylation factor 1 (ARF1). The encoded protein promotes hydrolysis of ARF1-bound GTP and is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is required for the fusion of these vesicles with target compartments. The activity of this protein is stimulated by phosphoinositides and inhibited by phosphatidylcholine.
The protein has two amphipathic lipid packing sensor motifs (ALPS), that let the protein sense the curvature of the membrane (<30 nm) or lipid packing defects, and in this way evaluate if the vesicle is mature and ready for coat disassembly.
Interactions
ARFGAP1 has been shown to interact with KDELR1 and LRRK2.
References
External links
Further reading |
https://en.wikipedia.org/wiki/HIST2H3PS2 | Histone cluster 2, H3, pseudogene 2, also known as HIST2H3PS2, is a human gene.
References
Further reading
Pseudogenes |
https://en.wikipedia.org/wiki/Cav1.1 | {{DISPLAYTITLE:Cav1.1}}
Cav1.1 also known as the calcium channel, voltage-dependent, L type, alpha 1S subunit, (CACNA1S), is a protein which in humans is encoded by the CACNA1S gene. It is also known as CACNL1A3 and the dihydropyridine receptor (DHPR, so named due to the blocking action DHP has on it).
Function
This gene encodes one of the five subunits of the slowly inactivating L-type voltage-dependent calcium channel in skeletal muscle cells. Mutations in this gene have been associated with hypokalemic periodic paralysis, thyrotoxic periodic paralysis and malignant hyperthermia susceptibility.
Cav1.1 is a voltage-dependent calcium channel found in the transverse tubule of muscles. In skeletal muscle it associates with the ryanodine receptor RyR1 of the sarcoplasmic reticulum via a mechanical linkage. It senses the voltage change caused by the end-plate potential from nervous stimulation and propagated by sodium channels as action potentials to the T-tubules. It was previously thought that when the muscle depolarises, the calcium channel opens, allowing calcium in and activating RyR1, which mediates much greater calcium release from the sarcoplasmic reticulum. This is the first part of the process of excitation-contraction coupling, which ultimately causes the muscle to contract. Calcium entry through Cav1.1 is not required in skeletal muscle, as it is in cardiac muscle; Cav1.1 undergoes a conformational change which allosterically activates RyR1.
Clinical significance |
https://en.wikipedia.org/wiki/PKN2 | Serine/threonine-protein kinase N2 is an enzyme that in humans and Strongylocentrotus purpuratus is encoded by the PKN2 gene.
Interactions
PKN2 has been shown to interact with:
AKT1,
NCK1,
PTPN13,
Phosphoinositide-dependent kinase-1, and
RHOA.
Further reading
References
EC 2.7.11 |
https://en.wikipedia.org/wiki/PROX1 | Prospero homeobox protein 1 is a protein that in humans is encoded by the PROX1 gene. The Prox1 gene is critical for the development of multiple
tissues. Prox1 activity is necessary and sufficient to specify a lymphatic endothelial cell fate in endothelial progenitors located in the embryonic veins.
Interactions
PROX1 has been shown to interact with EP300.
Production
PROX1 is produced primarily in the dentate gyrus in the mouse, and in the dentate gyrus and white matter in humans. Gene expression data for mouse, human and macaque from the Allen Brain Atlases can be found here.
Clinical significance
PROX1 is used as a marker for lymphatic endothelium in biopsy samples.
Homologous gene
PROX2
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/GeneMark | GeneMark is a generic name for a family of ab initio gene prediction programs developed at the Georgia Institute of Technology in Atlanta. Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of Haemophilus influenzae, and in 1996 for the first archaeal genome of Methanococcus jannaschii. The algorithm introduced inhomogeneous three-periodic Markov chain models of protein-coding DNA sequence that became standard in gene prediction as well as Bayesian approach to gene prediction in two DNA strands simultaneously. Species specific parameters of the models were estimated from training sets of sequences of known type (protein-coding and non-coding). The major step of the algorithm computes for a given DNA fragment posterior probabilities of either being "protein-coding" (carrying genetic code) in each of six possible reading frames (including three frames in complementary DNA strand) or being "non-coding". Original GeneMark (developed before the HMM era in Bioinformatics) is an HMM-like algorithm; it can be viewed as approximation to known in the HMM theory posterior decoding algorithm for appropriately defined HMM.
Prokaryotic gene prediction
The GeneMark.hmm algorithm (1998) was designed to improve gene prediction accuracy in finding short genes and gene starts. The idea was to integrate the Markov chain models used in GeneMark into a hidden Markov model framework, with tra |
https://en.wikipedia.org/wiki/PTPN7 | Protein tyrosine phosphatase non-receptor type 7 is an enzyme that in humans is encoded by the PTPN7 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 gene is preferentially expressed in a variety of hematopoietic cells, and is an early response gene in lymphokine stimulated cells. The noncatalytic N-terminus of this PTP can interact with MAP kinases and suppress the MAP kinase activities. This PTP was shown to be involved in the regulation of T cell antigen receptor (TCR) signaling, which was thought to function through dephosphorylating the molecules related to MAP kinase pathway. Two alternatively spliced transcript variants encoding different isoforms have been found for this gene.
Interactions
PTPN7 has been shown to interact with MAPK3 and MAPK1.
References
Further reading |
https://en.wikipedia.org/wiki/PTPRB | Receptor-type tyrosine-protein phosphatase beta or VE-PTP is an enzyme specifically expressed in endothelial cells that in humans is encoded by the PTPRB gene.
Function
VE-PTP is a member of the classical protein tyrosine phosphatase (PTP) family. The deletion of the gene in mouse models was shown to be embryonically lethal, thus indicating that it is important for vasculogenesis and blood vessel development. In addition, it was shown to participate in adherens junctions complex and regulate vascular permeability. Recently, Soni et al. have shown that tyrosine phosphorylation of VE-PTP via Pyk2 kinase downstream of STIM1-induced calcium entry mediates disassembly of the endothelial adherens junctions.
Interactions
VE-PTP contains an extracellular domain composed of multiple fibronectin type_III repeats, a single transmembrane segment and one intracytoplasmic catalytic domain, thus belongs to R3 receptor subtype PTPs.
The extracellular region was shown to interact with the angiopoietin receptor Tie-2 and with the adhesion protein VE-cadherin.
VE-PTP was also found to interact with Grb2 and plakoglobin through its cytoplasmatic domain.
Role in disease
Dysregulation of PTPRB correlates with the development of a variety of tumors. PTPRB promotes metastasis of colorectal cancer cells via inducing epithelial-mesenchymal transition (EMT).
References
Further reading |
https://en.wikipedia.org/wiki/PTPRN | Receptor-type tyrosine-protein phosphatase-like N, also called "IA-2", is an enzyme that in humans is encoded by the PTPRN gene.
Overview
The IA-2 protein encoded by PTPRN gene is a member of the protein tyrosine phosphatase (PTP) family and PTPRN subfamily. 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, a single transmembrane region, and a single catalytic domain, and thus represents a receptor-type PTP. This PTP was found to be an autoantigen that is reactive with insulin-dependent diabetes mellitus (IDDM) patient sera, and thus may be a potential target of autoimmunity in diabetes mellitus.
Structure
IA-2 and IA-2b belong to family of protein tyrosine phosphatase-like (PTP) molecules. IA-2 is a transmembrane protein with 979 amino acids encoded by a gene on human chromosome 2q35. Similarly, IA-2b has 986 amino acids, and it is located on human chromosome 7q36. The IA-2 is synthesised as a pro-protein of 110 kDa which is then converted by post-translational modifications into a 130 kDa protein.
The IA-2 and IA-2b shares 74% identity within the intracellular domains, but only 27% in the extracellular domains.
The IA-2 protein is expressed mainly in cells of neuroendocrine origin, such as pancreatic islets and brain. The IA-2 protein is localised in the membrane of secretory granules of pancreatic β-cell |
https://en.wikipedia.org/wiki/RBBP8 | Retinoblastoma-binding protein 8 is a protein that in humans is encoded by the RBBP8 gene.
Function
The protein encoded by this gene is a ubiquitously expressed nuclear protein. It is found among several proteins that bind directly to retinoblastoma protein, which regulates cell proliferation. This protein complexes with transcriptional co-repressor CTBP. It is also associated with BRCA1 and is thought to modulate the functions of BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. It is suggested that this gene may itself be a tumor suppressor acting in the same pathway as BRCA1. Three transcript variants encoding two different isoforms have been found for this gene. More transcript variants exist, but their full-length natures have not been determined.
Interactions
RBBP8 has been shown to interact with:
ATM,
BRCA1,
CTBP1,
LMO4,
RB1,
RBL1,
RBL2, and
SIAH1
References
Further reading |
https://en.wikipedia.org/wiki/RFC5 | Replication factor C subunit 5 is a protein that in humans is encoded by the RFC5 gene.
Function
The elongation of primed DNA templates by DNA polymerase delta and DNA polymerase epsilon requires the accessory proteins proliferating cell nuclear antigen (PCNA) and replication factor C (RFC). RFC, also named activator 1, is a protein complex consisting of five distinct subunits of 140, 40, 38, 37, and 36 kD. This gene encodes the 36 kD subunit. This subunit can interact with the C-terminal region of PCNA. It forms a core complex with the 38 and 40 kDa subunits. The core complex possesses DNA-dependent ATPase activity, which was found to be stimulated by PCNA in an in vitro system. Alternatively spliced transcript variants encoding distinct isoforms have been reported.
Interactions
RFC5 has been shown to interact with:
BRD4,
CHTF18,
PCNA,
RFC2, and
RFC4.
References
Further reading |
https://en.wikipedia.org/wiki/RTKN | Rhotekin is a protein that in humans is encoded by the RTKN gene.
This gene encodes a scaffold protein that interacts with GTP-bound Rho proteins. Binding of this protein inhibits the GTPase activity of Rho proteins. This protein may interfere with the conversion of active, GTP-bound Rho to the inactive GDP-bound form by RhoGAP. Rho proteins regulate many important cellular processes, including cytokinesis, transcription, smooth muscle contraction, cell growth and transformation. Dysregulation of the Rho signal transduction pathway has been implicated in many forms of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms.
References
Further reading |
https://en.wikipedia.org/wiki/S100A13 | S100 calcium-binding protein A13 (S100A13) is a protein that in humans is encoded by the S100A13 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. This protein is widely expressed in various types of tissues with a high expression level in thyroid gland. In smooth muscle cells, this protein co-expresses with other family members in the nucleus and in stress fibers, suggesting diverse functions in signal transduction. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene.
Interactions
S100A13 has been shown to interact with SYT1 and FGF1.
Pathology
Up-regulation of S100A13 was detected in cystic papillary thyroid carcinoma and association of S100A13 expression and chemotherapy resistance was shown in proteomics study of melanoma.
References
Further reading
S100 proteins |
https://en.wikipedia.org/wiki/SERPINB4 | Serpin B4 is a protein that in humans is encoded by the SERPINB4 gene.
See also
Serpin
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: I04.009
Serine protease inhibitors |
https://en.wikipedia.org/wiki/TRAPPC2 | Trafficking protein particle complex subunit 2 (TRAPPC2) also known as MBP-1-interacting protein 2A (MIP-2A) is a protein that in humans is encoded by the TRAPPC2 gene. A processed pseudogene of this gene is located on chromosome 19, and other pseuodogenes of it are found on chromosome 8 and the Y chromosome. Two transcript variants encoding the same protein have been found for this gene.
Function
Trafficking protein particle complex subunit 2 is thought to be part of a large multisubunit complex involved in the targeting and fusion of endoplasmic reticulum-to-Golgi transport vesicles with their acceptor compartment. In addition, the encoded protein can bind MBP1 and block its transcriptional repression capability.
Genetic Location
The TRAPPC2 gene is located on the X-chromosome at position 22 between base-pairs 13,712,241 to 13,734,634.
Clinical significance
Mutations in this gene are a cause of X-linked spondyloepiphyseal dysplasia tarda (SEDT).
Interactions
TRAPPC2 has been shown to interact with Alpha-enolase and CLIC1.
References
Further reading
External links
GeneReviews/NIH/NCBI/UW entry on X-Linked Spondyloepiphyseal Dysplasia Tarda
OMIM entries on X-Linked Spondyloepiphyseal Dysplasia Tarda |
https://en.wikipedia.org/wiki/SEPP1 | Selenoprotein P is a protein that in humans is encoded by the SEPP1 gene.
This gene encodes a selenoprotein containing multiple selenocysteine (Sec) residues, which are encoded by the UGA codon that normally signals translation termination. The 3' UTR of selenoprotein genes have a common stem-loop structure, the sec insertion sequence (SECIS), which is necessary for the recognition of UGA as a Sec codon rather than as a stop signal. This selenoprotein is an extracellular glycoprotein, and is unusual in that it contains 10 Sec residues (human, rat, mouse) per polypeptide, one located at the C-terminal side of protein and others at the N-terminal side. It is a heparin-binding protein that appears to be associated with endothelial cells, and has been implicated to function as an antioxidant in the extracellular space. Several transcript variants, encoding either the same or different isoform, have been found for this gene.
Animal models
Mice and dogs with knock-out variants in their SEPP1 homologues (Selenop and SELENOP respectively) may develop cerebellar ataxia phenotypes. SEPP1 and neural precursor cell levels in mouse brains increase post-exercise. Mice engineered to lack SEPP1 did not increase neural precursors.
See also
Selenium in biology
References
Further reading
Selenoproteins |
https://en.wikipedia.org/wiki/Delta-sarcoglycan | Delta-sarcoglycan is a protein that in humans is encoded by the SGCD gene.
Function
The protein encoded by this gene is one of the four known components of the sarcoglycan complex, which is a subcomplex of the dystrophin-glycoprotein complex (DGC). DGC forms a link between the F-actin cytoskeleton and the extracellular matrix. This protein is expressed most abundantly in skeletal and cardiac muscle. The mutations in this gene have been associated with autosomal recessive limb-girdle muscular dystrophy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding distinct isoforms have been observed.
In melanocytic cells SGCD gene expression may be regulated by MITF.
Interactions
SGCD has been shown to interact with FLNC.
References
Further reading
External links
LOVD mutation database: SGCD
Human proteins |
https://en.wikipedia.org/wiki/Homeobox%20protein%20SIX1 | Homeobox protein SIX1 (Sine oculis homeobox homolog 1) is a protein that in humans is encoded by the SIX1 gene.
Function
The vertebrate SIX genes are homologs of the Drosophila 'sine oculis' (so) gene, which is expressed primarily in the developing visual system of the fly. Members of the SIX gene family encode proteins that are characterized by a divergent DNA-binding homeodomain and an upstream SIX domain, which may be involved both in determining DNA-binding specificity and in mediating protein–protein interactions. Genes in the SIX family have been shown to play roles in vertebrate and insect development or have been implicated in maintenance of the differentiated state of tissues.[supplied by OMIM]
Interactions
SIX1 has been shown to interact with EYA1, DACH, GRO and MDFI.
References
Further reading
Transcription factors |
https://en.wikipedia.org/wiki/Neutral%20amino%20acid%20transporter%20B%280%29 | Neutral amino acid transporter B(0) is a protein that in humans is encoded by the SLC1A5 gene.
See also
Glutamate transporter
Solute carrier family
References
Further reading
Solute carrier family |
https://en.wikipedia.org/wiki/SS18 | Protein SSXT is a protein that in humans is encoded by the SS18 gene.
Function
SS18 is a member of the human SWI/SNF chromatin remodeling complex.
Clinical significance
SS18 is involved in a chromosomal translocation commonly found in synovial sarcoma.
Interactions
SS18 has been shown to interact with:
EP300,
MLLT10,
SMARCA2, and
SMARCB1.
References
Further reading |
https://en.wikipedia.org/wiki/TEAD1 | Transcriptional enhancer factor TEF-1 also known as TEA domain family member 1 (TEAD1) and transcription factor 13 (TCF-13) is a protein that in humans is encoded by the TEAD1 gene. TEAD1 was the first member of the TEAD family of transcription factors to be identified.
Structure
All members of the TEAD family share a highly conserved DNA binding domain called the TEA domain. This DNA binding domain has a consensus DNA sequence 5’-CATTCCA/T-3’ that is called the MCAT element. The three dimensional structure of the TEA domain has been identified [5]. Its conformation is close to that of the homeodomain and contains 3 α helixes (H1, H2 and H3). It is the H3 helix that enables TEAD proteins to bind DNA.
Another conserved domain of TEAD1 is located at the C terminus of the protein. It allows the binding of cofactors and has been called the YAP1 binding domain, because it is its ability to bind this well-known TEAD proteins co-factor that led to its identification. Indeed, TEAD proteins cannot induce gene expression on their own. They have to associate with cofactors to be able to act
Tissue distribution
TEAD1 is expressed in various tissues including skeletal muscle, pancreas, placenta, lung, and heart.
Orthologs
TEAD proteins are found in many organisms under different names, assuming different functions. For example, in Saccharomyces cerevisiae TEC-1 regulates the transposable element TY1 and is involved in pseudohyphale growth (the elongated shape that yeasts take |
https://en.wikipedia.org/wiki/Russellite%20%28mineral%29 | Russellite is a bismuth tungstate mineral with the chemical formula Bi2WO6. It crystallizes in the orthorhombic crystal system. Russellite is yellow or yellow-green in color, with a Mohs hardness of .
Russellite is named for the mineralogist Sir Arthur Russell, and the type locality is the Castle-an-Dinas Mine, near St Columb Major in Cornwall, where it was found in 1938 in wolframite.
It occurs as a secondary alteration of other bismuth bearing minerals in tin - tungsten
hydrothermal ore deposits, pegmatites and greisens. It typically occurs associated with native bismuth, bismuthinite, bismite, wolframite, ferberite, scheelite, ferritungstite, anthoinite, mpororoite, koechlinite, cassiterite, topaz, muscovite, tourmaline and quartz.
References
Tungstate minerals
Bismuth minerals
Orthorhombic minerals
Minerals in space group 29 |
https://en.wikipedia.org/wiki/THOP1 | Thimet oligopeptidase is an enzyme that in humans is encoded by the THOP1 gene.
References
Further reading |
https://en.wikipedia.org/wiki/TNNT1 | Slow skeletal muscle troponin T (sTnT) is a protein that in humans is encoded by the TNNT1 gene.
The TNNT1 gene is located at 19q13.4 in the human chromosomal genome, encoding the slow twitch skeletal muscle isoform of troponin T (ssTnT). ssTnT is an ~32-kDa protein consisting of 262 amino acids (including the first methionine) with an isoelectric point (pI) of 5.95. It is the tropomyosin binding and thin filament anchoring subunit of the troponin complex in the sarcomeres of slow twitch skeletal muscle fibers. TNNT1 gene is specifically expressed in slow skeletal muscle of vertebrates, with one exception that dry land toad (Bufo) cardiac muscle expresses ssTnT other than cardiac TnT.
Evolution
Three homologous genes have evolved in vertebrates, encoding three muscle type specific isoforms of TnT. Each of the TnT isoform genes is linked to one of the three troponin I isoform genes encoding the inhibitory subunit of the troponin complex, in chromosomal DNA to form three gene pairs: The fast skeletal muscle TnI (fsTnI)-fsTnT, ssTnI-cardiac (cTnT) and cTnI-ssTnT gene pairs. Sequence and epitope conservation studies suggested that genes encoding the muscle type specific TnT and TnI isoforms may have evolved from duplications of a fsTnI-like-fsTnT-like gene pair. Evolutionary lineage of the three TnI-TnT gene pairs shows that cTnI-ssTnT is the newest and most closely linked.
Protein sequence alignment demonstrated that TNNT1 genes are highly conserved among vertebrate specie |
https://en.wikipedia.org/wiki/Clear%20cell | In histology, a clear cell is a cell that shows a clear cytoplasm when stained with hematoxylin and eosin (H&E).
Normal histology
In the skin, some secretory cells in the epithelium appear as clear cells, and are one of the components of eccrine sweat glands. A clear cell's plasma membrane is highly folded, more so on the apical and lateral surfaces. The cytoplasm of clear cells contains large amounts of glycogen and many mitochondria. Melanocytes appear as clear cells when in the stratum basale of the skin, and Langerhans' cells appear as clear cells in the stratum spinosum.
C cells, more commonly referred to as parafollicular cells are type of cell found in the thyroid gland which stain clear using H&E.
Clear cell cancers
Clear-cell adenocarcinomas are adenocarcinomas that contain a preponderance of clear cells.
References
Tissues (biology)
Secretory cells |
https://en.wikipedia.org/wiki/UBE2D1 | Ubiquitin-conjugating enzyme E2 D1 is a protein that in humans is encoded by the UBE2D1 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. This enzyme is closely related to a stimulator of iron transport (SFT), and is up-regulated in hereditary hemochromatosis. It also functions in the ubiquitination of the tumor-suppressor protein p53 and the hypoxia-inducible transcription factor HIF1alpha by interacting with the E1 ubiquitin-activating enzyme and the E3 ubiquitin-protein ligases.
Interactions
UBE2D1 has been shown to interact with:
BARD1,
BRCA1, and
UBE3A.
References
Further reading |
https://en.wikipedia.org/wiki/UBE2D2 | Ubiquitin-conjugating enzyme E2 D2 is a protein that in humans is encoded by the UBE2D2 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. This enzyme functions in the ubiquitination of the tumor-suppressor protein p53, which is induced by an E3 ubiquitin-protein ligase. Two alternatively spliced transcript variants have been found for this gene and they encode distinct isoforms.
Interactions
UBE2D2 has been shown to interact with:
Baculoviral IAP repeat-containing protein 3,
NEDD4,
PJA1,
PJA2, and
UBE3A.
References
Further reading |
https://en.wikipedia.org/wiki/UGT2B15 | UDP-glucuronosyltransferase 2B15 is an enzyme that in humans is encoded by the UGT2B15 gene.
The UGTs are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. UGT2B8 demonstrates reactivity with estriol. See UGT2B4 (MIM 600067).[supplied by OMIM]
References
Further reading |
https://en.wikipedia.org/wiki/RAD18 | E3 ubiquitin-protein ligase RAD18 is an enzyme that in humans is encoded by the RAD18 gene.
Function
The protein encoded by this gene is highly similar to S. cerevisiae DNA damage repair protein Rad18. Yeast Rad18 functions through interaction with Rad6, which is a ubiquitin-conjugating enzyme required for post-replication repair of damaged DNA. Similar to its yeast counterpart, this protein is able to interact with the human homolog of yeast Rad6 protein through a conserved ring finger motif. Mutation of this motif results in defective replication of UV-damaged DNA and hypersensitivity to multiple mutagens.
Animal models
Model organisms have been used in the study of RAD18 function. A conditional knockout mouse line, called Rad18tm1a(EUCOMM)Wtsi, was generated as part of the EUCOMM program — a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists — at the Wellcome Trust Sanger Institute. Mice lacking Rad18 had no significant defects in viability or fertility, therefore male and female animals underwent a standardized phenotypic screen to determine the effects of deletion.
Twenty five tests were carried out and four significant phenotypes were reported:
Mutant male mice had a decreased body weight compared to wildtype control mice.
Mutant male mice showed increased activity, VO2 and energy expenditure, determined by indirect calorimetry.
Dual-energy X-ray absorptiometry (DEXA) showed mutant male mice had a |
https://en.wikipedia.org/wiki/NEIL1 | Endonuclease VIII-like 1 is an enzyme that in humans is encoded by the NEIL1 gene.
NEIL1 belongs to a class of DNA glycosylases homologous to the bacterial Fpg/Nei family. These glycosylases initiate the first step in base excision repair by cleaving bases damaged by reactive oxygen species (ROS) and introducing a DNA strand break via the associated lyase reaction.
Targets
NEIL1 recognizes (targets) and removes certain ROS-damaged bases and then incises the abasic site via β,δ elimination, leaving 3′ and 5′ phosphate ends. NEIL1 recognizes oxidized pyrimidines, formamidopyrimidines, thymine residues oxidized at the methyl group, and both stereoisomers of thymine glycol. The best substrates for human NEIL1 appear to be the hydantoin lesions, guanidinohydantoin, and spiroiminodihydantoin that are further oxidation products of 8-oxoG. NEIL1 is also capable of removing lesions from single-stranded DNA as well as from bubble and forked DNA structures. Because the expression of NEIL1 is cell-cycle dependent, and because it acts on forked DNA structures and interacts with PCNA and FEN-1, it has been proposed that NEIL1 functions in replication associated DNA repair.
Deficiency in cancer
NEIL1 is one of the DNA repair genes most frequently hypermethylated in head and neck squamous cell carcinoma (HNSCC). When 160 human DNA repair genes were evaluated for aberrant methylation in HNSCC tumors, 62% of tumors were hypermethylated in the NEIL1 promoter region, causing NEIL1 mes |
https://en.wikipedia.org/wiki/Cytidine%20deaminase | Cytidine deaminase is an enzyme that in humans is encoded by the CDA gene.
This gene encodes an enzyme involved in pyrimidine salvaging. The encoded protein forms a homotetramer that catalyzes the irreversible hydrolytic deamination of cytidine and deoxycytidine to uridine and deoxyuridine, respectively. It is one of several deaminases responsible for maintaining the cellular pyrimidine pool. Mutations in this gene are associated with decreased sensitivity to the cytosine nucleoside analogue cytosine arabinoside used in the treatment of certain childhood leukemias. Most cytidine deaminases act on RNA, and the few that act on DNA require ssDNA.
A related activation-induced (cytidine) deaminase (AID) regulates antibody diversification, especially the process of somatic hypermutation.
Interactive pathway map
References
Further reading
External links
EC 3.5.4 |
https://en.wikipedia.org/wiki/Aladin%20%28protein%29 | AladinTM, also known as adracalin, is a nuclear envelope protein that in humans is encoded by the AAAS gene. It is named after the achalasia–addisonianism–alacrima syndrome (triple A syndrome) which occurs when the gene is mutated.
Function
Aladin is a component of the nuclear pore complex, to which it is attached by nucleoporin NDC1. Mutant aladin causes selective failure of nuclear protein import and hypersensitivity to oxidative stress. Mutant aladin also causes decreased nuclear import of aprataxin, a repair protein for single-strand breaks, and DNA ligase I, employed in DNA base excision repair. These decreases in DNA repair proteins may increase the susceptibility of cells to oxidative stress by allowing accumulation of oxidative DNA damages that trigger cell death.
Clinical significance
Mutations in the AAAS gene are responsible for Triple A syndrome (also known as Allgrove Syndrome). Triple-A syndrome is an autosomal recessive neuroendocrinological disease.
Aladin is also employed in specific oocyte meiotic stages, including spindle assembly and spindle positioning. Female mice homozygously null for aladin are sterile.
References
Further reading
External links
Nuclear pore complex |
https://en.wikipedia.org/wiki/ELL%20%28gene%29 | RNA polymerase II elongation factor ELL is an enzyme that in humans is encoded by the ELL gene.
Interactions
ELL (gene) has been shown to interact with P53.
References
Further reading |
https://en.wikipedia.org/wiki/KLRC4 | NKG2-F type II integral membrane protein is a protein that in humans is encoded by the KLRC4 gene.
Natural killer (NK) cells are lymphocytes that can mediate lysis of certain tumor cells and virus-infected cells without previous activation. They can also regulate specific humoral and cell-mediated immunity. NK cells preferentially express several calcium-dependent (C-type) lectins, which have been implicated in the regulation of NK cell function. KLRC4 is a member of the NKG2 group which are expressed primarily in natural killer (NK) cells and encodes a family of transmembrane proteins characterized by a type II membrane orientation (extracellular C terminus) and the presence of a C-type lectin domain. The NKG2 gene family is located within the NK complex, a region that contains several C-type lectin genes preferentially expressed on NK cells. The 3' end of the KLRC4 transcript includes the first non-coding exon found at the 5' end of the adjacent D12S2489E gene transcript.
References
Further reading |
https://en.wikipedia.org/wiki/CUL4B | Cullin-4B is a protein that in humans is encoded by the CUL4B gene which is located on the X chromosome. CUL4B has high sequence similarity with CUL4A, with which it shares certain E3 ubiquitin ligase functions. CUL4B is largely expressed in the nucleus and regulates several key functions including: cell cycle progression, chromatin remodeling and neurological and placental development in mice. In humans, CUL4B has been implicated in X-linked intellectual disability and is frequently mutated in pancreatic adenocarcinomas and a small percentage of various lung cancers. Viruses such as HIV can also co-opt CUL4B-based complexes to promote viral pathogenesis. CUL4B complexes containing Cereblon are also targeted by the teratogenic drug thalidomide.
Structure
Human CUL4B is 913 amino acids long and shares a high degree of sequence identity (84%) with CUL4A with the exception of its unique N-terminal region. The extreme N-terminus of CUL4B is disordered and, currently, it is unclear what structural and functional qualities it possesses. CUL4B binds to the beta-propeller of the DDB1 adaptor protein which interacts with numerous DDB1-CUL4-Associated Factors (DCAFs). This interaction is crucial for the recruitment of substrates to the ubiquitin ligase complex. At the C-terminal end, CUL4B interacts with the RBX1/ROC1 protein via its RING domain. RBX1 is a core component of Cullin-RING ubiquitin ligase (CRL) complexes and functions to recruit E2 ubiquitin conjugating enzymes. Theref |
https://en.wikipedia.org/wiki/CUL3 | Cullin 3 is a protein that in humans is encoded by the CUL3 gene.
Cullin 3 protein belongs to the family of cullins which in mammals contains eight proteins (Cullin 1, Cullin 2, Cullin 3, Cullin 4A, Cullin 4B, Cullin 5, Cullin 7 and Cullin 9). Cullin proteins are an evolutionarily conserved family of proteins throughout yeast, plants and mammals.
Protein function
Cullin 3 is a component of Cullin-RING E3 ubiquitin ligases complexes (CRLs) which are involved in protein ubiquitylation and represent a part of ubiquitin–proteasome system (UPS). Added ubiquitin moieties to the lysine residue by CRLs then target the protein for the proteasomal degradation. Cullin-RING E3 ubiquitin ligases are involved in many cellular processes responsible for cell cycle regulation, stress response, protein trafficking, signal transduction, DNA replication, transcription, protein quality control, circadian clock and development.
Deletion of CUL3 gene in mice causes embryonic lethality.
Cullin 3-RING E3 ubiquitin ligases
Cullin 3-RING complex consists of Cullin 3 protein, RING-box protein 1 (RBX1), which recruits the ubiquitin-conjugating enzyme (E2), and a Bric-a-brac/Tramtrack/Broad (BTB) protein, a substrate recognition subunit. Cullin 3 protein is a core scaffold protein coordinating other components of the CRL complex. Cullin 3-RING complexes can also dimerise via their BTB domains which lead to creation of two substrate receptors and two catalytic RING domains.
Activation of the complex |
https://en.wikipedia.org/wiki/COP9%20signalosome%20complex%20subunit%203 | COP9 signalosome complex subunit 3 is a protein that in humans is encoded by the COPS3 gene. It encodes a subunit of the COP9 signalosome.
The protein encoded by this gene possesses kinase activity that phosphorylates regulators involved in signal transduction. It phosphorylates I-kappa-B-alpha, p105, and c-Jun. It acts as a docking site for complex-mediated phosphorylation. The gene is located within the Smith-Magenis syndrome region on chromosome 17.
See also
Signalosome
References
External links
Further reading |
https://en.wikipedia.org/wiki/MKNK1 | MAP kinase-interacting serine/threonine-protein kinase 1 is an enzyme that in humans is encoded by the MKNK1 gene.
Interactions
MKNK1 has been shown to interact with MAPK1 and Eukaryotic translation initiation factor 4 gamma.
References
Further reading
EC 2.7.11 |
https://en.wikipedia.org/wiki/SFRS9 | Splicing factor, arginine/serine-rich 9, also known as SFRS9, is a human gene encoding an SR protein involved in splice site selection in alternative splicing.
Interactions
SFRS9 has been shown to interact with Y box binding protein 1 and NOL3.
References
Further reading |
https://en.wikipedia.org/wiki/Death%20receptor%203 | Death receptor 3 (DR3), also known as tumor necrosis factor receptor superfamily member 25 (TNFRSF25), is a cell surface receptor of the tumor necrosis factor receptor superfamily which mediates apoptotic signalling and differentiation. Its only known TNFSF ligand is TNF-like protein 1A (TL1A).
Function
The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor is expressed preferentially by activated and antigen-experienced T lymphocytes. TNFRSF25 is also highly expressed by FoxP3 positive regulatory T lymphocytes. TNFRSF25 is activated by a monogamous ligand, known as TL1A (TNFSF15), which is rapidly upregulated in antigen presenting cells and some endothelial cells following Toll-Like Receptor or Fc receptor activation. This receptor has been shown to signal both through the TRADD adaptor molecule to stimulate NF-kappa B activity or through the FADD adaptor molecule to stimulate caspase activation and regulate cell apoptosis.
Multiple alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported, most of which are potentially secreted molecules. The alternative splicing of this gene in B and T cells encounters a programmed change upon T-cell activation, which predominantly produces full-length, membrane bound isoforms, and is thought to be involved in controlling lymphocyte proliferation induced by T-cell activation. Specifically, activation of TNFRSF25 is dependent upon previous engagement of the T |
https://en.wikipedia.org/wiki/Interleukin-18%20receptor | The interleukin-18 receptor (IL-18R) is an interleukin receptor of the immunoglobulin superfamily.
Endometrial IL-18 receptor mRNA and the ratio of IL-18 binding protein to interleukin 18 are significantly increased in adenomyosis patients in comparison to normal people, indicating a role in its pathogenesis.
References
External links
Clusters of differentiation
Immunoglobulin superfamily cytokine receptors |
https://en.wikipedia.org/wiki/CD84 | CD84 (Cluster of Differentiation 84) is a human protein encoded by the gene.
Function
Members of the CD2 (see MIM 186990) subgroup of the Ig superfamily, such as CD84, have similar patterns of conserved disulfide bonds and function in adhesion interactions between T lymphocytes and accessory cells.
Interactions
CD84 has been shown to interact with SH2D1A.
See also
Cluster of differentiation
References
Further reading
External links
Clusters of differentiation |
https://en.wikipedia.org/wiki/EIF2B4 | Translation initiation factor eIF-2B subunit delta is a protein that in humans is encoded by the EIF2B4 gene.
References
Further reading |
https://en.wikipedia.org/wiki/MBD4 | Methyl-CpG-binding domain protein 4 is a protein that in humans is encoded by the MBD4 gene.
Structure
Human MBD4 protein has 580 amino acids with a methyl-CpG-binding domain at amino acids 82–147 and a C-terminal DNA glycosylase domain at amino acids 426–580. These domains are separated by an intervening region that interacts with UHRF1, an E3 ubiquitin ligase, and USP7, a de-ubiquinating enzyme.
Function
DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 (this gene) comprise a family of nuclear proteins related by the presence in each of a methyl-CpG-binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene.
Deaminated bases as targets
Bases in DNA decay spontaneously, and this decay includes hydrolytic deamination of purines and pyrimidines that contain an exocyclic amino group (see image). Hypoxanthine and xanthine are generated at a |
https://en.wikipedia.org/wiki/AP3D1 | AP-3 complex subunit delta-1 is a protein that in humans is encoded by the AP3D1 gene.
Function
AP3D1 is a subunit of the AP3 adaptor-like complex, which is not associated with clathrin. The AP3D1 subunit is implicated in intracellular biogenesis and trafficking of pigment granules and possibly platelet dense granules and neurotransmitter vesicles.[supplied by OMIM]
Interactions
AP3D1 has been shown to interact with SYBL1.
References
External links
Further reading |
https://en.wikipedia.org/wiki/ARHGEF1 | Rho guanine nucleotide exchange factor 1 is a protein that in humans is encoded by the ARHGEF1 gene. This protein is also called RhoGEF1 or p115-RhoGEF.
Function
Rho guanine nucleotide exchange factor 1 is guanine nucleotide exchange factor (GEF) for the RhoA small GTPase protein. Rho is a small GTPase protein that is inactive when bound to the guanine nucleotide GDP. But when acted on by Rho GEF proteins such as RhoGEF1, this GDP is released and replaced by GTP, leading to the active state of Rho. In this active, GTP-bound conformation, Rho can bind to and activate specific effector proteins and enzymes to regulate cellular functions. In particular, active Rho is a major regulator of the cell actin cytoskeleton.
RhoGEF1 is a member of a group of four RhoGEF proteins known to be activated by G protein coupled receptors coupled to the G12 and G13 heterotrimeric G proteins. The others are ARHGEF11 (also known as PDZ-RhoGEF), ARHGEF12 (also known as LARG) and AKAP13 (also known as ARHGEF13 and Lbc). GPCR-regulated RhoGEF1 (and these related GEF proteins) acts as an effector for G12 and G13 G proteins. In addition to being activated by G12 or G13 G proteins, three of these four RhoGEF proteins (ARHGEF1/11/12) also function as RGS family GTPase-activating proteins (GAPs) to increase the rate of GTP hydrolysis of G12/G13 alpha proteins (which are themselves GTPase proteins). This action increases the rate of G protein deactivation, limiting the time during which these RhoGEFs |
https://en.wikipedia.org/wiki/ARHGEF2 | Rho guanine nucleotide exchange factor 2 is a protein that in humans is encoded by the ARHGEF2 gene.
Function
Rho GTPases play a fundamental role in numerous cellular processes that are initiated by extracellular stimuli that work through G protein-coupled receptors. The encoded protein may form complex with G proteins and stimulate rho-dependent signals.
Interactions
ARHGEF2 has been shown to interact with PAK1.
References
External links
Further reading |
https://en.wikipedia.org/wiki/MAGED1 | Melanoma-associated antigen D1 is a protein that in humans is encoded by the MAGED1 gene.
Function
This gene is a member of the melanoma antigen gene (MAGE) family. Most of the genes of this family encode tumor specific antigens that are not expressed in normal adult tissues except testis. Although the protein encoded by this gene shares strong homology with members of the MAGE family, it is expressed in almost all normal adult tissues. This gene has been demonstrated to be involved in the p75 neurotrophin receptor mediated programmed cell death pathway. Three transcript variants encoding two different isoforms have been found for this gene.
MAGED was found to be deleted in a group of children with an intellectual disability disorder caused by a Xp11.22 deletion.
Maged1 plays a role in controlling the reward circuitry in the brain of mice that is responsible for addictive behaviors.
Interactions
MAGED1 has been shown to interact with UNC5A, PJA1 and XIAP.
References
Further reading |
https://en.wikipedia.org/wiki/SCAMP1 | Secretory carrier-associated membrane protein 1 is a protein that in humans is encoded by the SCAMP1 gene.
Function
This gene product belongs to the SCAMP family of proteins which are secretory carrier membrane proteins. They function as carriers to the cell surface in post-golgi recycling pathways. Different family members are highly related products of distinct genes, and are usually expressed together. These findings suggest that the SCAMPs may function at the same site during vesicular transport rather than in separate pathways.
Interactions
SCAMP1 has been shown to interact with ITSN1 and AP1GBP1.
References
Further reading |
https://en.wikipedia.org/wiki/GTF2IRD1 | General transcription factor II-I repeat domain-containing protein 1 is a protein that in humans is encoded by the GTF2IRD1 gene.
The protein encoded by this gene contains five GTF2I-like repeats and each repeat possesses a potential helix-loop-helix (HLH) motif. It may have the ability to interact with other HLH-proteins and function as a transcription factor or as a positive transcriptional regulator under the control of Retinoblastoma protein. This gene is deleted in Williams syndrome, a multisystem developmental disorder caused by deletion of multiple genes at 7q11.23. Alternative splicing of this gene generates at least 2 transcript variants.
References
Further reading |
https://en.wikipedia.org/wiki/AKAP12 | A-kinase anchor protein 12, aka AKAP250, is an enzyme that in humans is encoded by the AKAP12 gene.
Function
The A-kinase anchor proteins (AKAPs) are a group of structurally diverse proteins, which have the common function of binding to the regulatory subunit of protein kinase A (PKA) and confining the holoenzyme to discrete locations within the cell. This gene encodes a member of the AKAP family. The encoded protein is expressed in endothelial cells, cultured fibroblasts, and osteosarcoma cells. It associates with protein kinase A and C and phosphatase, and serves as a scaffold protein in signal transduction. This protein and RII PKA colocalize at the cell periphery. This protein is a cell growth-related protein. Antibodies to this protein can be produced by patients with myasthenia gravis. Alternative splicing of this gene results in two transcript variants encoding different isoforms.
Interactions
AKAP12 has been shown to interact with Beta-2 adrenergic receptor.
References
External links
Further reading
A-kinase-anchoring proteins |
https://en.wikipedia.org/wiki/SART3 | Squamous cell carcinoma antigen recognized by T-cells 3 is a protein that in humans is encoded by the SART3 gene.
The protein encoded by this gene is an RNA-binding nuclear protein that is a tumor-rejection antigen. This antigen possesses tumor epitopes capable of inducing HLA-A24-restricted and tumor-specific cytotoxic T lymphocytes in cancer patients and may be useful for specific immunotherapy. This gene product is found to be an important cellular factor for HIV-1 gene expression and viral replication. It also associates transiently with U6 and U4/U6 snRNPs during the recycling phase of the spliceosome cycle. This encoded protein is thought to be involved in the regulation of mRNA splicing.
Interactions
SART3 has been shown to interact with RNPS1 and Androgen receptor.
References
Further reading
Spliceosome |
https://en.wikipedia.org/wiki/ELMO1 | Engulfment and cell motility protein 1 is a protein that in humans is encoded by the ELMO1 gene. ELMO1 is located on chromosome number seven in humans and is located on chromosome number thirteen in mice.
Structure
The human engulfment and cell motility protein 1, ELMO1, is 720 residues in length. The protein contains the following three domains:
N-terminal Armadillo domain (residues 82-262)
central ELMO (Engulfment and Cell Motility) domain (301-492)
C-terminal pleckstrin homology domain (residues 527-674)
ELMO1 also has a pro-rich motif at the extreme C terminus. Secondary structure analysis has predicted that there are alpha-helical regions at both the N and C-terminus.
The structure of the pleckstrin homology domain of ELMO1 has been determine by X-ray crystallography.
Function
The protein encoded by this gene interacts with the dedicator of cyto-kinesis 1 protein to promote phagocytosis and effect cell shape changes. Similarity to a C. elegans protein suggests that this protein may function in apoptosis and in cell migration. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms.
Interactions
ELMO1 has been shown to interact with Dock180 and HCK. ELMO1 directly interacts with the SH3 domain of HCK. The association between ELMO1 and HCK is dependent on polyproline interactions.
When ELMO1 is complexed with DOCK180, Rac GTPase-dependent biological processes are activated. The pH domain of ELMO1 functions i |
https://en.wikipedia.org/wiki/REEM | REEM is the latest prototype humanoid robot built by PAL Robotics in Spain. It is a 1.70 m high humanoid robot with 22 degrees of freedom, with a mobile base with wheels, allowing it to move at 4 km/hour. The upper part of the robot consists of a torso with a touch screen, two motorized arms, which give it a high degree of expression, and a head, which is also motorized.
REEM-A and REEM-B are the first and second prototypes of humanoid robots created by PAL Robotics. REEM-B can recognize, grasp and lift objects and walk by itself, avoiding obstacles through simultaneous localization and mapping. The robot accepts voice commands and can recognize faces.
Specifications
See also
ASIMO
Atlas
HUBO
Humanoid robot
iCub
Nao
QRIO
Robonaut
References
External links
Official Blog
Official REEM-C microsite
Bipedal humanoid robots
2005 robots
Robots of Spain
2008 robots |
https://en.wikipedia.org/wiki/AP1M2 | AP-1 complex subunit mu-2 is a protein that in humans is encoded by the AP1M2 gene.
Function
This gene encodes a subunit of the heterotetrameric adaptor-related protein complex 1 (AP-1), which belongs to the adaptor complexes medium subunits family. This protein is capable of interacting with tyrosine-based sorting signals.
Interactions
AP1M2 has been shown to interact with AP2B1.
References
Further reading
External links |
https://en.wikipedia.org/wiki/PANK2%20%28gene%29 | Pantothenate kinase 2, mitochondrial is an enzyme that in humans is encoded by the PANK2 gene.
This gene encodes a protein belonging to the pantothenate kinase family and is the only member of that family to be expressed in mitochondria. Pantothenate kinase is a key regulatory enzyme in the biosynthesis of coenzyme A (CoA) in bacteria and mammalian cells. It catalyzes the first committed step in the universal biosynthetic pathway leading to CoA and is itself subject to regulation through feedback inhibition by acyl CoA species. Mutations in this gene are associated with HARP syndrome and Pantothenate kinase-associated neurodegeneration (PKAN). Alternative splicing, involving the use of alternate first exons, results in multiple transcripts encoding different isoforms.
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Pantothenate Kinase-Associated Neurodegeneration |
https://en.wikipedia.org/wiki/ADCY3 | Adenylyl cyclase type 3 is an enzyme that in humans is encoded by the ADCY3 gene.
Function
This gene encodes adenylyl cyclase 3, which is a membrane-associated enzyme and catalyzes the formation of the secondary messenger cyclic adenosine monophosphate (cAMP).
The ADCY3 subtype likely mediates odorant detection (possibly) via modulation of intracellular cAMP concentration.
References
External links
Further reading
EC 4.6.1 |
https://en.wikipedia.org/wiki/Centromere%20protein%20E | Centromere-associated protein E is a protein that in humans is encoded by the CENPE gene.
Centromere-associated protein E is a kinesin-like motor protein that accumulates in the G2 phase of the cell cycle. Unlike other centromere-associated proteins, it is not present during interphase and first appears at the centromere region of chromosomes during prometaphase. CENPE is proposed to be one of the motors responsible for mammalian chromosome movement and/or spindle elongation.
CENPE is also called Kinesin-7.
Clinical significance
Mutations in CENPE result in autosomal recessive primary microcephaly type 13, which includes skeletal abnormalities and immunodeficiency.
See also
CENPF
CENPJ
CENPT
References
Further reading |
https://en.wikipedia.org/wiki/CISH%20%28protein%29 | Cytokine-inducible SH2-containing protein is a protein that in humans is encoded by the CISH gene. CISH orthologs have been identified in most mammals with sequenced genomes. CISH controls T cell receptor (TCR) signaling, and variations of CISH with certain SNPs are associated with susceptibility to bacteremia, tuberculosis and malaria.
Function
The protein encoded by this gene contains a SH2 domain and a SOCS box domain. The protein thus belongs to the cytokine-induced STAT inhibitor (CIS), also known as suppressor of cytokine signaling (SOCS) or STAT-induced STAT inhibitor (SSI), protein family. CIS family members are known to be cytokine-inducible negative regulators of cytokine signaling.
The expression of this gene can be induced by IL-2, IL-3, GM-CSF and EPO in hematopoietic cells. Proteasome-mediated degradation of this protein has been shown to be involved in the inactivation of the erythropoietin receptor.
CISH is induced by T cell receptor (TCR) ligation and negatively regulates it by targeting the critical signaling intermediate PLC-gamma-1 for degradation. The deletion of Cish in effector T cells has been shown to augment TCR signaling and subsequent effector cytokine release, proliferation and survival. The adoptive transfer of tumor-specific effector T cells knocked out or knocked down for CISH resulted in a significant increase in functional avidity and long-term tumor immunity. There are no changes in activity or phosphorylation of Cish's purported target |
https://en.wikipedia.org/wiki/CKMT2 | Creatine kinase S-type, mitochondrial is an enzyme that in humans is encoded by the CKMT2 gene.
Mitochondrial creatine kinase (MtCK) is responsible for the transfer of high energy phosphate from mitochondria to the cytosolic carrier, creatine. The "energy-rich" gamma-phosphate group of ATP that is generated by oxidative phosphorylation inside mitochondria is trans-phosphorylated to creatine (Cr) to give phospho-creatine (PCr), which then is exported from the mitochondria into the cytosol, where it is made available to cytosolic creatine kinases (CK) for in situ regeneration of the ATP that has been used for cellular work. Cr then is returning to the mitochondria where it stimulates mitochondrial respiration and again is charged-up by mitochondrial ATP via MtCK. This process is termed the PCr/Cr-shuttle or circuit.
MtCK belongs to the creatine kinase (CK) isoenzyme family. It exists as two isoenzymes, sarcomeric MtCK and ubiquitous MtCK, encoded by separate genes. Mitochondrial creatine kinase occurs in two different oligomeric forms: dimers and octamers, in contrast to the exclusively dimeric cytosolic creatine kinase isoenzymes. Sarcomeric mitochondrial creatine kinase has 80% homology with the coding exons of ubiquitous mitochondrial creatine kinase. This gene contains sequences homologous to several motifs that are shared among some nuclear genes encoding mitochondrial proteins and thus may be essential for the coordinated activation of these genes during mitochondrial b |
https://en.wikipedia.org/wiki/CLC%20%28gene%29 | Galectin-10 is an enzyme that in humans is encoded by the CLC gene.
Lysophospholipases are enzymes that act on biological membranes to regulate the multifunctional lysophospholipids. The protein encoded by this gene is a lysophospholipase expressed in eosinophils and basophils. It hydrolyzes lysophosphatidylcholine to glycerophosphocholine and a free fatty acid. This protein may possess carbohydrate or IgE-binding activities. It is both structurally and functionally related to the galectin family of beta-galactoside binding proteins. It may be associated with inflammation and some myeloid leukemias.
See also
Charcot-Leyden crystals
References
External links
Further reading |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.