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metadata
datasets:
  - multimolecule/gencode
library_name: multimolecule
license: agpl-3.0
pipeline: splice-site
pipeline_tag: other
tags:
  - Biology
  - Genomics
  - RNA
  - Splicing
  - rna
widget:
  - example_title: microRNA 21
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: UAGCUUAUCAGACUGAUGUUGA
  - example_title: microRNA 146a
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: UGAGAACUGAAUUCCAUGGGUU
  - example_title: microRNA 155
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: UUAAUGCUAAUCGUGAUAGGGGUU
  - example_title: RNA component of mitochondrial RNA processing endoribonuclease
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: >-
      GGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUAAAAAAAAA
  - example_title: 7SK small nuclear RNA
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: >-
      GGAUGUGAGGGCGAUCUGGCUGCGACAUCUGUCACCCCAUUGAUCGCCAGGGUUGAUUCGGCUGAUCUGGCUGGCUAGGCGGGUGUCCCCUUCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGCGCUCGGUCGAAGAGGACGACCAUCCCCGAUAGAGGAGGACCGGUCUUCGGUCAAGGGUAUACGAGUAGCUGCGCUCCCCUGCUAGAACCUCCAAACAAGCUCUCAAGGUCCAUUUGUAGGAGAACGUAGGGUAGUCAAGCUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGCAUGUGGCAGUCUGCCUUUCUUUU
  - example_title: telomerase RNA component
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: >-
      GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC
  - example_title: vault RNA 2-1
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: >-
      CGGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUUAUGCAA
  - example_title: brain cytoplasmic RNA 1
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: >-
      GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCUCUCAGGGAGGCUAAGAGGCGGGAGGAUAGCUUGAGCCCAGGAGUUCGAGACCUGCCUGGGCAAUAUAGCGAGACCCCGUUCUCCAGAAAAAGGAAAAAAAAAAACAAAAGACAAAAAAAAAAUAAGCGUAACUUCCCUCAAAGCAACAACCCCCCCCCCCCUUU
  - example_title: HIV-1 TAR-WT
    pipeline_tag: splice-site
    sequence_type: ncRNA
    task: splice-site
    text: GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACC
  - example_title: prion protein (Kanno blood group)
    pipeline_tag: splice-site
    sequence_type: mRNA
    task: splice-site
    text: AUGGCGAACCUUGGCUGCUGGAUGCUGGUUCUCUUUGUGGCCACAUGGAGUGACCUGGGCCUCUGC
  - example_title: interleukin 10
    pipeline_tag: splice-site
    sequence_type: mRNA
    task: splice-site
    text: AUGCACAGCUCAGCACUGCUCUGUUGCCUGGUCCUCCUGACUGGGGUGAGGGCC
  - example_title: Zaire ebolavirus
    pipeline_tag: splice-site
    sequence_type: mRNA
    task: splice-site
    text: >-
      AAUGUUCAAACACUUUGUGAAGCUCUGUUAGCUGAUGGUCUUGCUAAAGCAUUUCCUAGCAAUAUGAUGGUAGUCACAGAGCGUGAGCAAAAAGAAAGCUUAUUGCAUCAAGCAUCAUGGCACCACACAAGUGAUGAUUUUGGUGAGCAUGCCACAGUUAGAGGGAGUAGCUUUGUAACUGAUUUAGAGAAAUACAAUCUUGCAUUUAGAUAUGAGUUUACAGCACCUUUUAUAGAAUAUUGUAACCGUUGCUAUGGUGUUAAGAAUGUUUUUAAUUGGAUGCAUUAUACAAUCCCACAGUGUUAU
  - example_title: SARS coronavirus
    pipeline_tag: splice-site
    sequence_type: mRNA
    task: splice-site
    text: >-
      AUGUUUAUUUUCUUAUUAUUUCUUACUCUCACUAGUGGUAGUGACCUUGACCGGUGCACCACUUUUGAUGAUGUUCAAGCUCCUAAUUACACUCAACAUACUUCAUCUAUGAGGGGGGUUUACUAUCCUGAUGAAAUUUUUAGAUCAGACACUCUUUAUUUAACUCAGGAUUUAUUUCUUCCAUUUUAUUCUAAUGUUACAGGGUUUCAUACUAUUAAUCAUACGUUUGACAACCCUGUCAUACCUUUUAAGGAUGGUAUUUAUUUUGCUGCCACAGAGAAAUCAAAUGUUGUCCGUGGUUGGGUUUUUGGUUCUACCAUGAACAACAAGUCACAGUCGGUGAUUAUUAUUAACAAUUCUACUAAUGUUGUUAUACGAGCAUGUAACUUUGAAUUGUGUGACAACCCUUUCUUUGCUGUUUCUAAACCCAUGGGUACACAGACACAUACUAUGAUAUUCGAUAAUGCAUUUAAAUGCACUUUCGAGUACAUAUCU
  - example_title: insulin
    pipeline_tag: splice-site
    sequence_type: mRNA
    task: splice-site
    text: >-
      AUGGCCCUGUGGAUGCGCCUCCUGCCCCUGCUGGCGCUGCUGGCCCUCUGGGGACCUGACCCAGCCGCAGCCUUUGUGAACCAACACCUGUGCGGCUCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCCCUUGGCCCUGGAGGGGUCCCUGCAGAAGCGUGGCAUUGUGGAACAAUGCUGUACCAGCAUCUGCUCCCUCUACCAGCUGGAGAACUACUGCAACUAG
  - example_title: cyclin dependent kinase inhibitor 2A
    pipeline_tag: splice-site
    sequence_type: mRNA
    task: splice-site
    text: >-
      AUGGAGCCGGCGGCGGGGAGCAGCAUGGAGCCUUCGGCUGACUGGCUGGCCACGGCCGCGGCCCGGGGUCGGGUAGAGGAGGUGCGGGCGCUGCUGGAGGCGGGGGCGCUGCCCAACGCACCGAAUAGUUACGGUCGGAGGCCGAUCCAGGUCAUGAUGAUGGGCAGCGCCCGAGUGGCGGAGCUGCUGCUGCUCCACGGCGCGGAGCCCAACUGCGCCGACCCCGCCACUCUCACCCGACCCGUGCACGACGCUGCCCGGGAGGGCUUCCUGGACACGCUGGUGGUGCUGCACCGGGCCGGGGCGCGGCUGGACGUGCGCGAUGCCUGGGGCCGUCUGCCCGUGGACCUGGCUGAGGAGCUGGGCCAUCGCGAUGUCGCACGGUACCUGCGCGCGGCUGCGGGGGGCACCAGAGGCAGUAACCAUGCCCGCAUAGAUGCCGCGGAAGGUCCCUCAGACAUCCCCGAUUGA
  - example_title: human papillomavirus type 16 E6
    pipeline_tag: splice-site
    sequence_type: mRNA
    task: splice-site
    text: >-
      AUGCACCAAAAGAGAACUGCAAUGUUUCAGGACCCACAGGAGCGACCCAGAAAGUUACCACAGUUAUGCACAGAGCUGCAAACAACUAUACAUGAUAUAAUAUUAGAAUGUGUGUACUGCAAGCAACAGUUACUGCGACGUGAGGUAUAUGACUUUGCUUUUCGGGAUUUAUGCAUAGUAUAUAGAGAUGGGAAUCCAUAUGCUGUAUGUGAUAAAUGUUUAAAGUUUUAUUCUAAAAUUAGUGAGUAUAGACAUUAUUGUUAUAGUUUGUAUGGAACAACAUUAGAACAGCAAUACAACAAACCGUUGUGUGAUUUGUUAAUUAGGUGUAUUAACUGUCAAAAGCCACUGUGUCCUGAAGAAAAGCAAAGACAUCUGGACAAAAAGCAAAGAUUCCAUAAUAUAAGGGGUCGGUGGACCGGUCGAUGUAUGUCUUGUUGCAGAUCAUCAAGAACACGUAGAGAAACCCAGCUGUAA
  - example_title: NRAS proto-oncogene
    pipeline_tag: splice-site
    sequence_type: 5' UTR
    task: splice-site
    text: >-
      GGGGCCGGAAGUGCCGCUCCUUGGUGGGGGCUGUUCAUGGCGGUUCCGGGGUCUCCAACAUUUUUCCCGGCUGUGGUCCUAAAUCUGUCCAAAGCAGAGGCAGUGGAGCUUGAGGUUCUUGCUGGUGUGAA
  - example_title: amyloid beta precursor protein
    pipeline_tag: splice-site
    sequence_type: 5' UTR
    task: splice-site
    text: >-
      GUCAGUUUCCUCGGCAGCGGUAGGCGAGAGCACGCGGAGGAGCGUGCGCGGGGGCCCCGGGAGACGGCGGCGGUGGCGGCGCGGGCAGAGCAAGGACGCGGCGGAUCCCACUCGCACAGCAGCGCACUCGGUGCCCCGCGCAGGGUCGCG
  - example_title: RUNX family transcription factor 1
    pipeline_tag: splice-site
    sequence_type: 5' UTR
    task: splice-site
    text: >-
      ACUUCUUUGGGCCUCAUAAACAACCACAGAACCACAAGUUGGGUAGCCUGGCAGUGUCAGAAGUCUGAACCCAGCAUAGUGGUCAGCAGGCAGGACGAAUCACACUGAAUGCAAACCACAGGGUUUCGCAGCGUGGUAAAAGAAAUCAUUGAGUCCCCCGCCUUCAGAAGAGGGUGCAUUUUCAGGAGGAAGCG
  - example_title: fragile X messenger ribonucleoprotein 1
    pipeline_tag: splice-site
    sequence_type: 5' UTR
    task: splice-site
    text: >-
      CUCAGUCAGGCGCUCAGCUCCGUUUCGGUUUCACUUCCGGUGGAGGGCCGCCUCUGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGCGGCGGUGACGGAGGCGCCGCUGCCAGGGGGCGUGCGGCAGCGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCUGGGCCUCGAGCGCCCGCAGCCCACCUCUCGGGGGCGGGCUCCCGGCGCUAGCAGGGCUGAAGAGAAG
  - example_title: MYC proto-oncogene
    pipeline_tag: splice-site
    sequence_type: 5' UTR
    task: splice-site
    text: >-
      AACUCGCUGUAGUAAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGCCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUGAUCCCCCAGCCAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGCACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUAUUCUGCCCAUUUGGGGACACUUCCCCGCCGCUGCCAGGACCCGCUUCUCUGAAAGGCUCUCCUUGCAGCUGCUUAGACG
  - example_title: activating transcription factor 4
    pipeline_tag: splice-site
    sequence_type: 5' UTR
    task: splice-site
    text: >-
      CAUUUCUACUUUGCCCGCCCACAGAUGUAGUUUUCUCUGCGCGUGUGCGUUUUCCCUCCUCCCCGCCCUCAGGGUCCACGGCCACCAUGGCGUAUUAGGGGCAGCAGUGCCUGCGGCAGCAUUGGCCUUUGCAGCGGCGGCAGCAGCACCAGGCUCUGCAGCGGCAACCCCCAGCGGCUUAAGCCAUGGCGCUUCUCACGGCAUUCAGCAGCAGCGUUGCUGUAACCGACAAAGACACCUUCGAAUUAAGCACAUUCCUCGAUUCCAGCAAAGCACCGCAAC
  - example_title: Human GPI protein p137
    pipeline_tag: splice-site
    sequence_type: 3' UTR
    task: splice-site
    text: >-
      UUUUUAAAAGGAAAAGAUACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUUUGAAAGGCACCAGUAUGUGUUUUAGAUUGAUUUAAAUGUUUCAUUUAAAUCACGGACAGUAGUUUCAGUUCUGAUGGUAUAAGCAAAACAAAUAAAACGUUUAUAAAAGUUGUAUCUUGAAACACUGGUGUUCAACAGCUAGCAGCUUAUGUGAUUCACCCCAUGCCACGUUAGUGUCACAAAUUUUAUGGUUUAUCUCCAGCAACAUUUCUCUAGUACUUGCACUUAUUAUCUGAAUUC
  - example_title: nucleophosmin 1
    pipeline_tag: splice-site
    sequence_type: 3' UTR
    task: splice-site
    text: >-
      GAAAAUAGUUUAAACAAUUUGUUAAAAAAUUUUCCGUCUUAUUUCAUUUCUGUAACAGUUGAUAUCUGGCUGUCCUUUUUAUAAUGCAGAGUGAGAACUUUCCCUACCGUGUUUGAUAAAUGUUGUCCAGGUUCUAUUGCCAAGAAUGUGUUGUCCAAAAUGCCUGUUUAGUUUUUAAAGAUGGAACUCCACCCUUUGCUUGGUUUUAAGUAUGUAUGGAAUGUUAUGAUAGGACAUAGUAGUAGCGGUGGUCAGACAUGGAAAUGGUGGGGAGACAAAAAUAUACAUGUGAAAUAAAACUCAGUAUUUUAAUAAAGUAGCACGGUUUCUAUUGA
  - example_title: superoxide dismutase 1
    pipeline_tag: splice-site
    sequence_type: 3' UTR
    task: splice-site
    text: >-
      ACAUUCCCUUGGAUGUAGUCUGAGGCCCCUUAACUCAUCUGUUAUCCUGCUAGCUGUAGAAAUGUAUCCUGAUAAACAUUAAACACUGUAAUCUUAAAAGUGUAAUUGUGUGACUUUUUCAGAGUUGCUUUAAAGUACCUGUAGUGAGAAACUGAUUUAUGAUCACUUGGAAGAUUUGUAUAGUUUUAUAAAACUCAGUUAAAAUGUCUGUUUCAAUGACCUGUAUUUUGCCAGACUUAAAUCACAGAUGGGUAUUAAACUUGUCAGAAUUUCUUUGUCAUUCAAGCCUGUGAAUAAAAACCCUGUAUGGCACUUAUUAUGAGGCUAUUAAAAGAAUCCAAAUUCAAACUAAA
  - example_title: hemoglobin subunit alpha 2
    pipeline_tag: splice-site
    sequence_type: 3' UTR
    task: splice-site
    text: >-
      CUGGAGCCUCGGUAGCCGUUCCUCCUGCCCGCUGGGCCUCCCAACGGGCCCUCCUCCCCUCCUUGCACCGGCCCUUCCUGGUCUUUGAAUAAAGUCUGAGUGGGCAGCA
  - example_title: BRAF proto-oncogene
    pipeline_tag: splice-site
    sequence_type: 3' UTR
    task: splice-site
    text: >-
      AACAAAUGAGUGAGAGAGUUCAGGAGAGUAGCAACAAAAGGAAAAUAAAUGAACAUAUGUUUGCUUAUAUGUUAAAUUGAAUAAAAUACUCUCUUUUUUUUUAAGGUGAACCAAAGAACACUUGUGUGGUUAAAGACUAGAUAUAAUUUUUCCCCAAACUAAAAUUUAUACUUAACAUUGGAUUUUUAACAUCCAAGGGUUAAAAUACAUAGACAUUGCUAAAAAUUGGCAGAGCCUCUUCUAGAGGCUUUACUUUCUGUUCCGGGUUUGUAUCAUUCACUUGGUUAUUUUAAGUAGUAAACUUCAGUUUCUCAUGCAACUUUUGUUGCCAGCUAUCACAUGUCCACUAGGGACUCCAGAAGAAGACCCUACCUAUGCCUGUGUUUGCAGGUGAGAAGUUGGCAGUCGGUUAGCCUGGG
  - example_title: H3 clustered histone 1
    pipeline_tag: splice-site
    sequence_type: 3' UTR
    task: splice-site
    text: UUACUGUGGUCUCUCUGACGGUCCAAGCAAAGGCUCUUUUCAGAGCCACCACCUUUUC

OpenSpliceAI

Modular native-PyTorch reimplementation of SpliceAI for predicting pre-mRNA splice sites from nucleotide sequence.

Disclaimer

This is an UNOFFICIAL implementation of OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species by Kuan-Hao Chao, Alan Mao, et al.

The OFFICIAL repository of OpenSpliceAI is at Kuanhao-Chao/OpenSpliceAI.

The MultiMolecule team has confirmed that the provided model and checkpoints are producing the same intermediate representations as the original implementation.

The team releasing OpenSpliceAI did not write this model card for this model so this model card has been written by the MultiMolecule team.

Model Details

OpenSpliceAI is a deep dilated residual convolutional neural network that reimplements the SpliceAI architecture in native PyTorch. It predicts, for each nucleotide of a pre-mRNA transcript, whether the position is a splice acceptor, a splice donor, or neither. The model stacks dilated residual units with increasing kernel size and atrous rate so that a wide genomic context window contributes to each per-nucleotide prediction, while skip connections aggregate multi-scale features. OpenSpliceAI reproduces the predictive behavior of SpliceAI while providing an efficient, modular training pipeline that can be retrained on non-human species.

Variants

OpenSpliceAI ships trained model families for human MANE and four non-human species. Each family provides four flanking-context sizes.

Model Specification

Flanking Context Residual Blocks Hidden Size Num Parameters (M) FLOPs (G) MACs (G)
80 nt 4 32 0.09 0.95 0.47
400 nt 8 0.19 2.00 0.99
2,000 nt 12 0.36 5.03 2.50
10,000 nt 16 0.70 20.90 10.40

Model size is determined by flanking context and is shared across species for the same context. FLOPs and MACs are reported for a single 5,000-nucleotide output sequence.

Links

Usage

The model file depends on the multimolecule library. You can install it using pip:

pip install multimolecule

Direct Use

RNA Splicing Site Prediction

You can use this model directly to predict the splice sites of a pre-mRNA sequence:

>>> from multimolecule import RnaTokenizer, OpenSpliceAiForTokenPrediction

>>> model_id = "multimolecule/openspliceai-mouse.2000"
>>> tokenizer = RnaTokenizer.from_pretrained(model_id)
>>> model = OpenSpliceAiForTokenPrediction.from_pretrained(model_id)
>>> output = model(tokenizer("AGCAGUCAUUAUGGCGAA", return_tensors="pt")["input_ids"])

>>> output.keys()
odict_keys(['logits'])

Each output position carries three logits corresponding to neither, acceptor, and donor.

Interface

  • Input length: variable pre-mRNA sequence
  • Flanking context: 80 / 400 / 2,000 / 10,000 nt per variant family, split evenly on both sides of every predicted position
  • Padding: sequence ends padded with N
  • Output: per-position 3-class logits (neither, acceptor, donor)

Training Details

OpenSpliceAI was trained to predict the location of splice donor and acceptor sites from nucleotide sequence, following the SpliceAI training methodology.

Training Data

The MANE variants were trained on transcripts from the GENCODE/MANE human reference annotation. The non-human variants use the species annotations released by OpenSpliceAI for mouse, zebrafish, honeybee, and Arabidopsis. For each predicted nucleotide, the model receives a flanking context of 80, 400, 2,000, or 10,000 nucleotides, split evenly across the two sides of the output sequence, with sequence ends padded with N. Annotated splice donor and acceptor sites serve as positive labels; all other positions are negative.

Training Procedure

Pre-training

The model was trained to minimize a cross-entropy loss between predicted splice-site probabilities and the reference annotation.

  • Optimizer: Adam
  • Loss: cross-entropy

Please refer to the OpenSpliceAI paper for the full training protocol and hardware details.

Citation

@article{chao2025openspliceai,
  author    = {Chao, Kuan-Hao and Mao, Alan and Liu, Anqi and Salzberg, Steven L and Pertea, Mihaela},
  title     = {OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species},
  journal   = {eLife},
  volume    = 14,
  pages     = {RP107454},
  year      = 2025,
  doi       = {10.7554/eLife.107454.3},
  publisher = {eLife Sciences Publications, Ltd}
}

The artifacts distributed in this repository are part of the MultiMolecule project. If MultiMolecule supports your research, please cite the MultiMolecule project as follows:

@software{chen_2024_12638419,
  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},
  title     = {MultiMolecule},
  doi       = {10.5281/zenodo.12638419},
  publisher = {Zenodo},
  url       = {https://doi.org/10.5281/zenodo.12638419},
  year      = 2024,
  month     = may,
  day       = 4
}

Contact

Please use GitHub issues of MultiMolecule for any questions or comments on the model card.

Please contact the authors of the OpenSpliceAI paper for questions or comments on the paper/model.

License

This model implementation is licensed under the GNU Affero General Public License.

For additional terms and clarifications, please refer to our License FAQ.

SPDX-License-Identifier: AGPL-3.0-or-later