mRNABench
Collection
Collection of datasets re-hosted for mRNABench: https://github.com/morrislab/mRNABench • 13 items • Updated • 3
transcript_id string | gene string | chromosome string | sequence string | cds list | splice list | target int64 | description string |
|---|---|---|---|---|---|---|---|
NM_020451.2 | SELENON | 1 | CCCCGCCCCGCTCTTTCGCTTCCCGGGCCGCCGGCAGCCGCCGCCAGCCGCAGCCATGGGCCGGGCCCGGCCGGGCCAACGCGGGCCGCCCAGCCCCGGCCCCGCCGCGCAGCCTCCCGCGCCACCGCGCCGCCGCGCCCGTTCCCTGGCGCTGCTCGGAGCCCTGCTGGCCGCCGCCGCTGCCGCCGCCGTCCGGGTCTGCGCCCGCCACGCCGAGGCCCAGGCGGCCGCGCGGCAGGAACTGGCGCTGAAGACCCTGGGGACAGATGGCCTTTTTCTCTTTTCCTCCTTGGACACTGACGGGGATATGTACATCAGCC... | [
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NM_020451.2 | SELENON | 1 | CCCCGCCCCGCTCTTTCGCTTCCCGGGCCGCCGGCAGCCGCCGCCAGCCGCAGCCATGGGCCGGGCCCGGCCGGGCCAACGCGGGCCGCCCAGCCCCGGCCCCGCCGCGCAGCCTCCCGCGCCACCGCGCCGCCGCGCCCGTTCCCTGGCGCTGCTCGGAGCCCTGCTGGCCGCCGCCGCTGCCGCCGCCGTCCGGGTCTGCGCCCGCCACGCCGAGGCCCAGGCGGCCGCGCGGCAGGAACTGGCGCTGAAGACCCTGGGGACAGATGGCCTTTTTCTCTTTTCCTCCTTGGACACTGACGGGGATATGTACATCAGCC... | [
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0... | 1 | chr1:25816824 T:C,Impact on secondary structure |
NM_014017.3 | LAMTOR2 | 1 | GGTGGGGCGGGGTTGAGTCGGAACCACAATAGCCAGGCGAAGAAACTACAACTCCCAGGGCGTCCCGGAGCAGGCCAACGGGACTACGGGAAGCAGCGGGCAGCGGCCCGCGGGAGGCACCTCGGAGATCTGGGTGCAAAAGCCCAGGGTTAGGAACCGTAGGCATGCTGCGCCCCAAGGCTTTGACCCAGGTGCTAAGCCAAGCCAACACTGGAGGCGTCCAGAGCACCCTGCTGCTGAATAACGAGGGATCACTGCTGGCCTACTCTGGTTACGGGGACACTGACGCCCGGGTCACCGCTGCCATAGCCAGTAACATC... | [
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NM_014017.3 | LAMTOR2 | 1 | GGTGGGGCGGGGTTGAGTCGGAACCACAATAGCCAGGCGAAGAAACTACAACTCCCAGGGCGTCCCGGAGCAGGCCAACGGGACTACGGGAAGCAGCGGGCAGCGGCCCGCGGGAGGCACCTCGGAGATCTGGGTGCAAAAGCCCAGGGTTAGGAACCGTAGGCATGCTGCGCCCCAAGGCTTTGACCCAGGTGCTAAGCCAAGCCAACACTGGAGGCGTCCAGAGCACCCTGCTGCTGAATAACGAGGGATCACTGCTGGCCTACTCTGGTTACGGGGACACTGACGCCCGGGTCACCGCTGCCATAGCCAGTAACATC... | [
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0... | 1 | chr1:156058393 C:A,Impact on polyadenylation signal |
NM_000210.3 | ITGA6 | 2 | TTGATAAAACGCCTGCGAGTCTCCAGAGAACAACGGGCTCATTCAGCGGTCGCGAGCTGCCCGCGAGGGGGAGCGGCCGGACGGAGAGCGCGACCCGTCCCGGGGGTGGGGCCGGGCGCAGCGGCGAGAGGAGGCGAAGGTGGCTGCGGTAGCAGCAGCGCGGCAGCCTCGGACCCAGCCCGGAGCGCAGGGCGGCCGCTGCAGGTCCCCGCTCCCCTCCCCGTGCGTCCGCCCATGGCCGCCGCCGGGCAGCTGTGCTTGCTCTACCTGTCGGCGGGGCTCCTGTCCCGGCTCGGCGCAGCCTTCAACTTGGACACTCG... | [
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NM_000210.3 | ITGA6 | 2 | TTGATAAAACGCCTGCGAGTCTCCAGAGAACAACGGGCTCATTCAGCGGTCGCGAGCTGCCCGCGAGGGGGAGCGGCCGGACGGAGAGCGCGACCCGTCCCGGGGGTGGGGCCGGGCGCAGCGGCGAGAGGAGGCGAAGGTGGCTGCGGTAGCAGCAGCGCGGCAGCCTCGGACCCAGCCCGGAGCGCAGGGCGGCCGCTGCAGGTCCCCGCTCCCCTCCCCGTGCGTCCGCCCATGGCCGCCGCCGGGCAGCTGTGCTTGCTCTACCTGTCGGCGGGGCTCCTGTCCCGGCTCGGCGCAGCCTTCAACTTGGACACTCG... | [
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0... | 1 | chr2:172504156 AAAG:A |
NM_000207.2 | INS | 11 | AGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAG... | [
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NM_000207.2 | INS | 11 | AGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAG... | [
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0... | 1 | chr11:2159792 T:C,mRNA stability |
NM_000518.4 | HBB | 11 | ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGT... | [
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NM_000518.4 | HBB | 11 | ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGT... | [
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0... | 1 | chr11:5225482 TTTTTA:T,Impact on polyadenylation signal |
NM_000518.4 | HBB | 11 | ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGT... | [
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0... | 1 | chr11:5225484 T:C,Impact on polyadenylation signal |
NM_000518.4 | HBB | 11 | ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGT... | [
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NM_000518.4 | HBB | 11 | ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGT... | [
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NM_000518.4 | HBB | 11 | ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGT... | [
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NM_001281503.1 | SLITRK1 | 13 | CGCGCTCTCTTCCTCCCTCAGACAACTCGCCCCCCGCCCTCCGCCCCCCTCCACGTAATTCCGAAAGAGCAGAAGAAAGAGAAGGAGAACAGGAAAAGAAGAGCTAGTAAGCGAGAGCGAGAGCACAGAAAAGAAAAAAAAAAGCCTTAAGAGGACCGAAGGGGAGGAAAGGAAAAGGATGGACAACCACAAAACGCAGCGATTGCGGAAATTTTCCAGCGCCATTGGCTGGGCAGCGTGAGTCCTTCGGTCGGGCGTGATTTCAGCACCGGGGGAACTGGACAGCACCTCGGGGGGACTTCTGGGCAACCCGCAACCAC... | [
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End of preview. Expand in Data Studio
Overview
This utr variant effect prediction task measures the pathogenicity of single nucleotide polymorpism (SNPs) and indels (insertion-deletions) in 3' and 5' UTRs. This dataset is a reprocessing of the dataset from DeepGenomics (Bohn et al. Frontiers in Molecular Biosciences. 2023), see the original paper for the data generation process. We provide the mRNA transcript sequence context for the variant and wildtype sequences using the specified transcript id from RefSeq v109.
This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench
Data Format
Description of data columns:
target: Whether the specified sequence contains a pathogenic mutation.cds: Binary track which reports position of first nucleotide in each codon in CDS.splice: Binary track which reports position of the 3' end of each exon, indicating splice sites.description: Description of the sequence, either in the formatchr{chr}:{position} {ref_base}:{alt_base}[,optional variant impact]orwild-typefor the unmodified sequence.
Note: The position of the variant is 1-indexed (ClinVar notation) and refers to the position of the variant on the positive strand.
Data Source
This dataset is generated using a dataset collected by a team at DeepGenomics and is under a CC by 4.0 license.
Please attribute:
Original paper: https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2023.1257550/full
Original paper GitHub: https://github.com/deepgenomics/UTR_variants_DL_manuscript
3' UTR Variant data source: https://github.com/deepgenomics/UTR_variants_DL_manuscript/blob/main/data/utr3_plp_benchmark.tsv
5' UTR Variant data source: https://github.com/deepgenomics/UTR_variants_DL_manuscript/blob/main/data/utr5_plp_benchmark.tsv
Citation: Bohn E, Lau TTY, Wagih O, Masud T and Merico D (2023) A curated census of pathogenic and likely pathogenic UTR variants and evaluation of deep learning models for variant effect prediction. Front. Mol. Biosci. 10:1257550. doi: 10.3389/fmolb.2023.1257550
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