mRNABench
Collection
Collection of datasets re-hosted for mRNABench: https://github.com/morrislab/mRNABench • 13 items • Updated • 3
transcript_id stringlengths 17 23 | gene stringlengths 2 12 | chromosome stringclasses 24
values | sequence stringlengths 348 24.3k | cds sequencelengths 348 24.3k | splice sequencelengths 348 24.3k | target sequencelengths 8 8 |
|---|---|---|---|---|---|---|
ENST00000229416.10 | GCLC | 6 | ATAAAACCTGGAGCGCAGGATCGCGCCCAGGAGCGGCGAGCTAGCGGACGCAAAGACTGGGCATGCTCCGCGGCGGCGCAGGTTTTGGTCACAAGTAGGAAGAAGCCAGTGCACCAGACCGGCAAAGAGAAGCGGGAGCCGCCGCGGCAGCGCGGCCGTGGGGTCCGCCGCCGCCGCATCGGAGCGGGAGGAGGAGCAGCGGGGAGGGCGAGGCCGCCGGGCCGAGAGCCGTCCCGCCTGCTCTCGGTCTTCTGCCTTCGCCTCCGCGCGGTGCGTCGGACCCAGGGTCTGTCACCTGGGCGCCAGGGGCCGCCGCCGGG... | [
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ENST00000341376.10 | NFYA | 6 | GATTCCCCTTTGTTCGGGTTCGCCATTTTGCTAGGCAGCGGCAGTGGCGGCGGCAGCGGCGGCTGGAGCCTCTGATTGGGTTTCGGAGTCCGGTACTGGAGCCAATCAGCGCGGGCAGCGAACCGGGGGAGCGAGGCACGGAGTGTACCTCACAGCCTTCTAGGATCTCCAGAGTGGACAGGAATCTCACTTGGAGGGACCATGGAGCAGTATACAGCAAACAGCAATAGTTCGACAGAGCAGATTGTTGTCCAGGCAGGACAGATTCAGCAGCAGCAGCAGGGTGGTGTCACTGCTGTGCAGTTGCAGACTGAGGCCCA... | [
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ENST00000374399.8 | NIPAL3 | 1 | GCAGCTCTGAATTGGGAAGGGATGAAGGAGGCTGTGCCTCCGGGTTGCACGAAGAGTCCGAGTCATTTCTCAGAAGGTTTTGATAGGTGGGCCTTAGAGGAGACGCCGCCGAGCACCGCAAGAACTGGAAAACACACCCCTCTCTGTCTGCCTGGGAGAGCCACGGAAATTGGCACTTCTCTGAGTGAAGCTGAGGAGAAGGCTGTAAATCTGCCAAAACAGCCTTGAAGTATTCTTTTGTCATGAGGAAGTGACGGCTGCTGGAGGGAGGTGAACACCACAAGGAGAGATGGCATCTGGCCTGGGCCCCGCCTAGCAGC... | [
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ENST00000321037.4 | ENPP4 | 6 | GGAGCGCCCCGAGCGGCGCAGATAGGGACGTTGGGGCTGTGCCCCGCGGCGCGGCGCCTGCCACTGCGCAGGCGCCTCAGGAAGAGCTCGGCATCGCCCCTCTTCCTCCAGGTCCCCCTTCCCCGCAACTTCCCACGAGTGCCAGGTGCCGCGAGCGCCGAGTTCCGCGCATTGGAAAGAAGCGACCGCGGCGGCTGGAACCCTGATTGCTGTCCTTCAACGTGTTCATTATGAAGTTATTAGTAATACTTTTGTTTTCTGGACTTATAACTGGTTTTAGAAGTGACTCTTCCTCTAGTTTGCCACCTAAGTTACTACTA... | [
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ENST00000002829.7 | SEMA3F | 3 | AGCGCAGCGCAGGACCTGGGTACGCCGCGAGGAACCGTGCAGCCCAGCGCGGCCGCCCGGCCCGGGTCCAGCAGCCAGGAGAGCGCAGCGCTTCGAAGCCGAGTGCGCGCCACCGCCCGCGCCCCGCGCTGGGGAATGCGCCCTCGGCGCGCCGGCCAGGGGGCGCCCGCAGCCCACCCCAGGGGAGGCGGCCCCGAGCGCCCCTGAGCCTTCCCATGGCCCGGGCTGGGGCCCGGGCCCTCGGCTGCTGACGCGCCCGAAGCCCGCGGAACCGGTTAAGCCGCGGCCGCGGCGCCGATCCCGGCTGAGGCGCAGCGGCG... | [
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ENST00000381192.9_PAR_Y | CD99 | Y | ACCCCCTCTGTCTCCTCCCCGGGCCCGGCGTTCCCGCCCCTTCTGTGCGCGCGTGGAGGCCGGGGCGGGGCGGGCGCAGCCGGCGCTGAGCTTGCAGGGCCGCTCCCCTCACCCGCCCCCTTCGAGTCCCCGGGCTTCGCCCCACCCGGCCCGTGGGGGAGTATCTGTCCTGCCGCCTTCGCCCACGCCCTGCACTCCGGGACCGTCCCTGCGCGCTCTGGGCGCACCATGGCCCGCGGGGCTGCGCTGGCGCTGCTGCTCTTCGGCCTGCTGGGTGTTCTGGTCGCCGCCCCGGATGGTGGTTTCGATTTATCCGATGC... | [
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ENST00000318008.10 | LASP1 | 17 | GCAGTCAGCCTGAGAGCGCTGAGGCGCCAGCACCGCGGGCCCCGCCGTCCCCCCAGGAACCCGCCCCCGCGCAGCCCCACGTCGCCCGGAGAGCGCGCCTCGCTGCGCGTGCCCTTGCCCGCGCCCGAGGCGCGTGCCCGCCCCAGTGCAGCCCCTCCTCCCCGCTGTGTTTATTAGGGGAAGGAGGGCGGAGGCGGAGGCCAGTTCCCCAGCTCCAGCCGCCGTCGCTGCTGCCTGTGTAGTTGCAGCCGCGGCCGCCTCCCGCCAGCTCGCCTCGGGGAACAGGACGCGCGTGAGCTCAGGCGTCCCCGCCCCAGCTT... | [
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ENST00000000412.7 | M6PR | 12 | CCGGGAGCGGTCAGGCGCGTGACCCCGCGTGACCGGGGTGCGCGAGCCGAGAGGCCCTGGAAGCGGGACTCTGGGACCCCATTGAAAGAAAGGCAACCAGAAAAGGCGAAACGACAACCTCGATAGTGATTGGAGCTGATGGAACGAGGGCGGAGCTAAAGTCCCAGAATACTGGCCAATCAGAGTTTAAGATTATCAGGGAGCCCGGGAAGGGGAAAGGGGCGAAATGGTTCTATGGTCACATGCCGCGGGGTCTGGTGGGAGGAGCGGTTGCCCAGCGGCCTCTTGGCGCTTCCTGTTTCCGGTTCCCAGAGTGGGGC... | [
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ENST00000309955.7 | CFLAR | 2 | "TTTACTCCTAACGCGTGGAACTTGTGTCGACATCCACCCCCGGTTACTGCATACTCAGTCACACAAGCCATAGCAGGAAACAGCGAGCTTGCAGCCTCA(...TRUNCATED) | [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0(...TRUNCATED) | [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0(...TRUNCATED) | [
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ENST00000002125.8 | NDUFAF7 | 2 | "CCCAGCTCCTGGCGGAGCGAGCTAGCCTGCGAATTTCAGCATGAGTGTACTGCTGAGGTCAGGTTTGGGGCCGTTGTGTGCCGTGGCGCGCGCAGCCAT(...TRUNCATED) | [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,1,0,0,1(...TRUNCATED) | [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0(...TRUNCATED) | [
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End of preview. Expand in Data Studio
Overview
mRNA localization annotates the subcellular compartments that mRNA are found in. This task is a multilabel classification -- mRNA can be found in more than one compartment. This dataset was computed from experimental APEX RNA seq data collected by Fazal et al. 2019.
This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench
Data Format
Description of data columns:
target: Multihot labelling of cellular components that an mRNA appear in. The label positions correspond to:[Nucleus, Nucleolus, Lamina, Nuclear Pore, Cytosol, ERM, OMM, ER Lumen]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.
Data Source
This dataset was generated using Supplementary Table 3 from Fazal et al. 2024. Please provide proper attribution if you use this dataset, and contact the author for permission regarding further redistribution.
Please attribute:
Original paper: https://www.cell.com/cell/fulltext/S0092-8674(19)30555-0
Original dataset source: https://ars.els-cdn.com/content/image/1-s2.0-S0092867419305550-mmc3.xlsx
Citation: Fazal F et al., "Atlas of Subcellular RNA Localization Revealed by APEX-Seq.", Cell, 2019 Jul 11;178(2):473-490.e26
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