Sequence
atgc intronic sequence ATGC exonic sequence...tttagttacacaaatcattcacgcaacttgtcatgcttacaacagttacattttttaaaactttttgcacttggtgattgattatgaataccatctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g42300.1 (Oryza sativa), 3'ss of exon 5
tttagttacacaaatcattcacgcaacttgtcatgcttacaacagttacatt------ttttaaaact--ttttgcacttggtgattgattatgaataccatctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
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-------atacaa-ttgttcaagcaatacttcctgcttacagtagttgtattgtcactctttacacataattattgatttttggagtgtttttggatgtcatatgcagCTTCTTGCTGAGAAAGGTGAACTCCCAACAAGATTTGGCTCAGCTACACTGGGAATCCTCCTCCTGCAG
upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G30360.2 (Glycine max), 3'ss of exon 7
tttagttacacaaatcattca-cgcaacttgtcatgcttaca-acagttacattttt-taaaactttttgcacttggtgattgat-tatgaatac-catctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
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-----tgatatgtgacactaaatgcaacttatcaagcatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatttgtagCTTCTTGCAGAGAGAGGTGAGCTTCCTACGAGATTTGGTTCAGCAACTCTCGGAATACTTCTTTTGCAG
upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G06890.3 (Glycine max), 3'ss of exon 6
tttagttacacaaatcattcacgcaacttgtcatgct--tacaacagttacattttttaaaactttttgcacttggtgattgattatgaataccatctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
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-atggttttaggtgttccccatgcatgagtccattgtgatatgtgagtgacactaaatatggataatgtaacttatcaagcatatatgcatat-atttgtagCTTCTTGCAGAGAGAGGTGAGCTTCCTACAAGATTTGGCTCAGCAACTCTTGGAATACTTCTTTTGCAG
upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 6
-------tttagttacacaaa---tcattcacgca-acttgtcatgcttaca-acagttacattttttaaaactttttgcacttggtgattgattatgaataccatctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
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gtattagcacagttgcaataacttttagtcatctatatctagaatggtaatggagaggcaaactcaatcaagaatttagtacattcttattgacaattt-tgaaatgtatagCTTCTTGCAGAGAAAGGTGAGCTCCCTACAAGATTTGGCTCAGCAACCTTGGGAATTCTTCTTCTACAG
upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0282g00020.t01 (Vitis vinifera), 3'ss of exon 6
--tttagttacacaaatcattcacgcaacttgtcatgcttacaacagttacattttttaaaactttttgcacttggtgattgattatgaa-taccatctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
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gagtgaattatatgcagaaatttc-tttcttgtc-tgtagattagaat-attgctacaaagacttgatatagcagtctagatcttaccaagcacaatatatagCTTCTTGCAGAGAAAGGTGAGCTCCCAACACGATTTGGTTCAGCAACTTTGGGAATACTTCTACTACAG
upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ10924 (Selaginella moellendorffii), 3'ss of exon 5
tttagttacacaaatcattcacgcaacttgtcatgcttacaacagttacattttttaaaactttttgcacttggtgattgattatgaataccatct--gcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
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--------------------------------------------gtt-tgttgtccaaaatgcttc---tttgttaatttgttaagtgctgtatttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTTGGAATTCTTCTGTTTCAA
upper sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ25893 (Selaginella moellendorffii), 3'ss of exon 5
tttagttacacaaatcattcacgcaacttgtcatgcttacaacagttacattttttaaaactttttgcacttggtgattgattatgaataccatct--gcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
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--------------------------------------------gtt-tgttgtccaaaatgcttc---tttgttaatttgttaagtgctgtatttttgcagCTTCTTTCAGAGAAGGGAGAACTTCCAACAAGATTTGGCTCTGCCACCCTTGGAATTCTTCTCTTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacattttttaaaactttttgcacttggtgattgattatgaataccatctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
gattgat putative branch site (score: 4)
ttttttaaaacttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagttacacaaatcattcacgcaacttgtcatgcttacaacagttacattttttaaaactttttgcacttggtgattgattatgaataccatctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG