Sequence
atgc intronic sequence ATGC exonic sequencegttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgatgtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCTCGAATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0028g03050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgat-gtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCTCGAATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
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gtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcat-atatac-tgcgtagtactacattaattctt----cttttggttgagatgca--aatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC------
upper sequence: Vv12s0028g03050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g48130.2 (Oryza sativa), 3'ss of exon 1
gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgatgtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCTCGAATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
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----------------------------------------------------------------------------gtagctagctagagcttcctccctgctcgat-cgatcgatcggtctc-ctgtgtacatgttggatggcatt-----gagcatggtgtagagtcagTTGCAGGCAGCGGCGGC--GGCGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGGGTGAAGTTCGACCCGACGGACCAGGAGCTGCTGGAGCACCTGGAAG------------------
upper sequence: Vv12s0028g03050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g48130.1 (Oryza sativa), 3'ss of exon 1
gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgatgtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCTCGAATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
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----------------------------------------------------------------------------gtagctagctagagcttcctccctgctcgat-cgatcgatcggtctc-ctgtgtacatgttggatggcatt-----gagcatggtgtagagtcagttgcagGCAGCGGCGGC--GGCGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGGGTGAAGTTCGACCCGACGGACCAGGAGCTGCTGGAGCACCTGGAAGGGAAGG------------
upper sequence: Vv12s0028g03050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G058518_T01 (Zea mays), 3'ss of exon 1
gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgatgtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCT-CGA--ATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
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--------------------------------------------------------------------------------atgcatgggtcggtctctcacgtacatgcacgctccgagaataattaacgcacggtcgaataatctaatcgatcggccgtcgtcact--accatgcatgcagGTGCAGGCGGCGGCGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGCGTGAAGTTCGATCCGACGGACCAGGAGCTGCTGGAGCACCTGGAGGGGAAGG------------
upper sequence: Vv12s0028g03050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G134717_T01 (Zea mays), 3'ss of exon 1
gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgatgtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCTCGA--ATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
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--------------------------------------------------------------------------gttacccacaccacacgccatc--tagctagctagctacattcatgcatggaatggacgacaccactcactcacacgcacgctagcgatcggatcgtcgtccatcagGTGCAGCAGGCGGCGGCGATCCAGGACCTGCCGGGGCTGCCGGCGGGCGTGAAGTTCGATCCGACGGACCAGGAGCTGCTGGAGCACCTGGAGGGGAAGG------------
upper sequence: Vv12s0028g03050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G031200_T01 (Zea mays), 3'ss of exon 1
gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgatgtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctc-acttgt---gtcattgtttaattttgaattaaaaaa-------aaaaagGCTCGA--ATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
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------------gtacatactacgttgcgtacgcacgcgcgcgtcgatcgtgtgggcg-tg-catgcatgttagcttggtggtgctgggctagctagctcttctcgtccatgtcatgactcatgcatgcagttatatagcttgctgatgatcgacatgatcgatcgatgaacaaactgatattatataatgtggtcagAAGAGCACGACGATCCAGGACTTGCCGGGGCTGCCGGCCGGCGTGAAGTTCGACCCGACGGACCAGGAGCTGCTGGAGCACTTGGAGGGGAAGGCGAGGC------
upper sequence: Vv12s0028g03050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G031200_T02 (Zea mays), 3'ss of exon 1
gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgatgtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctc-acttg---tgtcattgtttaattttgaattaaaaaa-------aaaaagGCTCGA--ATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
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------------gtacatactacgttgcgtacgcacgcgcgcgtcgatcgtgtgggcg-tg-catgcatgttagcttggtggtgctgggctagctagctcttctcgtccatgtcatgactcatgcatgcagttatatagcttgctgatgatcgacatgatcgatcgatgaacaaactgatattatataatgtggtcagaagAGCACGACGATCCAGGACTTGCCGGGGCTGCCGGCCGGCGTGAAGTTCGACCCGACGGACCAGGAGCTGCTGGAGCACTTGGAGGGGAAGGCGAGGCCGG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCTCGAATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
ttgtgtcattgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgatgtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCTCGAATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT