Sequence
atgc intronic sequence ATGC exonic sequencegtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 4
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttag-ttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
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--------------------------------------------------------------------tttagtttttgtattgggttttggctctcaaaattctagtcttactgg-----tgatattgcaaaatcttgatgtataacttcaaat---attccatcacatttt----cagTGACCAGCTACCTGTCAGTACAAAGTTTGATATGCGTAGCGATCCTGGCGTTGTAAGGAATTATGGTCGGCTCTTGCTGGAGATGGCTTCTGCTGTGCCA
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G097605_T01 (Zea mays), 3'ss of exon 4
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaat--ttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
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----------------------------------------------------------------------------cttatgttaagctt--ttataacatctttagttgtttccaacatttcatattactggta---gcattgtacactgtgtaaacaccaaccattccatcatcttcagTGATCAGCTACCTGTGAGTACAAAGTTCGATATGCGTAGTGATCCTGGTGTTGTGAGGAATTATGGCCGCCTCTTGCTGGAAATGGCTTCTGCTGTTCCA
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G008524_T01 (Zea mays), 3'ss of exon 1
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagac---attacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
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-----------------------------------------------------------------------------ttatgttaagctcttatgaaagctttagttatttccaacatttcatatt-actggtagcattgtatgcttgtgtattcatcaact---attccatcat-ttttagTGATCATCTACATGTGAGTACAAAGTTTGATATGAATAGTGATCCTGGTGTTGTGAGGAATTATGACCACCTTTTGCTGGAAATGGCTTCTGCTATTCAA
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 5
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
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-----------------gtattcccataatttactaccctgtattttaaaacagaccttgttaattgttaatacgttacattttaaatct--ccgat-----ttgcttgaaagtgacctcttttacttcccc--ctttgttttatttttaatgtttaat-cggtttctt---gtttcagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCG
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 5
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
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------------------------gtattcccataatttgctcccctg--tattttaaaacagactttgttaattgttaatac--attacattttaaatccctgattttcttgaaagagacctcttttacttccccct-ttattctatttctaatgttttaatatgtttattgttttagTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTATTGGAAATGGCTTCAGTTGTTCCA
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
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---------------------------------------------------------------------------------gtatgtggtatataaaaagaatcctgaacacttaac-----ttattttttaattttatatgtcttgacattattgg------ttgttttctttttcagTGATCAGCTTCCTGTTAGCACCAAATTTGACATGAGAAGTGATCCTGGTGTTGTGAGGAATTACGGAAAGCTTTTGGTAGAGATGGTATCTATTGTTCCT
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S145_26V6.3 (Physcomitrella patens), 3'ss of exon 7
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatct-tagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
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---------------------------------------------------------------------------ctgcatggcattccattgttagaacaggtcaaatg-gttgcatagatatttaagatttgtaatcattttttatttcttatt----ccaattttattacaatgcagTGACCAGCTGCCTGTCAGCACGAAATTTGATATGCGGAGTGATCCTGGAGTTGTTCGCAATTACGGTCGTCTGCTACTAGAGATGGTCACTGCTGTTCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
tttctttttatttc CT-rich tract
ttattgaattcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggggttaaattaaggtttgattcttttttctattcaataatttgggtgtcttagtttctattactacaacctttcttattaatcttagttgaaagacattacttccattaggtcatttttatttatttatttttgtttctttctccttattgaattcaatttctttttatttcagTGACCAGCTTCCTGTGAGTACAAAATTTGATATGAGAAGTGATCCTGGTGTTGTAAGGAATTATGGGAGGCTCCTGCTGGAGATGGTGTCTGTTGTTCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG