Sequence
atgc intronic sequence ATGC exonic sequencegtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 5
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
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---------gtaggaatgtagctactagccagcatagagcaattgctcaaaaatgttattctaata-ttcgttatccattatactg---------atattatagttatg-------------tgtcaagGCCTTAACAGATCCATACTTTACTGGATTGGCAAATTCGGAACGTGAACCCATAGCACAACCCATCTCAAAACTCGAGTTTGAGTTTGAGAGAAGGAAGC----------------------------------------
upper sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G375975_T01 (Zea mays), 3'ss of exon 5
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
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-----------------------------------gtagtagcaatgtcagcaag--aagcggtag---tttcaaacgatgtattat-tagttatgctcaatactgatattacaatagtggaattcaagGCCTTGACAGATCCATACTTCACTGGGTTAGCAAATTCTGCACGTGAACCAGTAGCACAACCTATCTCAAAATTTGAGTTTGAGTTTGAAAGAAGGAAGC----------------------------------------
upper sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 6
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
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---------------------------gttaatctcctatca-----cctatatataatttcattgataatt-acctaagagtatatttcattatttctg----tcatgtttgtgatatc-------agGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGTGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT----------------------------------------
upper sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 6
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
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---------------------------gttgatctcctatca-----cctatatataatttcattgataatt-acctaagagtatatttcattatttctg----tcatgtttgtgatatc-------agGCATTATCTGATCCTTACTTCACTGGCTTGGCGAACATGGACCGCGAACCATCCACTCAACCCATTTCAAAACTTGAGTTTGAATTTGAGAGAAGGAAAT----------------------------------------
upper sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 6
---gtaccatgcgtaaaaaaaaaaccatccattccct--tctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCT---TCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
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gttgatcttcatttacctagataactaccaaaggcggaatctttttgaatgtaccaaatgatgatcaattatgcagataatttccaaggt---tccttacttct--------ttgtcatgcctgtgtttgc-agGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAACCCATTTCAAAGCTCGAGTTTGAGTTTGAGAGGAGAA-------------------------------------------
upper sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 6
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaa----aaattccct--gatgttaatccgttggctcttcaactactggaatgtctccttgcatttgat-cctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCT---TCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
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----------------gttgttcttcagttacctagataaaaggggaaattttgttgaatgtgtaccaaatga-tgatcaattatgcagataatttccaaggttccttacttctttgttatgcctgtgtttgc-agGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAGCCCATTTCAAAGCTTGAATTTGAGTTTGAGAGGAGAA-------------------------------------------
upper sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
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-------------gttagctcctctatacttgttttttctagcgtttccacttcaaaatttcagagcagtttcaatcgctctcagaaaaggaaacattatatatacatgtgtgtgtgtatat---acagGCACTGGCAGATCCTTACTTCTATGGTCTGGCAAACGTTGATCGGGAACCATCTACTCAACCGATTCCGAAACTCGAGTTTGAGTTTGAAAGAAGGAAGA----------------------------------------
upper sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------gtaccatgcgtaaaaa----aaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgt---ccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
| || ||| | | || ||| | | | |||| | || | || | || ||||| | | || | || || |||| || || | || | |||| ||||||||||| || ||| ||||| || || | || || ||||| || || || || |||||||| ||||| |||||||||||||||| |||||
gtatgcttaaattttgctttatttcttacatgaggtagatggaactatgtttgagaacgttgaaatgtgacagtactagaggcacatagatgcagaacctagaagatgatgaaaattcaaagaacaaactgaaattctatgttccctcttaatatatgtgtgcctatatttttacagGCATTAGCTGATCCATACTTTAATGGTCTGTCAAGTAAAGTGCGGGAACCATCGACACAGCCGATTTCAAAGCTTGAATTTGAGTTTGAGAGAAAGAAAT---------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
ttttgat putative branch site (score: 4)
ttattttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaaaaattccctgatgttaatccgttggctcttcaactactggaatgtctccttgcatttgatcctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCTTCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG