Sequence
atgc intronic sequence ATGC exonic sequence...ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgt-tctgattttaatttccacatccta---tttatgctta-cagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
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---atatgctacacctatgctggagcag--ttcttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgt-tctgattttaatttccacatccta---tttatgctta-cagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
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---atatgctacacctatgctggaacagtttttaaa--agtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
ttgttgttt-tacttggttgttgggaaatc----tttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
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---ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatat--tattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
ttgttgttt-tacttggttgttgggaaatc----tttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
|| | | | | |||| ||| | | | | | || | | | || || ||| ||||| ||| ||||| || ||||||| || | || || || || ||||| ||||||||||| || || || |||||||| ||||||||||||||||| |||||||| ||| ||||||
---ttatctgtgtataattgtacaagaattgtgatctttttaccatgaatttaacaagcctgatctattttggttt--atttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgttctgat----tttaatttccacatcctat-ttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
||| | ||||| ||| ||| | | || |||||| | | |||| |||||| ||| ||| || | | || | || |||||||||| | || ||||| || ||||| || |||||||| ||||| || || || || ||||||||||| |||||||||||||| || || |||
--attgggattgttggtccttga-aaacaatcatggtc--ttttttactataactcctataagtctgatctagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA
upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
---ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
||| | || || | || | | | ||| | ||| || | | || ||| ||| | ||| |||| | |||| ||||| | || ||||| |||||||||||||||||||| || || || || || || || |||||||| ||||||||||| || || ||||||
gtagggttcctgcaccacgtattaggttgaattaagacatca-taacggcagtcatgttgtatatttttgacgg-aatcttgtcat--tattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
------ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgct-tacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
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gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttca----tgttgtagattcttgactgatcttgtcat-tattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
ttttaat putative branch site (score: 3)
ttctgattttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - -tacttgg
- - - - - - - - -tgttggg
- - - - - - - - - - - - - - - -tctcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacatc