Sequence
atgc intronic sequence ATGC exonic sequencegtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G020146_T01 (Zea mays), 3'ss of exon 3
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
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--------tcggtttattgtttgattgtgttgggtt-----catttaggaaaa-------aaacaaaagagtcatagcctct-------catgggtgttatttaattgc------tctaaa---ctgctatttcagGTGTTCTTTAAGAAGCACCCAGAATTTGCAAAGAATGACTTCTTTATAACTGGAGAATCTTATGCTGGGCACTACATTCCAGCATTTGCAAGCAGAGTTC
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G19950.3 (Glycine max), 3'ss of exon 3
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgta-tacctctttg--tgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
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------------------------------------------------gtaataattatttgaatgcaagataacatcttattgtgtataat--taagattcactcaactcaattaattttaa-----tataatggcagGAGTTTTTCAAGGCTCATCCTAAGTTCGTTAAGAATGACTTTTATATTACCGGAGAATCATACGCTGGACACTATATTCCGGCTCTTGCATCCCGGATAA
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G19960.1 (Glycine max), 3'ss of exon 3
------gtcactctgcgtctccttatctttctgtgccaaatctaaaacattta--cgtatacctctttgtgcaaatcac-tcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
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gtaacaattaattataatctactaatctccct-tctcaatttcatctcatttatccgaatacaagataattaatatcttgttgtgtataaaataagatccaataaatta---attt------gatttactac----taatggcagGAGTTTTTCAAGGCGCATCCTGAGTTTGTTAAGAATGATTTTTATATTACTGGAGAATCATACGCTGGGCACTATGTTCCGGCACTTGCATCCCGGGTTA
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G16790.1 (Glycine max), 3'ss of exon 3
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
| | | ||| || | ||| ||| ||| | ||| | | |||| || ||| | | || || | ||| || ||||| |||| ||||| |||||| | ||||| |||||||||||||| || |||||||||||||||||||| || || ||| || |||| | || |||
------------caattgttgccactgggctcatcctagtgggttt---------tctgaatacaatataattttgttgtctataag--------------taacatgcactaaat-taatttactataatgacagGAGTTTTTCAAGGCACATCCTCAATTCGTTAAGAATGACTTTTATATCACTGGAGAATCATACGCTGGACATTATGCTCCAGCTCTTGCATCCCGTGTTA
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G05470.1 (Glycine max), 3'ss of exon 3
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
| || |||| | | | ||| | ||| | |||||| |||||| | ||| | | | || | | || ||||| |||| ||||| ||||||||| || || ||||||||||||||||| || ||||||||||| ||||| ||||| |||| || |||| | ||||||
----------------------------actgtatttaaattgtcttttctgaaatctgaatccaagataatcttgttttgtgtaaa--------tattaataagatgccctaaattaattttactataatgacagGAGTTTTTCAAGGCGCATCCTGAATTTGTTAAGAATGACTTTTACATTACCGGAGAATCATATGCTGGACACTATGTTCCAGCTCTTGCATCCCGGGTTA
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G30160.1 (Glycine max), 3'ss of exon 3
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccct---gtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
||| | | || || ||| | | | |||| || || | ||| | | || | ||| | || | || | | || | ||||| ||||||||||| |||| ||| || || |||||||||||||| || |||||||| ||||| ||||| ||||||||||| || |||| | ||||||
-------------------------------aaaaatgcaggatg---gtgtacatact-atctaaatt--tcaagttatatgttagactctgc-cgttgtgcatcat-aggatccatttaattttacaataatgacagGCATTTTTCAAGGAGCACCCTCAGCTCACTAAGAATGACTTTTATATTACTGGAGAGTCATATGCTGGACACTACATTCCAGCTCTTGCATCCAGGGTTC
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G39730.1 (Glycine max), 3'ss of exon 3
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaacc--ctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
|||| || | | ||||| | |||| || || | ||| | | || | || | || | ||| | || | ||||| ||||||||||| |||| ||| | ||| |||||||||||||| || |||||||| ||||| ||||| || |||||||| || |||| | ||||||
-----------------------------aaaaatgcaagatggt-gtacataccatct-----aaatt--tcaagttatatgttagactctgc-cgtggtgcatcataagatccactcaattttacaataatgacagGCATTTTTCAAGGAGCACCCTCAATTCACTAAGAATGACTTTTATATTACTGGAGAGTCATATGCTGGACATTACATTCCAGCTCTTGCATCCAGGGTTC
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G08500.1 (Glycine max), 3'ss of exon 5
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGG----CCACTACATTCCTGCGTTTGCTGCTCGGGTTC-----------------------------
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------------------------------------------------------------------------------------------------------------------------------------------gtttttcaaggcgcatccttagtttgtcaagAATGATTTTTATATTACTGGAGAATCATATGCTGGAAATTAACTATGTTCTGGCGCTTGCCTCCCGGGTTAACCAAGGCAATAAAAGAAAACAAGGAATC
upper sequence: Vv06s0061g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G45010.1 (Arabidopsis thaliana), 3'ss of exon 3
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaat-cactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
|| | | || | | || |||| | | ||| ||| | || | || | | | ||||| ||||| | ||||||| | || ||||||||||| |||||||| || || ||||| |||||||| || |||||||| || || ||| | || ||||
------------------------------------------------------------gttcggtttcaattctttcctctgt----ttcatcacattaaaaacatgttcttgacgtgacacattttctttgcagGCGTTTTTCAAAGAGCATCCACAATTTGTGAAGAATGATTTTTACATTACCGGTGAATCCTACGCTGGACATTACATTCCGGCATTGGCTTCACGTGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
tattgat putative branch site (score: 3)
ttattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcactctgcgtctccttatctttctgtgccaaatctaaaacatttacgtatacctctttgtgcaaatcactcttgtcaactgtaaaatccttcatgttattgattctcagaaagtgtaaaaccctgtaatgtcagGCATTTTTTGCAAAGCATCCTGAGTTCGTGAAGAATGACTTTTACATAACTGGAGAATCATACGCTGGCCACTACATTCCTGCGTTTGCTGCTCGGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT