Sequence
atgc intronic sequence ATGC exonic sequence...ttgtggatccggttggtcaatctaataacaaaatgaagaggcaaaagtaatttgccttttgaacttacactattggttttcatcgtgaaactatgagcagGTTGGCTGCATCAAACTGGAGTGGTGAAGGTTCTTTCCTATTCACATCTAGTTCTGCACCATTTGATTGCAATGACAATGGATCATGTGATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g01880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G09370.2 (Glycine max), 3'ss of exon 2
-----ttgtggatccggttggtcaatctaataacaaaatgaagaggcaaaagtaatttgccttttgaacttacactattggttttcatcgtgaaactatgagcagGTTGGCTGCATCAAACTGGAGTGGTGAAGGTTCTTTCCTATTCACATCTAGTTCTGCACCATTTGATTGCAATGACAATGGATCATGTGATGAG
|| || | | || ||| | || | |||| || | ||| |||||| | ||||| | | || | || || |||| | ||||||| || ||||| |||||||||||||||| |||| ||||| || ||| |||| |||||| ||||| |||||| |||||||||||
gttagagaaaaatgatattagcttaatgaaaggaaaatttgtgatggtgtagtagtt-gtcttatgaactcatg-tattgatgtggattgccaactaat---cagGCTAGCTGCATTAAGCTGGAATGGTGAAGGTTCTTTCTTATTTACATCAAGCAGTGCTCCATATGATTGTAATGATAATGGACCATGTGATGAG
upper sequence: Vv05s0020g01880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G26450.1 (Glycine max), 3'ss of exon 2
-----ttgtggatccggttggtcaatctaataacaaaatgaagaggcaaaagtaatttgccttttgaacttacactattggttttcatcgtgaaactatgagcagGTTGGCTGCATCAAACTGGAGTGGTGAAGGTTCTTTCCTATTCACATCTAGTTCTGCACCATTTGATTGCAATGACAATGGATCATGTGATGAG
|| |||| | || ||| | || |||| ||| ||| |||||| | ||||| | | || | || || |||| | ||||||| || ||||| ||||||||||||||| |||| ||||| || ||| |||| |||||| ||||| |||||| |||||||||||
gttagagaaaaatgatattggcttaatgaaaggaaaatttgtgatagtgtagtagttt-tcttatgaactcatg-tattgatgtggattgccaactaat---cagGCTAGCTGCATTAAGCTGGAACGGTGAAGGTTCTTTCTTATTTACATCAAGCAGTGCTCCATATGATTGTAATGATAATGGACCATGTGATGAG
upper sequence: Vv05s0020g01880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G10460.4 (Glycine max), 3'ss of exon 2
----------ttgtggatccggtt--ggtcaatctaataacaaaatgaaga-ggcaaaagtaatttgcctttt-gaacttacactattggttttcatcgtgaaactatgag-------------------cagGTTGGCTGCATCAAACTGGAGTGGTGAAGGTTCTTTCCTATTCACATCTAGTTCTGCACCATTTGATTGCAATGACAATGGATCATGTGATGAG
|| | | || | || || ||||| || | | | | | |||||| | || || | || ||||| || |||| |||| | |||| ||||||||||| ||||| |||||||||| |||| || || ||||| || ||||| || | |||||| ||||| ||||||| ||| | |||
gttagcaatcttatccttgaaatttaaattaaagaggaaataaaataaaaacaattataaaagtcaacctttttgtgtttgcaattgtgtttttcttc-tgaacttatgtggggtggactgtcaaccaatcagGCTGGCTGCATCATGCTGGAATGGTGAAGGTGCTTTGCTGTTTACATCAAGCTCTGCTCCTTATGATTGTAATGATAATGGATTGTGTCACGAG
upper sequence: Vv05s0020g01880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G28660.1 (Glycine max), 3'ss of exon 3
--------------------------ttgtggatccggttg----gtcaatctaataacaaaatgaagaggcaaaagtaatttgcc--ttttga-acttacact----attg-gttttcatcgtgaaactatgag-------------------cagGTTGGCTGCATCAAACTGGAGTGGTGAAGGTTCTTTCCTATTCACATCTAGTTCTGCACCATTTGATTGCAATGACAATGGATCATGTGATGAG
||| || ||| | ||| ||||| ||||| || | | | | || | ||| | | | || |||| ||||| | |||| |||| | |||| ||||||||||| ||||| |||||||||| |||| || || ||||| || ||||| || | |||||| ||||| ||||||| ||| |||||
gtgatcttaggttatcaatcttgtccttgaaaattaaattgaagaggaaataaaataaaaaaattaaaaaaaaggtattgtgtgttagtattgttattcatgcttggaattgtgtttttcttctgaacttatgtgtggtggactgtcaaccaatcagGCTGGCTGCATCATGCTGGAATGGTGAAGGTGCTTTGCTGTTTACATCAAGCTCTGCTCCTTATGATTGTAATGATAATGGATTGTGTCATGAG
upper sequence: Vv05s0020g01880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G39080.1 (Arabidopsis thaliana), 3'ss of exon 3
--ttgtggatcc--ggttggtcaatctaataacaaaatgaagaggcaaaagtaatttgccttttgaacttacactattggttttcatcgtgaaactatgagcagGTTGGCTGCATCAAACTGGAGTGGTGAAGGTTCTTTCCTATTCACATCTAGTTCTGCACCATTTGATTGCAATGACAATGGATCATGTGATGAG
||||| | | | | || | | |||| | || | | ||| || | || | || || | | | | || |||| || ||||||||||||| ||| ||||| || ||| |||||||||||||||||||||| | ||||||| ||| || ||| ||| | |||
atttgtgctttttagttcatcctatgtgacaacagtaaaaacatttgcct-tcattcaactgtctaatatgtgtgtatgcttgtgtttacaa---tcggatcagGAATGCAGCATCAAACTGGAATGGCGAAGGATCATTCTTATTCACATCTAGTTCTGCACCTTATGATTGCTTTGATAACGGAGAATGCAACGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaatttgccttttgaacttacactattggttttcatcgtgaaactatgagcagGTTGGCTGCATCAAACTGGAGTGGTGAAGGTTCTTTCCTATTCACATCTAGTTCTGCACCATTTGATTGCAATGACAATGGATCATGTGATGAG
aacttac putative branch site (score: 2)
ttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtggatccggttggtcaatctaataacaaaatgaagaggcaaaagtaatttgccttttgaacttacactattggttttcatcgtgaaactatgagcagGTTGGCTGCATCAAACTGGAGTGGTGAAGGTTCTTTCCTATTCACATCTAGTTCTGCACCATTTGATTGCAATGACAATGGATCATGTGATGAG
- -tggatcc
- - - - - ggttggt
- - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - -ggcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctattgg