Sequence
atgc intronic sequence ATGC exonic sequencegtaaagatccagtagtttgccatcaactcgattttcatccagcagattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 6
gtaaagatccagtagtt----tgccatcaactcgattttcatccagca-gattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
|| | ||| || || | | || | | | || | | | || | || ||| | || |||||||| |||||||| ||||| ||||| | || |||||||| ||||| ||||||||||||||||| || |||||||||||||||| | |||||||| |
gtgatgattcactaatgctggtagcaatgatataacctccagatcttatgcctttacttaacaaacatttcgatcgtttattcagGATGGCAAAATTAGCTATGAAGAATTCGTAGCAATGATGAAGACTGGCACAGATTGGAGAAAGGCGTCACGGCATTATTCAAGAGGACGTTTCAACAGCC
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 6
---gtaaagatccagtagtttgccatcaactcgat--tttcatccagcagat-------tataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
| | | | | | |||| | | | | || | || | | | ||||| || | || ||| || || |||||||||| || ||||| ||||| ||||||| || |||||||| || || ||||||||||||||||| || ||||||| || ||||| ||||||||||| |
gtgatgatatttctgaatacaaccattcttttggtaatatcgttcaaaacttttttttatctaaataacat-atgttttcttttcactgcagGATGGCAAGATTAGCTATGACGAATTTGTAGCAATGATGAAGACGGGCACAGATTGGAGAAAGGCGTCCCGGCATTACTCTAGAGGAAGATTCAACAGCC
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 6
-------------gtaaagatccagtagtttgccatcaac--tcgattttcatccagcagattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
||| | || | | | | | || | | |||| | | || || | | || || | |||||||||| |||||||| || || ||||||| || |||||||| ||||||||||||||||| ||||| || ||||||||||||||||| | ||||| || |
gttaacggttcacctaaggcccctgagatagctctgctgccttcaaatctcattaatta--tttcaagtcgcaataacctttgttgtttctgcagGATGGTAAAATTAGCTACGAAGAATTTGTAGCGATGATGAAGACTGGAACAGATTGGAGGAAGGCGTCGCGGCATTATTCAAGAGGGCGCTTCAATAGCC
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G088361_T01 (Zea mays), 3'ss of exon 6
---------------------------gtaaagatccagtagtttgccatcaactcgattttcatccagcagattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
| | | |||| |||| || | || | ||| || | |||| |||| | ||||||||||||||||||| || || ||||||| || |||||||||||||| || || ||||| ||||| || |||| |||||||||||| | ||||| || |
gttaacgatccaccaccgaaggctcctgcgatagcttgtggctgtgccttcaaatc--ctatcgttagtcaggccgcaa-taacttc-ccgttgtttc----tgcagGATGGGAAAATTAGCTACGACGAATTTGTAGCGATGATGAAAACTGGCACGGACTGGAGGAAGGCATCGCGGCACTATTCAAGAGGGCGCTTCAATAGCC
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 6
--gtaaagatcc-agtagtttgccatcaactcgattttcatccagcagattataaatgactttatttttgtcttacaat-gcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
|| || || | || ||| | | | | | | || ||| || || || || | ||| | ||||||||| || || || |||||||||| |||||||||||||||||||||||||||||||| || || |||||||| ||| | || |||||||| ||
gtgtgaatattcgagagatttttctttacatataggcttgattaggggatcttacc---ctctaaaattcttgaacacttgcagGATGGACGTATCAGCTACGATGAATTTGTTGCTATGATGAAAACTGGAACAGATTGGAGAAAAGCATCAAGGCATTACTCACGTGGAAGATTCAATAGCT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 8
gtaaagatcc-agtagtttgccatcaactcgattttcatccagcagattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC-
| | || || ||| | | | | | | || ||| || | ||| ||| |||||||||| || || ||||||||||||| |||||||||||||||||||| ||||||||||| || || |||||||| || | || |||||||||||
-tggatatttgagagatttctctttacatataggcttgattaggggatcttaccatataaaattcttgaacact--tgcaggATGGACGTATCAGCTATGATGAATTTGTTGCTATGATGAAAACTGGAACGGATTGGAGAAAAGCATCAAGGCATTACTCGCGTGGAAGATTCAACAGCTT
upper sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------gtaaagatccagtagtttgccatcaactcgattttcatccagcagattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
| | | || | | | | | | | | | || | |||| | |||| | ||| | ||||||||| ||| || || || || |||||||| ||||||||||| ||||| |||||||||||||| ||| | ||||| ||||||||||||||||| || |
agagagttcacttctcatatcgttaaacagaaccttagagactatagttagtgtaaaaatgtttcttctggttgtgcctgacatggatttt---tgacatt--agGATGGGAGAATAAGCTACGAAGAGTTTGCGGCAATGATGAAAACAGGAACGGATTGGAGAAAGGCGTCTCGTCATTACTCAAGAGGGAGATTCAATAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcgattttcatccagcagattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
gtcttac putative branch site (score: 3)
ctttatttttgtctt CT-rich tract
attataaatgacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagatccagtagtttgccatcaactcgattttcatccagcagattataaatgactttatttttgtcttacaatgcagGATGGGAAAATTAGTTATGATGAATTTGCGGCTATGATGAAAACTGGAACAGATTGGAGAAAGGCTTCTAGGCATTATTCAAGAGGGAGATTCAACAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT