Sequence
atgc intronic sequence ATGC exonic sequence...ttttattatttatatacctcttaagattgatgataatcattacatttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g11330.1 (Oryza sativa), 3'ss of exon 4
-------ttttattatttatatacctcttaagattgatgataatcattacatttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
|| || | | | || ||| | ||| || | || | | | || || ||| | || || || | | | ||||| ||||| |||||||||||||||||||| | ||||| || |||| |||||||||||| | ||||| || ||| | || | || || || ||||| |
tgaaactggataatagctgtgttacttttacagctactgacaaatgaaagatatggcctacccatctttctttagctgatg--atattatttatttata-----cagCTTTTTCCGAACCTCAACAAGGTGGTCTTTCTTGATGACGACATTGTTATTCAGCGTGATTTGTCTCCCCTTTGGAAGATCAATCTCGAAGGGAAGGTGA
upper sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G113506_T01 (Zea mays), 3'ss of exon 4
ttttattatttatatacc-tcttaagattgatgataatcattacatttctgtttttgtttttgtttgcgctatt--tttatgttgattgtgtgcatgtaa-cagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
|||| | || || | | || | ||| | | || | | | || | | |||||| | || || | | | | | || ||||||||||| ||||||||||||||||||||| | |||||||| |||| |||||||||| | ||||| || |||| || | ||||| || ||||| |
--ttat-acttgtactctgtagcaaagattgtgaaatttatcatgta-caattgtagattttgtacatctttttaacctaattcgttcacttctcttcaatcagCTCTTTCCCAACCTCAACAAGGTGGTCTTCCTCGATGATGACATTGTTGTTCAGCGTGACTTGTCTCCCCTTTGGGCGATCAATCTTGAAGGGAAGGTGA
upper sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G107854_T01 (Zea mays), 3'ss of exon 4
ttttattatttatatacctcttaagattgatgata-atcattacatttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
| || |||| | || | | || || | | |||| | ||| | | | | || | | || | | | | | ||||||||||| ||||||||||||||||| ||| | |||||||| |||| |||||||||| | ||||| || |||| || | ||||| || ||||| |
agctgcacttaccatacagtacagctttaaagctagattgtgaaatttgtagatttttgtgcatcttt-ttaatctgatccattcacttttctttaaccagCTCTTTCCCAACCTCAACAAGGTGGTTTTCCTCGATGATGACATTGTTGTTCAGCGTGACTTGTCTCCCCTTTGGGCTATCAATCTTGAAGGGAAGGTAA
upper sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G49960.1 (Glycine max), 3'ss of exon 4
---ttttattatttatatacctcttaagattgatgataatcattacatttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
|| || | | | || | | | | | ||| | | | | || || | | |||| | | || ||||| | || | ||||||| || |||||||| |||||||||| || || ||||||||||| || ||||||||||| | ||||| || |||||||||||||| || ||||| ||||
gtgttagataaaatgt-tattgttgtctttctcttttgaacataaattgtgttttgtttgatatatttgtgttgatt--atgtttgctttgcatgtcaaacagCTTTTCCCAAACCTTGACAAGGTGGTTTTTTTGGATGATGATGTGGTGATTCAGCGTGACTTGTCTCCGCTTTGGGAAATTGACCTGGAAGGAAAAGTTA
upper sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G26480.1 (Glycine max), 3'ss of exon 4
--------ttttattatttatatacctcttaagattgatgataatcattacatttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
| || |||| | || | |||| |||| | | |||||||| | | |||| ||| || ||||| | | | | ||||||| || |||||||| |||||||||| || || ||||||||||| || ||||||||||| | |||||||| ||||||||||| || || ||||| ||||
atgttagataaaatgttttagttgtctttctcttttgaacataaactgtg---ttctgtttga---tatatttgagctgatt--atgtttgtcttatttgtcaaacagCTTTTCCCAAACCTTGACAAGGTGGTTTTTTTGGATGATGATGTGGTGATTCAGCGTGACTTGTCTCCACTTTGGGAAATTGATCTGGAAGGAAAAGTTA
upper sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G03460.1 (Glycine max), 3'ss of exon 4
ttttattatttatatacctcttaagattgatgataatcattacatttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
|||| ||| | | | || | | || | | || | || ||| ||| || | | | ||| |||| | ||||||| || |||||||| |||||||||| || | ||||||||||||||| |||| ||||| | |||||||||||||||||||| | | ||||| ||||
tttttatatgagccaatttgagcacatgaacattttatgttggagaaattttccatctcttatttatgctgattgtgtttccattatgtgtgttgaacagCTTTTCCCAAACCTTGACAAGGTGGTTTTTCTGGATGATGATGTTGTAGTTCAACGTGACTTGTCTCCACTCTGGGAAATTGATATGAATGGAAAAGTTA
upper sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G05950.1 (Glycine max), 3'ss of exon 4
----ttttattatttatatacctcttaagattgatgataatcattacatttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
| || || || |||| | ||| | | || ||| ||| | | | || ||| || | ||||| | | | ||| ||||||| ||||||| || |||||||| |||||||||| || | |||||||||||||| |||| ||||| | |||||||||||||||||||| | | ||||| ||||
aagatgttttttcctaaatacat-ttagcacttat-atagcaattgtaacttc--tcttatttatgctgaatgtatttatgtttgcattatgtgcattgaacagCTTTTCCCAAACCTTGACAAGGTGGTTTTTCTGGATGATGATGTTGTGGTTCAACGTGACTTGTCTCCACTCTGGGAAATTGATATGAATGGAAAAGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
tgttgat putative branch site (score: 4)
tatttttatgttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttattatttatatacctcttaagattgatgataatcattacatttctgtttttgtttttgtttgcgctatttttatgttgattgtgtgcatgtaacagCTCTTTCCAAACCTCAACAAGGTGGTCTTCTTAGATGATGATGTTGTAATTCAGCGTGATCTCTCTCCACTCTGGGAAATTGACCTTGAGGGAAAGGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgtg