Sequence
atgc intronic sequence ATGC exonic sequence...agatccagtgtgtttatggtcttttctttatttattactggtttgagagtaatggcactttggatatagatacaattttctaattctttgtgtattttagGCGTGGGGTAATTTCTGTGACTATGTATAACTTTGGATCTCCTAGAGTTGGAAACAAAAGATTTGCTGAAGTTTACAATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g43030.1 (Oryza sativa), 3'ss of exon 12
--agatccagtgtgtttatggtcttttctttatttattactggtttgagagtaatggcactttggatatagatacaattttctaattctttgtgtattttagGCGTGGGGTAATTTCTGTGACTATGTATAACTTTGGATCTCCTAGAGTTGGAAACAAAAGATTTGCTGAAGTTTACAATGAG
|| | | | || | | | || || | || | || | || | | || || | || |||| ||||||| || | |||||| ||||| |||||||| ||||||||||||||||| | ||| || |||||||| ||||||| |
tgcaattgacaatctgtaaaattgcattaaagacagcttctatttccctacatccttttctacgatcattcgttca--tatttatccgttcaccttttatagGAGTGGGGTCATATTTGTGACAATGTACAACTTTGGCTCTCCTAGAGTTGGAAATAGAAGGTTCGCTGAAGTCTACAATGCG
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G26510.1 (Glycine max), 3'ss of exon 4
-----agatccagtgtgtttatggtctt--ttctttatttattactggtttgagagtaatggcactttggatatagatacaattttctaattctttgtgtattttagGCGTGGGGTAATTTCTGTGACTATGTATAACTTTGGATCTCCTAGAGTTGGAAACAAAAGATTTGCTGAAGTTTACAATGAG
| || | | | || | | ||| | ||| | | ||| | | | |||||| || ||| | | ||| | | ||| ||| ||||| || | ||||||| | |||||||||||||| || |||||||| ||||| |||||||||||||| |||||||||||||||
actgcaaattaatttactgtaatatttaaattcactctttctgccctattttatattcatggcagttactgtatgca-ataatcattttattgtttac------cagGCGGGGAGCAATTTCTATTACTATGTATAACTTCGGTTCTCCTAGGGTTGGTAACAAAAGATTTGCAGAAGTTTACAATGAG
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G20890.1 (Glycine max), 3'ss of exon 10
-----agatccagtgtgtttatggtctt--ttctttatttattactggtttgagagtaatggcactttggatatagatacaattttctaattctttgtgtattttagGCGTGGGGTAATTTCTGTGACTATGTATAACTTTGGATCTCCTAGAGTTGGAAACAAAAGATTTGCTGAAGTTTACAATGAG
| || | | | || | | ||| | ||| | || ||| | | | |||||| || ||| | | ||| | | ||| | | ||||| || | ||||||| | |||||||||||||| || ||||| || ||||| |||||||||||||| |||||||||||||||
agtgcaaattaatttactgtaatatttaaattcactctttctgcctcattttatattcatggcagttactgtatgca-ataatcattttattgtctac------cagGCGGGGAGCAATTTCTATTACTATGTATAACTTCGGTTCTCCCAGGGTTGGTAACAAAAGATTTGCAGAAGTTTACAATGAG
upper sequence: Vv05s0077g00480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G13550.1 (Arabidopsis thaliana), 3'ss of exon 12
agatccagtgtgtttatggtcttttctttatttattactggtttgagagtaatggcactttggatatagatacaattttctaattctttgtgtattttagGCGTGGGGTAATTTCTGTGACTATGTATAACTTTGGATCTCCTAGAGTTGGAAACAAAAGATTTGCTGAAGTTTACAATGAG
||| ||| | || | | | || ||| || ||| || || || || | | | |||| | |||| ||||||| ||| |||| || ||||| |||||||||||||| ||||| || |||||| |||||||||| |||| ||| ||
---gtaagtac-tttgagaactcccttctcctacatatcaccctgacgacaa--gcagctta-atgggcatttaacat----gatttgtgtgcttgttagACGTGGGGCAATCACTGTTACCATGTACAACTTTGGATCTCCAAGAGTAGGCAACAAACAATTTGCTGAAATTTATAATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagtaatggcactttggatatagatacaattttctaattctttgtgtattttagGCGTGGGGTAATTTCTGTGACTATGTATAACTTTGGATCTCCTAGAGTTGGAAACAAAAGATTTGCTGAAGTTTACAATGAG
ttctaat putative branch site (score: 2)
ttctttgt CT-rich tract
atatagatacaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatccagtgtgtttatggtcttttctttatttattactggtttgagagtaatggcactttggatatagatacaattttctaattctttgtgtattttagGCGTGGGGTAATTTCTGTGACTATGTATAACTTTGGATCTCCTAGAGTTGGAAACAAAAGATTTGCTGAAGTTTACAATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - ccagtgt
- - - - - - - - - - - - - - - - - ttactgg
- - - - - - - - - - - - - - - - - - - - - - - - - aatggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatacaa