Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgcccatggtagctactttaatcgtttcttgaattctctttattaattatctcagccttttgctgtgtgttttagGCCCTTGATTTGATTCGAGACAGAAATCTTCAGACTCTAACCGATTCCTGCTTGGAGGGACAATTTTCAGACAGTGATGGTACGGAGTTAGTACGCCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01740.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G01300.2 (Glycine max), 3'ss of exon 7
----------gtaagtgcccatggtagcta--ctttaatcgtttcttgaa---ttctctttattaatt-----atctcagccttttgctgtgtgttttagGCCCTTGATTTGATTCGAGACAGAAATCTTCAGACTCTAACCGATTCCTGCTTGGAGGGACAATTTTCAGACAGTGATGGTACGGAGTTAGTACGCCTGA
| ||| | | | ||||||| | | || | | | | | | || | | | | || | || | ||||||| ||| ||||||| | ||||||||||||| ||||| ||||| |||||||| ||||||||||| || |||||| || ||||| |||||| ||
ttcttctcccatgtccgccatctacaacaaatctttaatagctagttatatattaccatatgtaaacttgcatgtgtaattattagaaaatttggtgcagGCCCTCGATGTGATTCGTGGAAGAAATCTTCAGATGCTAACAGATTCTTGCTTGGAAGGACAATTTTCCGATGATGATGGAACTGAGTTGGTACGCTTGG
upper sequence: AT1G01740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G07850.2 (Glycine max), 3'ss of exon 7
------------gtaagtgcccatggtagctactt--taatcgtttcttgaattctctttattaattatctcagccttttgct------gtgtgttttagGCCCTTGATTTGATTCGAGACAGAAATCTTCAGACTCTAACCGATTCCTGCTTGGAGGGACAATTTTCAGACAGTGATGGTACGGAGTTAGTACGCCTGA
|| | || ||||| || || | | | | | | | || | | | | || | | || | ||||||||||| ||||||| | ||||||||||||| || || ||||| || ||||| |||||||||||||| ||||| || |||||||||||| ||
aacatatccttaatagccatttttttgaggtacttaatagctaattatgtattaccatatgtaaacttgcatggtgtaatgattagaaaatttggtgcagGCCCTTGATGTGATTCGTGGAAGAAATCTTCAGATGCTGACAGATTCTTGTTTGGAAGGACAATTTTCAGATGACGATGGAACTGAGTTAGTACGCTTGG
upper sequence: AT1G01740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv15s0046g02900.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtgcccatggtagct---actttaatcgtttctt----------gaatt---ctctttattaattatctcagccttttgct------gtgtgttttagGCCCTTGATTTGATTCGAGACAGAAATCTTCAGACTCTAACCGATTCCTGCTTGGAGGGACAATTTTCAGACAGTGATGGTACGGAGTTAGTACGCCTGA
||||| ||| || | ||| ||| || || || || || |||||| || || | || |||| | || | ||||||||||| |||| |||||||| ||||| |||| || || |||||||||||||| ||||| ||| | | |||||| || ||||||||||| |
--tagtgcaaatgttattttgtgcttcaatgtttcttttggggttatagagttgacctttttatttatgatttacatctaatgcttgaataatttgaatcagGCCCTTGATCTGATACGAGACAGGAATCTGCAGATGCTGACAGATTCCTGCTTGGAAGGACAGTTTACTAATGATGATGGAACTGAGTTAGTACGGTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcgtttcttgaattctctttattaattatctcagccttttgctgtgtgttttagGCCCTTGATTTGATTCGAGACAGAAATCTTCAGACTCTAACCGATTCCTGCTTGGAGGGACAATTTTCAGACAGTGATGGTACGGAGTTAGTACGCCTGA
tattaat putative branch site (score: 2)
ttgaattctctttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgcccatggtagctactttaatcgtttcttgaattctctttattaattatctcagccttttgctgtgtgttttagGCCCTTGATTTGATTCGAGACAGAAATCTTCAGACTCTAACCGATTCCTGCTTGGAGGGACAATTTTCAGACAGTGATGGTACGGAGTTAGTACGCCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG