Sequence
atgc intronic sequence ATGC exonic sequence...ttttgacggtttctgcgaaaaccatcccgttatatacctcttaagcgttgttgtcccatgttttagtctttgtctcttatcttcttaattatacttgcagGCCATATCAGCTTATACTTTCCAGGATCACGAGCGATCTTCACCGGGGACACGATGTTTAGCTTATCATGTGGTAAACTCTTTGAAGGCACTCCTAAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G31350.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G31350.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 4
------ttttgacggtttctgcgaaaaccatccc-------gttatatacctcttaagcgttgt-tgtcccatgttttagtctttgtctcttatcttct---taattatact---tgcagGCCATATCAGCTTATACTTTCCAGGATCACGAGCGATCTTCACCGGGGACACGATGTTTAGCTTATCATGTGGTAAACTCTTTGAAGGCACTCCTAAGCA
|| | | | ||| | || | ||| || | | || | | | | | || | | | | | ||| | |||| || ||||||| |||||||||||| ||||| || ||||| ||||| | || || || || || ||||| ||||||||||||||||||| || ||||||||||| || || ||||
gtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
upper sequence: AT2G31350.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G03320.1 (Glycine max), 3'ss of exon 4
------ttttgacggtttctgcgaaaaccatccc-------gttatatacctcttaagcgttgttgtcccatgttttagtctttgtctctta----tcttcttaattatact---tgcagGCCATATCAGCTTATACTTTCCAGGATCACGAGCGATCTTCACCGGGGACACGATGTTTAGCTTATCATGTGGTAAACTCTTTGAAGGCACTCCTAAGCA
|| | | | ||| | || | || || | | || | | || | | | | | || | | || ||| ||| ||||||| |||||||||||| ||||| || ||||| ||||| | || || || || || ||||| |||| |||||||||||||| || ||||||||||| || || ||||
gtcacattcatgctctatttgcattagtaattcttcttaatattgtaaagtattaaaaaaatctggtttcttttatgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTCAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgttgttgtcccatgttttagtctttgtctcttatcttcttaattatacttgcagGCCATATCAGCTTATACTTTCCAGGATCACGAGCGATCTTCACCGGGGACACGATGTTTAGCTTATCATGTGGTAAACTCTTTGAAGGCACTCCTAAGCA
tcttaat putative branch site (score: 3)
ttatcttcttaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgacggtttctgcgaaaaccatcccgttatatacctcttaagcgttgttgtcccatgttttagtctttgtctcttatcttcttaattatacttgcagGCCATATCAGCTTATACTTTCCAGGATCACGAGCGATCTTCACCGGGGACACGATGTTTAGCTTATCATGTGGTAAACTCTTTGAAGGCACTCCTAAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG