Sequence
atgc intronic sequence ATGC exonic sequencegtataatctacgtccttatttcttacaggcagcggttcctcttctttatccatgcacacgaataatgtactgtctgtttctctttaatttcgtagAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G36160.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 7
-----gtataatctacgtccttatttcttacaggcagcggttcctcttctttatccatgcacacgaataatgtactgtctgtt-tctctttaatttcgtagAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATC
| ||| | || || ||| || | ||| |||| ||| | | || | | ||| | | | | | | |||| |||||||||| || |||||||| | |||||||||||||| |||||| ||||| |||||||||| ||| |||| ||||||||||||||| ||||| |||||
caaatgaatagtgtaacctattctttactattatttact-ttcttcttgtttgctatttgatttgatttcttacatgtatttcatgtgtctcatttaatagAGATAAGGCGTTTCTATGGGGTGGAACATGGTGGAGGGTATGATGCTTGGAGAAAAACATCCGTTTTAGCTACCCCTTTTGATTTTGACAAAGCACAATC
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 7
-gtataatctacgtccttattt---cttacaggcagcggttcctcttctttatccatgcacacgaat--aatgtactgtctgtttctctttaatttcgtagAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATC
||| | | | || | | || | ||| | | |||||| | || | ||| | | | | | | | | | |||| |||||||||| || |||||||| | |||||||||||||| |||||| | ||| |||||||||||||| |||| |||||| |||||||| ||||| |||||
agtagggaccaaatgaatagtgaaacctattctttactattctt-tactttattcttgtttgctaattgatttgatttcttacatgtgtctcatttaatagAGATAAGGCGTTTCTATGGGGTGGAACATGGTGGAGGGTATGATGCCTGGAGAAAAACATCTGTTTTAGCTACCCCTTTCGATTTTGACAAAGCACAATC
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 8
gtataatctac---gtccttatttcttacaggcagcggttcctcttcttta--tccatgc-acacgaataatgta-ctgtctgtttctct---ttaatttcgtagAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATC
|||| ||| || | |||| || | | ||| ||||| | | || | | || || | ||| || | | | | || |||| ||||| | ||||||||||| |||||||| ||||| |||||| ||||| | | |||||| ||||| || ||||||||||||||| ||||| | ||
gtatgctcttatcgatcttcatttttttctagacctttttctcagtctttcacttcttgttatgtgtatgctgcatctgactatattattgactgtcttaaatagAAATAAGGAGATTCTATGGAATGGAACATGGCGGAGGATATGATGCTTGGAGGAGAACATCAGTTGTTGCTACCCCTTTTGATTTTGACAAAGCAGAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctttatccatgcacacgaataatgtactgtctgtttctctttaatttcgtagAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATC
ctttaat putative branch site (score: 4)
tttctctttaatttc CT-rich tract
tttctctttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatctacgtccttatttcttacaggcagcggttcctcttctttatccatgcacacgaataatgtactgtctgtttctctttaatttcgtagAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA