Sequence
atgc intronic sequence ATGC exonic sequence...cataatgattgatgtcaacctcgttttcttctgttatctttcacaaatatatatttatcaactgggttttcactttctttttatggtgttccacaactagATTGGAGAGGAACTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCTCCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 10
----cataatgattgatgtcaacctcgttttcttctgttatctttcacaaatatatatttatcaactgggttttcactttctttttatggtgttccacaactagATTGGAGAGGAACTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCTCCAAG
|| || || | || | || | ||||||| || | || | ||||| | | ||||| | | | | || | |||||||||| || ||||| ||||| ||||||||||| || || ||||||||||| ||
ctggca-aagaatagctgctatttctgtaggacacacttatcttgattaactgaattatc--taactgatatgggtcattcttctattcctaatgca-attcagATTGGAGATGAGCTTGGTGATATCTATGACTATGTTGCACCATGTTTTCCTCCTAG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 12
cataatgattgatgtcaacctcgttttcttctgttatctttcaca-----aatatatatttatcaactgggttttcactttctttttatggtgttccacaactagATTGGAGAGGAACTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCTCCAAG
| ||| || || | || | || | | || | ||||| || | | || | | | | || |||||||| || || ||||||||| | ||||||||||| ||||| || |||||||||||
-----taatttattcaaaatatcgtatcatttgcagcttcctgtacatgagatccacttttattccctattactgatggaaccttgtttcttttgtggcatatagATTGGGGAAGAGCTTGGAGATGTCTATGACTATGTAGCTCCCTGCTTTCCTCCAAG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 11
cataatgattgatgtcaacctcg--ttttcttctgttatcttt-cacaaatatatatttatcaactgggttttcactttctttttatggtgttccacaactagATTGGAGAGGAACTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCTCCAAG
| | | || || | | ||| | || ||| | || | ||| || | | || | ||| || || || || ||||||||||| || |||||||||||||||||||||||||||||||||||||| |||||
--ttcttaatgctgctagttttaaactttaataggtcctctctattcataagcccttttttcctgcaaatgatgcctctggtttgattgt-tttgacttttagATTGGAGAAGAGCTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCCCCAAG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 11
cataatgattgatgtcaacctcgttttcttctgttatctttcacaaatatatatttatcaactg-ggttttcactttctttttatggtgttccacaactagATTGGAGAGGAACTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCTCCAAG
| | | || || | | | | | | || | ||| | | ||| | | | ||| | || || ||||||||||| || |||||||||||||||||||||||||||||||||||||| |||||
-tttcttaatgctgctagttttaaactttaatagtcctttctattcataagccactttttcctgcaaatgatgcctctggtttggtttttttgacttttagATTGGAGAAGAGCTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCCCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatatatttatcaactgggttttcactttctttttatggtgttccacaactagATTGGAGAGGAACTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCTCCAAG
atatttatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataatgattgatgtcaacctcgttttcttctgttatctttcacaaatatatatttatcaactgggttttcactttctttttatggtgttccacaactagATTGGAGAGGAACTTGGAGATATTTATGACTATGTGGCTCCTTGTTTTCCTCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT