Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcaaaagatatgactcttttgatgacactatttctttctcccattttcagacgaatatttatatgttaatattgactacagATAAACAACAACCTTCGCTGCTACGACCTTGCCATGGAGTTAAGTAATAGCACTTTAGAAGCTCTTCCACAAAATTATGCAGAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.2 |
intron # | 17 |
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 17
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 17
---------gtatgtcaaaagatatgactcttttgatgacactatttctttctcccattttcagacgaatatttatatgttaatattgactacagATAAACAACAACCTTCGCTGCTACGACCTTGCCATGGAGTTAAGTAATAGCACTTTAGAAGCTCTTCCACAAAATTATGCAGAGCAG
| | || | | | | | ||| | || || || | | || | | || ||| || ||| |||| | |||| |||||||| | |||||||| |||||||| |||||| ||||||||||||| ||||||| |||||||| || || || ||||||
gttagtgtaatttttctgtaagtgttgcgttattgttt-caacataagattgttttctgttgacatgag-attcat---ctaacattgtatttagATTAACAACAATTTGCGCTGCTATGACCTTGCAATGGAGCTAAGTAATAGCACCATAGAAGCCCTTCCACAGAACTACGCTGAGCAG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 16
gtatgtcaaaagatatgactcttttgatgacactatttctt--tctcccattt--tcagacgaatatttatatgttaatattgac------tacagATAAACAACAACCTTCGCTGCTACGACCTTGCCATGGAGTTAAGTAATAGCACTTTAGAAGCTCTTCCACAAAATTATGCAGAGCAG
|| |||| | | | |||| |||| |||| | | | | | | | | |||| | | | ||||||| | ||||| |||||||| || |||||||| || || || ||||| | |||| ||||| || |||||||||||||| |||||||| ||||||
gtttgtctctcttaaacaagttccatgtgactctatctcttggttttctactaaattaagtcaccatttctttactgctattgacattgtatccagATTAACAACAATCTACGCTGCTATGATCTAGCATTGGAGCTGAGTAGCAGCACCTTGGAAGCTCTTCCACAGAATTATGCTGAGCAG
upper sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 16
gtatgtcaaaagatatgactcttttgatgacactatttctt--tctcccattt--tcagacgaatatttatatgttaatattgac------tacagATAAACAACAACCTTCGCTGCTACGACCTTGCCATGGAGTTAAGTAATAGCACTTTAGAAGCTCTTCCACAAAATTATGCAGAGCAG
|| |||| | | | |||| |||| |||| | | | | | | | | | || | | | ||||||| | ||||| |||||||| || |||||||| || || || ||||| | |||| ||||| || |||||||||||||| |||||||| ||||||
gtttgtctctcttaaacaagttccacgtgactctatctcttggttttctactaaattaagtcaccaattctttactgctattgacattgtatccagATTAACAACAATCTACGCTGCTATGATCTAGCATTGGAGCTGAGTAGCAGCACCTTGGAAGCTCTTCCACAGAATTATGCTGAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actatttctttctcccattttcagacgaatatttatatgttaatattgactacagATAAACAACAACCTTCGCTGCTACGACCTTGCCATGGAGTTAAGTAATAGCACTTTAGAAGCTCTTCCACAAAATTATGCAGAGCAG
tattgac putative branch site (score: 2)
aatatttatatgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcaaaagatatgactcttttgatgacactatttctttctcccattttcagacgaatatttatatgttaatattgactacagATAAACAACAACCTTCGCTGCTACGACCTTGCCATGGAGTTAAGTAATAGCACTTTAGAAGCTCTTCCACAAAATTATGCAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG