Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttccttttttgtttatatccacttctttcctcgatgatttcgctggattccgattatggacttcaacggttcgattttattcttcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08590.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
gtatgtttccttttttgtttatatccacttctttcctcgatgatttcgctggatt--------ccgatta--tggacttcaacggttcgattttattct-tcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC
|| ||| ||||| | | | || | | | | | | | | | ||| || | || | | | ||||||| | | |||||| || || ||||| ||| | | |||||||||||||| || || || || | ||||| |||||||| || ||||||||||| ||||||||||
----gtgtccatttttagtagccgacggtgtttcaaacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggat--ttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
-gtatgtttccttttttgtttatatccacttctttcctcgatgatttcgctg----gattccgattatggacttcaacggttcgattttattcttcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC
||| | | |||| | | | |||| | | || | | || ||| |||| ||| | || | |||||||||| || || | |||||| ||| | || |||||||| | || || || || || | || || |||||||| ||||||||||||||||| |||||||
ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S193_45V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtatgtttcct--tttttgtttatatccacttctttcctcgatgatttcgctggattccg--attatggacttcaacggttcgattttattcttcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC
|| | | | | || ||| | | || || ||| | || | | ||| || | | || | | || | || | || | || || |||| || | | ||| ||||| | || || || |||||||| || ||||||||||||||||| ||||||||||| ||||
cctcatcatccatgatcttaagttacaaactagaattgaatccgtgagcttcctacctgttggaattctgtagtagaaagtgttaatgct-ttttctgtagACGGCACCGGATCGATGGCGGCTTGTGCGAGCCCATGGCCTTTCTGTAGGCCTTCCCAGCGACGAAGACATGGGAAACAGTGAGGTTGGCCACAACGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatttcgctggattccgattatggacttcaacggttcgattttattcttcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC
ttttattcttc CT-rich tract
attttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttccttttttgtttatatccacttctttcctcgatgatttcgctggattccgattatggacttcaacggttcgattttattcttcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA