Sequence
atgc intronic sequence ATGC exonic sequence...aacacagttctgcatgtgttcacttcttaaattatgtggttttgacgccttttttcccaatgaattttttttcttaagtgggaatactatgatgttgcagGTGATAGAAGCACAAGAAGACATGCCTATTCTGAGTGCAGTAACCCTATATTCCTCCCTTCTCAAGTTTACTCTTCACGTTCACCCTGATCGGCTTGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17790.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 9
-aacacagttctgcatgtgtt---cacttcttaaattatgtggttttgacgccttttttcccaatgaattttttttcttaagtgggaatactatgatgttgcagGTGATAGAAGCACAAGAAGACATGCCTATTCTGAGTGCAGTAACCCTATATTCCTCCCTTCTCAAGTTTACTCTTCACGTTCACCCTGATCGGCTTGATT
|| | |||| | | | || || || || || | || || || | | || | | | | | | || | | || ||||||||||||| ||||| |||||||| | | | | | ||||| ||||||| |||||||||| || |||||||| |||||||||||||| |||||||
aaatgtacttctttacatccttctcattttttctatgatacaatgttattgctgttatgctcatcaattgtgaaatatgatgtc----ttcaattgctatgcagGTGATAGAGGCACAGCCTGACATGCCCACTGTTGGAGTTGTAACTTTATATTCGTCCCTTCTCACCTTCACTCTTCATGTTCACCCTGATCGACTTGATT
upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 9
-aacacagttctgcatgtgtt---cacttcttaaattatgtggttttgacgccttttttcccaatgaattttttttcttaagtgggaatactatgatgttgcagGTGATAGAAGCACAAGAAGACATGCCTATTCTGAGTGCAGTAACCCTATATTCCTCCCTTCTCAAGTTTACTCTTCACGTTCACCCTGATCGGCTTGATT
|| | |||| | | | || || | || || | || | || | | || | | | | | | || | | || | ||||||||||||| ||||| |||||||| | | | | | ||||| ||||||| |||||||||| || |||||||| || ||||||||||| |||||||
aaatgtacttctttacatccttctcattttatgcatgatacaatgttattgttgttatgctcatgggttgtgaaatatgatgtc----ttcaattgttatgcagGTGATAGAGGCACAGCCTGACATGCCCACTGTTGGAGTTGTAACTTTATATTCGTCCCTTCTCACCTTCACTCTTCATGTCCACCCTGATCGACTTGATT
upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 10
aacacagttctgcatgtgttcacttcttaaattatgtggttttgacgccttttttcccaatgaattttttttcttaagtggg-aatacta----tgatgttgcagGTGATAGAAGCACAAGAAGACATGCCTATTCTGAGTGCAGTAACCCTATATTCCTCCCTTCTCAAGTTTACTCTTCACGTTCACCCTGATCGGCTTGATT
||| | ||| | ||||| ||| | || || | | |||| | | | | | |||||| || | | ||||| || |||||||| | |||||||||||| | | || ||||| |||||||| || ||||||| |||||||| || || |||||||||||||||||||
----ttcttccctttatgtctatttcttcg-ttacacgtttgtgcaattaggtatataaatggactaaagtaggagaaaatgtaatacttaatctgttcattcagGTCATCGAAGCACAGGTTGACATGCCTATTTTTGGAGCTGTAACTCTATATTCATCTCTTCTCACTTTTACTCTGCATGTGCACCCTGATCGGCTTGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgccttttttcccaatgaattttttttcttaagtgggaatactatgatgttgcagGTGATAGAAGCACAAGAAGACATGCCTATTCTGAGTGCAGTAACCCTATATTCCTCCCTTCTCAAGTTTACTCTTCACGTTCACCCTGATCGGCTTGATT
aatgaattttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacacagttctgcatgtgttcacttcttaaattatgtggttttgacgccttttttcccaatgaattttttttcttaagtgggaatactatgatgttgcagGTGATAGAAGCACAAGAAGACATGCCTATTCTGAGTGCAGTAACCCTATATTCCTCCCTTCTCAAGTTTACTCTTCACGTTCACCCTGATCGGCTTGATT
aacacag
- - - - - - - - - - - - - - - - - - -ggttttg