Sequence
atgc intronic sequence ATGC exonic sequencegtcattaactcctcttttcaacattactttctaaccgctatttcggttttttttttaaaactcacggatcaatctctatcgttttgtgtagGTTGATGAAAGGGCAGTTCTTAAACACTTTGACTGGCCAGAAGGTAAAGCTGATGCGCTACGAGAAGCAGCTTTTGAATATCAAGATCTTATGAAACTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25690.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G11260.1 (Glycine max), 3'ss of exon 5
-------gtcatt-aactcctcttttcaacattactttctaaccgctatttcggttttttttttaaaactcacggatcaatctctatcgttttgtgt---agGTTGATGAAAGGGCAGTTCTTAAACACTTTGACTGGCCAGAAGGTAAAGCTGATGCGCTACGAGAAGCAGCTTTTGAATATCAAGATCTTATGAAACTGG
|| ||| || ||| ||| || | ||| | | || | | || ||| |||| || | | | || | | ||||||||||| | || || || ||||||||||||||||| ||||| ||||| ||||| ||| | || ||||||||||||||||| ||| | |||||| |||
acctaaagttatttaagtcccaatttttttatgattttatggtt--cacttttaatctcattagaaatctcattttccatttcattttattccttatgcaagGTTGATGAACGAGCCGTCCTCAAACACTTTGACTGGCCTGAAGGGAAAGCAGATGCACTAAGGGAGGCAGCTTTTGAATATCAGGATTTGATGAAATTGG
upper sequence: AT3G25690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G22620.1 (Glycine max), 3'ss of exon 5
----gtcattaactcctcttttcaacattactttc--taaccgctatttcggttttttttttaaaactcacggatcaatctc-tatcgttttgtgt---agGTTGATGAAAGGGCAGTTCTTAAACACTTTGACTGGCCAGAAGGTAAAGCTGATGCGCTACGAGAAGCAGCTTTTGAATATCAAGATCTTATGAAACTGG
|| | ||| | | || | | |||| || | | ||| | | | | || || ||||| | | || | | ||||||| ||| | || || || || |||||||||||||| ||||| ||||| ||||| ||| | || ||||||||||||||||| ||| | |||||| |||
ccacatc-taaacagaaaatataaatctcattttccatatcaataacttcacatccagtaccactgcatacttattcatctcattttattccttatgcaagGTTGACGAACGAGCCGTCCTCAAGCACTTTGACTGGCCTGAAGGAAAAGCAGATGCACTAAGGGAGGCAGCTTTTGAATATCAGGATTTGATGAAATTGG
upper sequence: AT3G25690.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g02860.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------gtcattaactcctctt-------ttcaacattactttcta-------accgctatttcggttttttttttaaaactcacggatcaatctctatcgttttgtgtagGTTGATGAAAGGGCAGTTCTTAAACACTTTGACTGGCCAGAAGGTAAAGCTGATGCGCTACGAGAAGCAGCTTTTGAATATCAAGATCTTATGAAACTGG
| ||| | || || | ||||| | | | | | ||| || | | ||| || || | |||||| | | || | ||||||||||| |||| ||||| || |||||||| ||||| ||||| ||||| ||||| || |||||||||| |||||||||||||| | |||||| |||
gtatgcctttaaaacttcatctgttaaactggctattcttttcttttatagctgctaaacatgattctatgtcatggtattcctaatttgatcatttattccaacccttttcatcaatttttttcccatc----agGTTGATGAACGGGCCGTTCTCAAGCACTTTGATTGGCCTGAAGGGAAAGCAGATGCATTAAGAGAAGCAGCCTTTGAATATCAAGACTTGATGAAATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctatttcggttttttttttaaaactcacggatcaatctctatcgttttgtgtagGTTGATGAAAGGGCAGTTCTTAAACACTTTGACTGGCCAGAAGGTAAAGCTGATGCGCTACGAGAAGCAGCTTTTGAATATCAAGATCTTATGAAACTGG
aactcac putative branch site (score: 2)
tcgtttt putative PPT
ttttttttttaaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcattaactcctcttttcaacattactttctaaccgctatttcggttttttttttaaaactcacggatcaatctctatcgttttgtgtagGTTGATGAAAGGGCAGTTCTTAAACACTTTGACTGGCCAGAAGGTAAAGCTGATGCGCTACGAGAAGCAGCTTTTGAATATCAAGATCTTATGAAACTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT