Sequence
atgc intronic sequence ATGC exonic sequence...tttgcttgcttttgctgctaattaaggaaacacggttatgtgctttttccttgagagcattgtatgaaagtaacatattacttactctcagcttcaacagGACCACAAGGGAATCCACACCATGCAGTTTGATAAGAAGGCCTGAAATCATGACAACCCCGGGATCGTCTACAAAGCTTAACATTTGTGTAAGTGAAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32710.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32710.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G34090.1 (Glycine max), 3'ss of exon 1
------tttgcttgcttttgctgctaattaaggaaacacggttatgtgctttttccttgagagcattgtatgaaagtaacatattacttactctcagcttcaacagGACCACAAGGGAATCCACACCATGCAGTTTGATAAGAAGGCCTGAAATCATGACAACCCCGGGATCGTCTACAAAGCTTAACATTTGTGTAAGTGAAAGC---
||||| | | ||| | || | | || | | || | | | | ||| | | ||||| ||| || | || || | ||| |||||||||||||| |||||||||||||| | || | | | || ||||| || |||| | || || |||| | ||||
ttgccttttgccactaatatgctttcattttttgtgtgtgtttctattctactactttacggttaaattgttaaattgatatatttattattcgctgc------agAAGCACTAGGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGTCAGGACTCCGGGTTCAACTACCAGGCCTA---CTTGTTCAGCTGAAGCTTAT
upper sequence: AT2G32710.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0029g00040.t01 (Vitis vinifera), 3'ss of exon 1
--tttgcttgcttttgctgctaattaaggaaacacggttatgtgctttttccttgagagcattgtatgaaagtaacatattacttactctcagcttcaacagGACCACAAGGGAATCCACACCATGCAGTTTGATAAGAAGGCCTGAAATCATGACAACCCCGGGATCGTCTACAAAGCTTAACATTTGTGTAAGTGAAAGC
| ||| || || || || | || || | | | | || ||||| | | | | | | ||| ||||||| ||| |||||| ||||||| ||||||||||||||| || |||| ||| | |||||| || || |||| |||| | || | | | |
tgatacagagctcttact-ttagttctgcaattcttattgtcctggtgatagtgtcga-tattgttttcttatgaatggattcattgtctttataaaaacagGAGCACTAGGGAAACCACACCTTGCAGTTTGATAAGAGATCCAGAAACCATAAGAACCCCTGGTTCTACTACTAAGCCTGCCAGCTCGTCTGGCATTAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccttgagagcattgtatgaaagtaacatattacttactctcagcttcaacagGACCACAAGGGAATCCACACCATGCAGTTTGATAAGAAGGCCTGAAATCATGACAACCCCGGGATCGTCTACAAAGCTTAACATTTGTGTAAGTGAAAGC
tacttac putative branch site (score: 1)
aaagtaacatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcttgcttttgctgctaattaaggaaacacggttatgtgctttttccttgagagcattgtatgaaagtaacatattacttactctcagcttcaacagGACCACAAGGGAATCCACACCATGCAGTTTGATAAGAAGGCCTGAAATCATGACAACCCCGGGATCGTCTACAAAGCTTAACATTTGTGTAAGTGAAAGC
- - - -gcttttg
- - - - - - - ctgctaa
- - - - - - - - - - - - - -aaacacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtaaca