Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttaaactcacacctcaataacctctccttttgtgacctctgcacagaaaaactgtttagatcttattcatcaattttcctaactttttttatgaagGTTCTTGGCTCAGTTGGGCATCCTATTAAAGATACAGAGTTCAAAATTGTAGATCATGAGACTGGTACTGTTCTTCCACCTGGTTCAAAGGGCATTGTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23790.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23790.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA11G36690.1 (Glycine max), 3'ss of exon 12
----gtaagtttaaa-ctcacacctcaataacctctccttttgtgacctctgcacagaaaaactgtttagatcttattcatcaattttcctaactttttttatgaagGTTCTTGGCTCAGTTGGGCATCCTATTAAAGATACAGAGTTCAAAATTGTAGATCATGAGACTGGTACTGTTCTTCCACCTGGTTCAAAGGGCATTGTCA
||| | ||| | || ||| | | | | |||||| ||| | || ||| |||| | | | | | | || |||| ||||||| |||| || ||||| ||||| ||||| ||||||| |||||| | |||||| |||||||| | ||||||||||||||||||||||| || | |
cataataattacaaaatttgcattcttttaattagtttgtattttgtgtctgcaaagagtag-tgcttatatctgaatgttatagatgc--aatctttt----gaagGTTATTGGGTCTGTTGGCCATCCAATTAAGCATACAGAATTCAAAGTCGTAGATTCTGAGACTGATGAAGTTCTTCCACCTGGTTCAAAGGGAATATTAA
upper sequence: AT3G23790.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA05G28390.1 (Glycine max), 3'ss of exon 12
gtaagtttaaactcacacctcaataacctctccttttgtgacct-ctgcacagaaaaactgtttagatcttattcatcaattttcctaacttt-ttttatgaagGTTCTTGGCTCAGTTGGGCATCCTATTAAAGATACAGAGTTCAAAATTGTAGATCATGAGACTGGTACTGTTCTTCCACCTGGTTCAAAGGGCATTGTCA
| | | || | | || | || || || | ||| | | |||| ||| || | | |||| | |||||| |||| || ||||||||||| ||| ||||||| |||||||| |||||| ||| |||| | ||||||||||||||||||||||||||| | |
----cataacaagtacttatttgcattctttagattagtagtaaattgaatcatcaaagagaggtgcatttatctgagaatgttacagatggaattttttaaagGTTATTGGATCTGTTGGGCATCCAATTCGTCATACAGAATTCAAAATAGTAGATTCTGAAACTGATGAAGTTCTTCCACCTGGTTCAAAGGGCATTTTGA
upper sequence: AT3G23790.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv08s0032g00050.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtttaaactcacacctcaataacctctcc--ttttgtgacctctgcacagaaaaactgtttagatcttattcatcaattttcctaactttttttatgaagGTTCTTGGCTCAGTTGGGCATCCTATTAAAGATACAGAGTTCAAAATTGTAGATCATGAGACTGGTACTGTTCTTCCACCTGGTTCAAAGGGCATTGTCA
|| | || | || ||| | || | ||| || | ||| ||| ||| || | | |||| || | | || || |||||||||||||||||||||||||||| ||| | ||||||| |||||||||||||| ||| |||| | |||| ||||||||||||||||||||||| |
gttcctgtatggtttcat-tcatttgccatttgggtttagtcatatctctttccaaatggggtt---atatcacatgacaatattacagatttaacttttgaagGTTCTTGGCTCAGTTGGGCATCCAATTCGACATACAGAAATCAAAATTGTAGATTCTGAAACTGATGAACTTCTGCCACCTGGTTCAAAGGGCATTGTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacagaaaaactgtttagatcttattcatcaattttcctaactttttttatgaagGTTCTTGGCTCAGTTGGGCATCCTATTAAAGATACAGAGTTCAAAATTGTAGATCATGAGACTGGTACTGTTCTTCCACCTGGTTCAAAGGGCATTGTCA
tcctaac putative branch site (score: 1)
ttttcctaactttttt CT-rich tract
aattttcctaactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttaaactcacacctcaataacctctccttttgtgacctctgcacagaaaaactgtttagatcttattcatcaattttcctaactttttttatgaagGTTCTTGGCTCAGTTGGGCATCCTATTAAAGATACAGAGTTCAAAATTGTAGATCATGAGACTGGTACTGTTCTTCCACCTGGTTCAAAGGGCATTGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA