Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagaaccaaccaagaaaagaaaaaaactcttaactctcaaaatttgaaactaatggagttttgttttgttttgtttgatcagTTCGCACATAGAAACTGCATACAACGTTGGTGTAATGAAAAAGGAAACACAACTTGTGAAATCTGTCTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02075.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02075.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G01680.1 (Glycine max), 3'ss of exon 1
gtaaaagaaccaaccaagaaaagaaaaaaactctta-actctcaaaatttgaaactaatggagttttgttttgttttgtttgatcagTTCGCACATAGAAACTGCATACAACGTTGGTGTAATGAAAAAGGAAACACAACTTGTGAAATCTGTCTTCAG
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-------gtaaatccacattctcttaacaacttttatgtttactttgtttttcatgaatcttgtcatgattagttttatt-gttcagTTTGCTCACAGAGATTGCATTCAGACTTGGTGCAATGAGAAAGGAAATACAACTTGTGAAATATGTCTCCAG
upper sequence: AT4G02075.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g01360.t01 (Vitis vinifera), 3'ss of exon 1
gtaaaagaaccaaccaagaaaagaaaaaaactcttaa-----ctctcaaaatttgaaactaatggagtttt---------gttttgttttgtt-tgatcagTTCGCACATAGAAACTGCATACAACGTTGGTGTAATGAAAAAGGAAACACAACTTGTGAAATCTGTCTTCAG
|| |||||| | | |||| || || ||||||| | || |||| |||||||||| || | | |||| || |||||| | || ||||| | ||||| ||||||||||| ||||||||||||||||||||||| |||
--------gtaaagaaagaaagggggtattttcttggttttgctttcggaatttgaggtttggtgatttttctgatttgggttttgtttttttgtctttagTTTGCTCATAGAGATTGTATACAGAGGTGGTGCAATGAAAAAGGGAACACAACTTGTGAAATCTGTCTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttaactctcaaaatttgaaactaatggagttttgttttgttttgtttgatcagTTCGCACATAGAAACTGCATACAACGTTGGTGTAATGAAAAAGGAAACACAACTTGTGAAATCTGTCTTCAG
aactaat putative branch site (score: 2)
ttttgttt putative PPT
aaaatttgaaactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagaaccaaccaagaaaagaaaaaaactcttaactctcaaaatttgaaactaatggagttttgttttgttttgtttgatcagTTCGCACATAGAAACTGCATACAACGTTGGTGTAATGAAAAAGGAAACACAACTTGTGAAATCTGTCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA