Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcacttcacacattattactgtcttcctaagattcttgattgtttataaaaccaaatctcattgtctttgttgtgtattgtttgcagGTAACTGAGAGTGGAAAGCAAGAGAGACACATAGTAGCAACAGTGGGGAAATTCAGTGTGATATGGGACTTGGAGCGGGTGAAGAACAGTGCACACGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19240.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G14960.1 (Glycine max), 3'ss of exon 1
----------gtaagtttcacttcacacattattactgtcttcctaagattcttgattgtttataaaaccaaatctcattgtctttgttgtgtattgtttgcagGTAACTGAGAGTGGAAAGCAAGAGAGACACATAGTAGCAACAGTGGGGAAATTCAGTGTGATATGGGACTTGGAGCGGGTGAAGAACAGTGCACACGAAT
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gaattagaaaatatatgtaaactgatg-ataattagtagtttaccgag-tccattaccttgcagcaacctgcaagtatctgacctg--tgtttttgtctttcagGTCACTGAGAATGGTAAACAAGAACGCCACCTCGTTGCGACTGTGGGCAAGTTTAGTGTGATATGGGATTTTCAGCGGGTGAAGAACAGTGCACATGAAT
upper sequence: AT3G19240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv03s0063g00480.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtttcacttc------acacattattactgtcttcctaagattcttgattgtttataaaaccaaatctcattgtctttgttgtgtattgtttgcagGTAACTGAGAGTGGAAAGCAAGAGAGACACATAGTAGCAACAGTGGGGAAATTCAGTGTGATATGGGACTTGGAGCGGGTGAAGAACAGTGCACACGAAT
| |||| || | | | | |||| | || | | | | || || | | | | || | | | ||| ||||| ||||||| ||| || |||||| | || |||| ||||||||||| || ||||| ||||||||| |||| ||| |||||| |||||| || || |
ttcagttccagtcgtcaaagataaactattggactactcgtcaaaaaaaaaaaaagcaattggactgatggatgtgttgcattttatattgtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgattgtttataaaaccaaatctcattgtctttgttgtgtattgtttgcagGTAACTGAGAGTGGAAAGCAAGAGAGACACATAGTAGCAACAGTGGGGAAATTCAGTGTGATATGGGACTTGGAGCGGGTGAAGAACAGTGCACACGAAT
tcttgat putative branch site (score: 4)
tttataaaaccaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcacttcacacattattactgtcttcctaagattcttgattgtttataaaaccaaatctcattgtctttgttgtgtattgtttgcagGTAACTGAGAGTGGAAAGCAAGAGAGACACATAGTAGCAACAGTGGGGAAATTCAGTGTGATATGGGACTTGGAGCGGGTGAAGAACAGTGCACACGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC