Sequence
atgc intronic sequence ATGC exonic sequencegtatataccaatcttgctcaactagtgttctctgtttggttggttttgacatgaagataggttcttttgtagATCTTGAATGCTCTGGAATATGTGCGTCAAGGTGCTGATGTGATGCCAAGGAGTCAACTTAATCCAGTTTTGGATGCTGAGTTAGGTTCCAATTGGCAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01660.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01660.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G27970.1 (Glycine max), 3'ss of exon 3
------------------------gtatataccaatct-tgctcaactagtgttc-tctgtttggttggttttgacatgaagataggttct---tttgtagATCTTGAATGCTCTGGAATATGTGCGTCAAGGTGCTGATGTGATGCCAAGGAGTCAACTTAATCCAGTTTTGGATGCTGAGTTAGGTTCCAATTGGCAAT
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attgaagggtcatgagttcagttcgt-tggaggaatctgtaaattacttttgtttatatttttatgtgactttaaacgaactcttaatcctatatatgtagATCCTGGCTGCATTAGAAATTGTTCGTCAAGGTGCAGATGTGATGCCAAAGAGCCAGCTTAATCAAGTTTTAAATGCTGAATTAGGTCCTGGCTGGTCAT
upper sequence: AT4G01660.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G00920.1 (Glycine max), 3'ss of exon 2
---------------------gtatataccaatct-tgctcaactagtgttctctgtttggttggttttgacatgaaga---taggttcttt---tgtagATCTTGAATGCTCTGGAATATGTGCGTCAAGGTGCTGATGTGATGCCAAGGAGTCAACTTAATCCAGTTTTGGATGCTGAGTTAGGTTCCAATTGGCAAT
|| | ||||| | | | |||| ||| | | || | ||| | | | | |||| |||||||| || ||| | ||| ||| ||||||||||| ||||||||||||| ||| || ||||||| |||||| ||||||| |||||| | ||| ||
tgaaaggtcatgcgttcagttccatggaggaatctgtaaattatttttgtttatatttttatgtgactttaaatgtaaactcttaatcctttatatgtagATCCTGGCTGCATTAGAAATTGTTCGTCAAGGTGCAGATGTGATGCCAAAGAGCCAGCTTAATCAAGTTTTAAATGCTGAATTAGGTCCTGGCTGGTCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaactagtgttctctgtttggttggttttgacatgaagataggttcttttgtagATCTTGAATGCTCTGGAATATGTGCGTCAAGGTGCTGATGTGATGCCAAGGAGTCAACTTAATCCAGTTTTGGATGCTGAGTTAGGTTCCAATTGGCAAT
ttttgac putative branch site (score: 3)
ttcttttgt putative PPT
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatataccaatcttgctcaactagtgttctctgtttggttggttttgacatgaagataggttcttttgtagATCTTGAATGCTCTGGAATATGTGCGTCAAGGTGCTGATGTGATGCCAAGGAGTCAACTTAATCCAGTTTTGGATGCTGAGTTAGGTTCCAATTGGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG