Sequence
atgc intronic sequence ATGC exonic sequencegtacatactactcactcattgtctagattcctgttggttaagtgaaacattaaaaggacagattttttaattaaaattttgactttgttataacttttgggattaacagGATGTGGAAGAGCTAATGAGTTTACCACCTGAGAAGATCTTATTGAGATGGATGAATTTTCAGTTGAGAAAAACTGAATACAAGAAAACCGTCACAAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G48460.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G48460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0333g00010.t01 (Vitis vinifera), 3'ss of exon 2
gtacatactactcactcattgtctagattcctgttggttaagtgaaacattaaaaggacagatttt--ttaattaaaattttgactttgttataact---tttgggattaacagGATGTGGAAGAGCTAATGAGTTTACCACCTGAGAAGATCTTATTGAGATGGATGAATTTTCAGTTGAGAAAAACTGAATACAAGAAAACCGTCACAAACT
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gtgaagatatttctcccaat-tagaagttattggttcttagctactggcttaaagggttttatatgaataatttctagtataaacatgatttcaattatattgaaaatcaacagGATGTGGAGGAGCTGATGAGTCTACCACCAGAGAAGATCTTACTTCGGTGGATGAATTTTCAACTGAAGAAAGCAGGATATAAGAGAATAGTTACAAACT
upper sequence: AT5G48460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 3'ss of exon 4
----gtacatactactcactcattgtcta--gattcct-gttggttaagtgaaacattaaaaggacagattttttaattaaaattttgactttgttataacttttgggattaacagGATGTGGAAGAGCTAATGAGTTTACCACCTGAGAAGATCTTATTGAGATGGATGAATTTTCAGTTGAGAAAAACTGAATACAAGAAAACCGTCACAAACT
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gtgaagatatttctcccaattagaagttattggttcttagctactcgcttaaagggttttatatgaataatttctagtataaacatgatttcaattata---ttgaaaatcaacagGATGTGGAGGAGCTGATGAGTCTACCACCAGAGAAGATCTTACTTCGGTGGATGAATTTTCAACTGAAGAAAGCAGGATATAAGAGAATAGTTACAAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggacagattttttaattaaaattttgactttgttataacttttgggattaacagGATGTGGAAGAGCTAATGAGTTTACCACCTGAGAAGATCTTATTGAGATGGATGAATTTTCAGTTGAGAAAAACTGAATACAAGAAAACCGTCACAAACT
ttataac putative branch site (score: 2)
agattttttaattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatactactcactcattgtctagattcctgttggttaagtgaaacattaaaaggacagattttttaattaaaattttgactttgttataacttttgggattaacagGATGTGGAAGAGCTAATGAGTTTACCACCTGAGAAGATCTTATTGAGATGGATGAATTTTCAGTTGAGAAAAACTGAATACAAGAAAACCGTCACAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA