Sequence
atgc intronic sequence ATGC exonic sequencegtaggccgactgaaaaatctcaaagtgcaaagaggtctgatgattttattgaactttccaatccatgcaacttatcttacaagtttcgtttctgttatagACTGCTGAGAAGTTACTGGCGGATGTAAAACTGACAGGAGCGGCGAAAGTTAGAGCAGGAAGTTACAGTGGTGGAATGAAACGTCGACTCAGTGTTGCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61690.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61690.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os08g30740.1 (Oryza sativa), 3'ss of exon 11
gtaggccgactgaaaaatctcaaagtgcaaagaggtctgatg-attttattgaactttccaatccatgcaacttatcttacaagtttcgtttctgttatagACTGCTGAGAAGTTACTGGCGGATGTAAAACTGACAGGAGCGGCGAAAGTTAGAGCAGGAAGTTACAGTGGTGGAATGAAACGTCGACTCAGTGTTGCGG
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gtatgtttctttagaactgattacacgtactcctccctaaagcacttaatttaattgtct--tgcattgatcttcctctgattgttcaa---ccaatgcagGTAGCAGAACAATCCTTAATCCAAGTGAAGCTCAGCCAGGCAGCTAATGTTAGAGCAGGTAGCTACAGTGGGGGAATGAAACGCCGGCTAAGTGTTGCAA
upper sequence: AT5G61690.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G34140.1 (Glycine max), 3'ss of exon 11
-----------------------------gtaggccgactgaa-aaatctcaaagtgcaaag---aggtctgatgattttattgaactttccaatccatgcaacttatcttacaagtttcgtttctgttatagACTGCTGAGAAGTTACTGGCGGATGTAAAACTGACAGGAGCGGCGAAAGTTAGAGCAGGAAGTTACAGTGGTGGAATGAAACGTCGACTCAGTGTTGCGG
|| | ||| | | | |||||| | | | | || | | | ||| | ||| | | ||| | | |||| | | ||| | | | || || || | ||| || | || | ||||| ||||| |||||||||||||| ||||||||||| || |||||| ||||
gtatgtctgcacatgcctgaaattgttccatacaatcaatgattatgtgtgtgtgtgcaatatttgaaattattagctattatggatactgcctctcattccttttaattcaagttcttctgtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTGAGACTCACGGATGCATCCAAAGTGAGAGCTGGAAGTTACAGTGGAGGAATGAAACGCCGTCTCAGTTTTGCTA
upper sequence: AT5G61690.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 11
-------------------------------------------gtaggccgactgaaaaatctcaaagtgcaaag---aggtctgatgattttattgaactttccaatccatgcaacttatcttacaagtttcgtttctgttatagACTGCTGAGAAGTTACTGGCGGATGTAAAACTGACAGGAGCGGCGAAAGTTAGAGCAGGAAGTTACAGTGGTGGAATGAAACGTCGACTCAGTGTTGCGG
|| | | || | |||||| | | | | ||| | |||| | ||| | | || | | | |||| | | ||| | | | || || |||| ||| || | || || ||||| ||||| ||||||||||| || ||||||||||| || |||||||||||
gtatgtataatccaggccttaaatcgttttgtaaaatcaatgattatgggtgtgtgcacatatgtgtgtgcaatatttgaaattattagctattaagaatacggcctcccattccttttaattcaagttctttggtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTGAGAGCTGGAAGTTACAGCGGAGGAATGAAACGCCGTCTCAGTGTTGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattgaactttccaatccatgcaacttatcttacaagtttcgtttctgttatagACTGCTGAGAAGTTACTGGCGGATGTAAAACTGACAGGAGCGGCGAAAGTTAGAGCAGGAAGTTACAGTGGTGGAATGAAACGTCGACTCAGTGTTGCGG
atcttac putative branch site (score: 3)
tttcgtttct putative PPT
ttatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggccgactgaaaaatctcaaagtgcaaagaggtctgatgattttattgaactttccaatccatgcaacttatcttacaagtttcgtttctgttatagACTGCTGAGAAGTTACTGGCGGATGTAAAACTGACAGGAGCGGCGAAAGTTAGAGCAGGAAGTTACAGTGGTGGAATGAAACGTCGACTCAGTGTTGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA