Sequence
atgc intronic sequence ATGC exonic sequence...ctaaatagaaactattttaatgtaactttactagtcatgatgtttaatgttttaatttagctctaataaaatttatgaattctgatgaaattaattacagGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
------------------------------------ctaaatagaaactattttaatgtaactttactagtcatgatgtttaatgttttaatttagctctaataaaatttatga--------attctgatga-aatta----------attacagGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG
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gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
upper sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------ctaaatagaaactattttaatgtaa--ctttacta-gtcatgatgtttaatgtt-ttaatttagctctaataaaatttatga-attctgatgaaattaat------------tacagGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG
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gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
upper sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G30460.1 (Glycine max), 3'ss of exon 1
ctaaatagaaactattttaatgtaactttactagtcatgatgtttaa-----tgttttaatttagctctaataa--aatttatgaattctgatgaaattaattac-agGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG
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---tggaggacttgtttt----taatttcattaattctgaggactaaaaggatggtgtgtgacaaatttgaggactaaattgtctatt-tactcaatttattttccagGAGATTAATCATGCTGGCGCAGGGGGACTGTGGGCTGAACTTGTTATCAATAGAG
upper sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 2
ctaaatagaaactattttaatgta-actttactagtcatgatgtttaatg----ttttaatttagctctaataaaatttatgaattctgatgaaattaattacagGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG
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----tttgggattatgggaatgtgcatttgattttgtattcaatttgatgatgcctcttatccaaatatcagaaaatgaccagtttatgg-aatttcatctacagGAAATTAATCATGCTGGAGCTGGGGGATTGTGGGCTGAGCTTGTGAGCAACAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgttttaatttagctctaataaaatttatgaattctgatgaaattaattacagGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG
aattaat putative branch site (score: 3)
tctaataaaatttatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaaatagaaactattttaatgtaactttactagtcatgatgtttaatgttttaatttagctctaataaaatttatgaattctgatgaaattaattacagGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - -gaaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgaaa