Sequence
atgc intronic sequence ATGC exonic sequence...gagggctaatatctatgaagcctttccctagctggaataaacaatgcagcacttttcatagaatttaataatttgacattaaacttttcttcacgtgcagCGATTATTTTGGCCTCTATGCAGATGCTTGTTTTGCCAATTTTGGTGATAGAGTGAAGCACTGGATCACATTAAATGAACCTCTTCAGACCTCGGTGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G36890.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G36890.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 6
----gagggctaatatctatgaagcctttccctagctg-gaataaacaatgcagcacttttcatagaatttaataatttgacattaaacttttcttcacgtgcagCGATTATTTTGGCCTCTATGCAGATGCTTGTTTTGCCAATTTTGGTGATAGAGTGAAGCACTGGATCACATTAAATGAACCTCTTCAGACCTCGGTGAAT
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ccttgtaaatttgtttcc-tagtacctttattaagatgagtgtagttgatttttcaatattc-tattattgaatggtgtggttctgatgtggcatatgc---cagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT
upper sequence: AT5G36890.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0220g00070.t01 (Vitis vinifera), 3'ss of exon 5
---gagggctaatatctatgaagcctttccctagctg--gaataaacaatgcagcacttttcatagaatttaataatttgacattaaacttttcttcacgt-gcagCGATTATTTTGGCCTCTATGCAGATGCTTGTTTTGCCAATTTTGGTGATAGAGTGAAGCACTGGATCACATTAAATGAACCTCTTCAGACCTCGGTGAAT
| | || | | | || || | | | | || || || | | |||||| | ||| |||| || | ||| | || | |||| | ||||||| | ||||| || |||| ||||| | ||||||||||||||| ||| ||||||||||||||||||| |||||||| || ||||||||
ttttaaaatttatctttgctattccaaacctcacatactggttgaaggatccattattgttcataca---taaatgtttggtat---attttggtaaacattgcagAAAATATTTTGCAATTTATGCGGAAACTTGCTTTGCAAGTTTTGGTGATAGAGTAAAGAACTGGATCACATTAAATGAGCCTCTTCAAACTGCGGTGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagcacttttcatagaatttaataatttgacattaaacttttcttcacgtgcagCGATTATTTTGGCCTCTATGCAGATGCTTGTTTTGCCAATTTTGGTGATAGAGTGAAGCACTGGATCACATTAAATGAACCTCTTCAGACCTCGGTGAAT
atttgac putative branch site (score: 4)
cttttcttcac putative PPT
ttttcatagaatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagggctaatatctatgaagcctttccctagctggaataaacaatgcagcacttttcatagaatttaataatttgacattaaacttttcttcacgtgcagCGATTATTTTGGCCTCTATGCAGATGCTTGTTTTGCCAATTTTGGTGATAGAGTGAAGCACTGGATCACATTAAATGAACCTCTTCAGACCTCGGTGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC