Sequence
atgc intronic sequence ATGC exonic sequence...ctaaaatcttgcttttagttttgtcattaaatggggcatcatgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g66730.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 5
--------ctaaaatcttgcttttagttttgtcattaaatggggcatcatgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
||| || || | | ||||| |||| || || || |||| || |||| | |||| |||| | | || || |||||||||||| ||||| || ||||| |||||||||||||||||| ||||||| ||| |||||||||| ||||| |||||||| || || |||||| ||
gggctttgctagaagctagatgactgtttttatgttaattg---tattttgcctgcgatcatgcaatgtatttt-----cttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCAAG
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 5
--------ctaaaatcttgcttttagttttgtcattaaatggggcatcatgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
| | || || | ||||| |||| || || || |||| ||| |||| | |||| |||| | | || || |||||||||||| ||||| || ||||| |||||||||||||||||| ||||||| ||| |||||||||| ||||| |||||||| || || |||||||||
gggctttgcaagaagctagacgactgtttttatgttaattg---tattttgcctgtgatcatgcgatgtatttt-----cttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 3
-----------ctaaaatcttgcttttagttttgtcattaaatggggcatcatgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
|| || || | | || ||||| | ||| || || | || | |||| | || | ||||||||| | | || || |||||||||||| ||||| || ||||| |||||||||||| |||| |||| || |||||||||||||||||||| |||||||| || |||||||| |||
atgggcttttggtagaaactagatatttgtttttt------atgttaaataattgtttttttcctgtgatgtgtttt-----ctttgctgaaatagctttcgttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGCCCTTCCTACCGGTGCTTGCATTTGAAGGTGGTACAAGGAGAAACATACCAAAGTTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
ttcttac putative branch site (score: 2)
ttctgtc putative PPT
atatgatatattctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaaaatcttgcttttagttttgtcattaaatggggcatcatgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA