Sequence
atgc intronic sequence ATGC exonic sequence...ctaaaatcttgcttttagttttgtcattaaatgaggcatcacgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g47256.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 5
--------ctaaaatcttgcttttagttttgtcattaaatgaggcatcacgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
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gggctttgctagaagctagatgactgtttttatgttaattg---tattttgcctgcgatcatgcaatgtatttt-----cttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCAAG
upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 5
--------ctaaaatcttgcttttagttttgtcattaaatgaggcatcacgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
| | || || | ||||| |||| || | | || |||| ||| |||| | |||| |||| | | || || |||||||||||| ||||| || ||||| |||||||||||||||||| ||||||| ||| |||||||||| ||||| |||||||| || || |||||||||
gggctttgcaagaagctagacgactgtttttatgttaattgtattttgcctgtga---tcatgcgatgtatttt-----cttttctgaaatagctttggttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGGCCTTTCTACCAGTACTTTCATTTGAAGGCGGTACAAGGAGAAACATACCCAAGTTCGAG
upper sequence: LOC_Os01g47256.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 3
ctaaaatcttgcttttagttttgtcattaaatgaggcatcacgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
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atgggcttttggtagaaactagatatttgttttttatgttaaataattgtttttttcctgtgatgtgttttctttgctgaaatagctttcgttattacagAACTTTTTGGTAGACATAAAGGGTCCTAATTTGCCCTTCCTACCGGTGCTTGCATTTGAAGGTGGTACAAGGAGAAACATACCAAAGTTTGAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58653630|gb|CK042310.1|CK042310EST: CTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT AACTTCTTGGTGGATATAAAAGGTCCTAATTGGGCCTTTTTACCAGTTCTT
genomic: CTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGATgtaagtacat ... gtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaaaatcttgcttttagttttgtcattaaatgaggcatcacgatgcacctcatatgatatattcttacctctttgctgagctggattctgtcattacagAACTTCTTGGTGGATATAAAAGGTCCTAATTTGGCCTTTTTACCAGTTCTTGCATTTGAAGGTGGTACCAGGAGAAATATTCCAAAGTTCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA