Sequence
atgc intronic sequence ATGC exonic sequenceGTATGCAATGATTAGGTTAGCTCAGAAGCTGCAGAAATCCAAGAGAAATAAGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAGgtgcgctcatcaatacgtttttctgtttatattgtgatcaaatcaaagtgacaactgaccataatgacatcaattgtcttgatgtttcacag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g12670.5 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G009438_T01 (Zea mays), 5'ss of exon 1
GTATGCAATGATTAGGTTAGCTCAGAAGCTGCAGAAATCCAAGAGAAATAAGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAGgtgc-gctcatcaat---acgtttt-----tctgtttata---ttgtgatcaaatcaaagtgac------aactgaccata-----------------atgacatcaattgtcttgatgtttcacag
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GTCGGTGATGGTTAGGTTGACTCAGAAGCTGCAGAAATCTAAGAGAAATAAGTGGTGGCGGCAGAGGAGAAGGAAGCATGTTGCAGAGCTTTTTCAGAAGgtgccactcgccgctgtcaccttttatacgtctcattatacatttctggttcattccaaacagccaaaaaaaccaaccatgtgaattgtgaaatgtggatggcatctcttgtcttgttgtttcatag
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G058366_T01 (Zea mays), 5'ss of exon 2
GTATGCAATGATTAGGTTAGCTCAGAAGCTGCAGAAATCCAAGAGAAATAAGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAGgtgc-gctcatcaatacgtttttctgtttatattgtgatcaaatcaaagtgac--------aactgaccataatgacatcaattgtcttgatgtttcacag--------------------------------
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GTCGGCGATGGTTAGGTTGACTCAGAAGCTGCAGAAATCTAAGAGAAATAAGCGGTGGCGGCAGAGGAGAAGGAAGCATGTTGCGGAGCTTTTTCAGAAGgtgccactcgtcactgtcaccttttatacagctcataatacatttctggttccttcattccaaacagccaaaaaaaacccaaccgtgtgaattgtgaattgtggatgacatctcttgtcttgttgtttcatag
upper sequence: LOC_Os01g12670.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G174489_T01 (Zea mays), 5'ss of exon 1
GTATGCAATGATTAGGTTAGCTCAGAAGCTGCAGAAATCCAAGAGAAATAAGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAGgtgc-gctcatca------------atacgtttttctgtttatattgtgatca---aatcaaagtgac-------aactgaccata-----------------atgacatcaattgtcttgatgtttcacag
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GTCGGCGATGGTTAGGTTGACTCAGAAGCTGCAGAAATCTAAGAGAAATAAGCGGTGGCGGCAGAGGAGAAGGAAGCATGTTGAAGAGCTTTTTCAGAAGgtgccactcgtcgctgtcaccttttatacgtctcattatacatttctggttccttcattccaaacagccaaaaaaaaccaaccatgtgaattgtgaaatgtggatggcatctcttgtcttgttgtttcatagMapped 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|29678139|gb|CB674414.1|CB674414EST: AGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAG GAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCT
genomic: AGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAGgtgcgctcat ... tgtttcacagGAGCATGCAGATTATGACAGAATTGATCAGGAAGCTGATGAATGGAGGGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTATGCAATGATTAGGTTAGCTCAGAAGCTGCAGAAATCCAAGAGAAATAAGCGATGGAGAAAGAGAAAAAGAAAGCATGTTGCAGAGCTTTTCCAGAAGgtgcgctcatcaatacgtttttctgtttatattgtgatcaaatcaaagtgacaactgaccataatgacatcaattgtcttgatgtttcacag
- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT