Sequence
atgc intronic sequence ATGC exonic sequenceAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacatattgtcagtctttttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 6
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacata-ttgtcagtctttttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact--
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AGATGGTTCTGATGATCAAAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAAATACAAATGTACACTGAAACAAAGAATAATAAAAAGCTTAAGgtaagacatccttgtttgcctattcgcaagtgactctttgg---tgggtaatatcccaagttaaattatcattgtgaattatgatgcattatttctttttttt
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 6
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacata-ttgtcagtctttttacacgtgattattt--tggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact
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AGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAATGTACACTGAAACAAAGAATAATAAAAAGCTTAAGgtatggcgtccttgtttgcccatttgcaagtgactctttggtgggtattatcttatta--aattatccttgtgaattgtgatgatgtatgtttctgaaaaat-
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA19G17660.3 (Glycine max), 5'ss of exon 6
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgt-aagacatattgtc--------agtctt-tttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact
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AGATGGCACAGATGACCATAAGAAAGGAACCCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACTGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttgttttatagaagaaattcttgttcttgcatgacttaagtagttaagtaattatgtcttttcaaattcttttattgtgtttgcctgcaatt----------
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA19G30100.1 (Glycine max), 5'ss of exon 6
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacatattgtcagtctttttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact---
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AGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAATGTACACAGAGATGAAGAACAACAAAAAACTCAAGgtcagcatttgttttagaaaataaattc-ttattatgc-aacttgcataggagtaataatgtgcctttccaatttattact-gtcttttcctacaattttagc
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 6
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacatattgtcagtctttttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact-
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AGATGGCACAGATGACCACAAAAAAGGAACTCAACTTTTGGAGGTATATGCTGTAGAGATTCAAATGTACACAGAGACCAAGAACAACAAAAAACTTAAGgtcaggatttcttttacagaagaaactcttgttcttgcatgact-taagtaattatgtcttttcaattgcttttagtgtgtttgcctgcaatttatcattg
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 6
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacatattgtcagtctttttacacgtgattattt-tggattacaggttactactgttcaagattttgtgtcagtttctt-gttcaatattgcagtact
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AGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAATGTATACTGAGACCAAGAATAACAAAAAACTCAAGgtcagg-gtttcttgaatgtttgtttccatattgatttgtaaatcatttttttcagtaattttgtatatttctatagtatttaagttccatgagttaaaat-
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ29478 (Selaginella moellendorffii), 5'ss of exon 6
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacatattgtcagtctttttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact
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AGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGATGTACACGGAGACAAAGAACAACAAGAAGCTAAAGgta-----tctatgcagttctttt-tatgatattttgctgaacctcggcctcag----------------------------------------------
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ28052 (Selaginella moellendorffii), 5'ss of exon 6
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacatattgtcagtctttttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact
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AGATGGCTCTGATGATCAGAAGAAAGGAACTCAGCTTCTGGAAGTATACGCCATTGAGATTCAGATGTACACGGAGACAAAGAACAACAAGAAGCTAAAGgta-----tctatgcagttttttt-tatgatattctactgaacctcggcctcag----------------------------------------------Mapped 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|55827482|gb|AU032236.2|AU032236EST: CTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAG GAACTATATACANAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGA
genomic: CTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacata ... tctgctgcagGAACTATATACAAAAGCTCTTTCCATCAAATCAGCGATACCTCATCCAAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAATGTACACTGAAACAAAGAACAACAAAAAATTGAAGgtaagacatattgtcagtctttttacacgtgattattttggattacaggttactactgttcaagattttgtgtcagtttcttgttcaatattgcagtact
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG