Sequence
atgc intronic sequence ATGC exonic sequenceTTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaagatttgtgaggtatttctgtagtacatggttttaggactacctatgttagcagaacagttgtat...
Basic information
species | Oryza sativa |
transcript | LOC_Os09g07830.3 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 9
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaagatttgtgaggtatttctgtag-tacatggt----tttaggactacctatgttagcagaacagttgtat
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TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaact-tcttggcatttacgtta--ttattacttagcccttttaattttatcttcagctgtattataattcttgtgatttaccatggtgctagtgaacttct--
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 9
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaagatttgtgaggtatttctgtagtacatggttttaggac-tacctatgttagcagaacagttgtat------
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TTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt-gaaatatttctgaggccttttgt----cctacaaagtctttctg-agaccttgtttttcggccatatgttgtttagctga-cagatatgaaggaca
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G830250_T01 (Zea mays), 5'ss of exon 7
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaagatttgtgaggtatttctgtagtacatggttttaggactacctatgttagcagaacagttgtat----
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TTTGACCCAGTAAAGCTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATTGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgcttgaa--cttatttctgat-acctttttgtcctataaagggtttctgagaccttgtttttctgcaacattttgtttagctga-cagatctgaagga
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA14G00760.1 (Glycine max), 5'ss of exon 8
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgt--gcttgctttgacacttattttaatttatttttaagatttgtgaggtatttctgtagtacatggttttaggactacctatgttagcagaacagttgtat-
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TTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAGgttaatatattttcgaaatttgttaaactttttcctaca--taacgatttgtatttggatgcccttgtcgattattttgttataa-aatactatatatatata
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G47860.1 (Glycine max), 5'ss of exon 8
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgt--gcttgct-ttgacacttattttaatttatttttaagatttgtgaggtatttctgtagtacatggttttaggactacctatgttagcagaacagttgtat
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TTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACTGCTGGCAATGCTTCCAGCATAAGgttaatatattattgaaatttgcttaacttttttcctagtgtgtgtgtg-tgtgtgaatga-aaatgctcttgctaacag-----------------------
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G48230.1 (Arabidopsis thaliana), 5'ss of exon 8
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaagatttgtgaggtatttctgtagtacatggttttaggactacctatgttagcagaacagttgtat-----------------------------
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TTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAGgtccttttcctagc---tgaccatatatatgttcttagcttttagagaactcatgtaacgtatgaagtggatcttggttagatttgcaacttttttttctctttagtaaattttgtctctctttgacag
upper sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 9
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaag-atttgtgaggtatttctgtagtacatggttttagg-actacctatgttagcagaacagttgtat
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TTTGACCCTGTGAAATTAAAGAAGCTCCGACCCAGTTTTAAGGAGAATGGAGGTTCTGTCACTGCAGGCAATGCTTCTAGCATAAGgtatattatcttatttatacttctgttcatctttatttacttattgtttgatgc--cagtaccttcttgtgtttatggtccttgttgccggtataaactcacMapped 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|33678061|gb|CF306300.1|CF306300EST: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAG TGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
genomic: TTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctt ... catggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaagatttgtgaggtatttctgtagtacatggttttaggactacctatgttagcagaacagttgtat
- - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - TGGTGG