Sequence
atgc intronic sequence ATGC exonic sequenceTTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaaccagtttgatctgttacag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g45280.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g45280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G157115_T01 (Zea mays), 5'ss of exon 5
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaacca--gtttgatctgttacag
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TTTGGTCTCGCAAGAACAGGTCCTAGTGGAGACCAAACCCATGTGTCAACTCGGGTCATGGGAACTTATGGATACGCAGCTCCAGAATATGTCATGACTGgtaagcaaggg--tttcc---tatcgtcaa---gccaacgatttgaggataaaaatgagct--tgtccccaagaatgaatagacac-tcatgttacttgacttggtccaaat-attttaatcctcaaatcaccatttaacttgacgcag
upper sequence: LOC_Os06g45280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G050701_T02 (Zea mays), 5'ss of exon 5
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaac-cagtttgatctgttacag
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TTTGGTCTCGCAAGAACAGGTCCTAGTGGAGACCAAACCCACGTGTCAACTCGTGTTATGGGAACTTATGGATACGCGGCTCCAGAATATGTCATGACTGgtaagcaa--ggatttcc---tatcatcaagccaacaattcgaggata--aaaatgaactt---gtccccaagaatgaatagacac-tcatggtacttgacctagtcca-attatgttaatcctcaatcaccaattaacttgacgcag
upper sequence: LOC_Os06g45280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G03070.1 (Glycine max), 5'ss of exon 5
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaaccagtttgatctgttacag
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TTTGGCCTTGCAAAGGATGGTCCGATGGGGGACCAAACCCATGTTTCAACACGAGTAATGGGCACATATGGATACGCTGCTCCTGAGTATGTCATGACTGgtgagtta---------cccgaagctattgatggtgaatttttccattt-------catttctaatttctcag---aaatatggagaat-tcataaacgata--aaaaaggtgcaattactc-------------------------
upper sequence: LOC_Os06g45280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G36500.2 (Glycine max), 5'ss of exon 5
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaaccagtttgatctgttacag
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TTTGGCCTTGCAAAGGATGGTCCGATGGGGGACCAAACCCATGTTTCAACACGAGTAATGGGCACATATGGATATGCTGCTCCTGAGTATGTCATGACTGgtgagttactcaaagctattg----------atgctgatt--tttttcctttcatttttctaat-ttctcaga----aatatggat-ttatcataaatgata--aaaaaagtgcaattct---------------------------
upper sequence: LOC_Os06g45280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv11s0065g00470.t01 (Vitis vinifera), 5'ss of exon 5
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaaccagtttgatctgttacag
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TTTGGGCTTGCAAAGGATGGACCTATGGGAGACCAGACCCATGTGTCAACACGTGTGATGGGCACATATGGATATGCAGCTCCTGAGTATGTAATGACTGgtgag----------tctttgaattgccaaaaattgcacttaattgc-cttgtaagggtttcttttcccca--caaaaacac-taaatcttttccattaaataaaagtatttta---------------------------------
upper sequence: LOC_Os06g45280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S31_254V6.1 (Physcomitrella patens), 5'ss of exon 5
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgag---caatggaatctccctgtat-ttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctg-acatcatgtatgttaaattgttactctaaccagtttgatctgttacag
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TTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATGCTGCCCCTGAGTATGTGATGACAGgtgtgattcttccctattcattcgtgtcttttcgaaaatgtattcaggcgctttgccgagtactcgcggaaacttatcttgtatatgcagcgatctgattttgtgtaggttcttcattcggttgcttcatttaactatgtattgatttgcag
upper sequence: LOC_Os06g45280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ35779 (Selaginella moellendorffii), 5'ss of exon 4
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaaccagtttgatctgttacag
|| || | ||| ||| || || ||| |||| || || || || || || ||||| |||||||||||||||||||| ||||| || ||||||||| | | |||| | | | || | | | ||||| ||| || | | |||| | || | | ||| || | | | | | |
TTCGGTTTGGCAAAGGATGGTCCGGAAGGTGACAAAACGCACGTTTCGACGCGCGTAATGGGGACTTATGGCTATGCAGCTCCAGAATACGTAATGACAGgta--ctttttcttctcgttcttgctcgagtgaagctctctttcgtttcttcagtcgtttcgacgatctt--gcgagagtgagagc----ttgcgactcatgcctttccggctttgcag----------------------------
upper sequence: LOC_Os06g45280.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ10730 (Selaginella moellendorffii), 5'ss of exon 4
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaaccagtttgatctgttacag
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TTCGGTTTGGCAAAGGATGGTCCGGAAGGTGACAAAACGCACGTTTCGACGCGCGTAATGGGGACTTATGGCTATGCAGCTCCAGAATACGTAATGACAGgta--ctttttcttctcgttcttgctcgagtgaagctgtctttcgtttcttcagccgtttcgacgatctt--gcgagagtgagagc----ttgcgactcatgcctttccggctttgcag----------------------------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|33381081|gb|CF196424.1|CF196424EST: TACTTATGGCTATGCAGCTCCTGAATATGTCATGACAG GCCATCTGACAGCACGAAGTGATGTCTATGGCTTTGGTGTCGTCCTTCTCG
genomic: TACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatg ... tctgttacagGCCATCTGACAGCACGAAGTGATGTCTATGGCTTTGGTGTCGTCCTTCTCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTGGCCTAGCACGAACTGGACCTAGTGGAGACCAAACCCATGTATCAACTCGGGTCATGGGTACTTATGGCTATGCAGCTCCTGAATATGTCATGACAGgtgagcaatggaatctccctgtatttttagaatgccaacccgttcattcttgagtgcatttaatgttcttaagtatgaatatgcatatcattgtagctgacatcatgtatgttaaattgttactctaaccagtttgatctgttacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC