Sequence
atgc intronic sequence ATGC exonic sequenceATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaattgtagaagtattagttgtccaagagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt...
Basic information
species | Oryza sativa |
transcript | LOC_Os08g17820.2 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g17820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AC197714.3_FGT005 (Zea mays), 5'ss of exon 6
ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaattgtagaagtattagttgtccaagagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt
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ATACGAGGTTCAGTCAAGTTGAAAAGGATTATGCAGACAATTCTTTCTCTCGGAAATGCATTGAACCAAGGCACTGCTAGAGgtaagcaaaattgt-gaattgatacttcttaag-------------------------------------------------------------------
upper sequence: LOC_Os08g17820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ36895 (Selaginella moellendorffii), 5'ss of exon 11
ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaattgtagaagtattagttgtccaagagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt
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GTGAAAGAGTCTGCGAAGCTTAAAAGAGTAATGCAAACGGTTCTATCCTTGGGAAATGCGCTAAACCAAGGAACTGCTAGAGgtaa-gacctgtgctggggaacttg--agctaactatatgttgagctaacattccag-------------------------------------------
upper sequence: LOC_Os08g17820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ37653 (Selaginella moellendorffii), 5'ss of exon 11
ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaat-tgtagaagtattagttgtccaa-gagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt
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GTGAAAGAGTCTCCTAAGCTTAAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaagcagagtgcccgggagcttgagctaagtaacaagtgtggctgttgttccag-----------------------------------------------
upper sequence: LOC_Os08g17820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ33545 (Selaginella moellendorffii), 5'ss of exon 11
ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaattgtagaagtattagttgtccaagagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt
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GTGAAAGAGTCTGCTAAGCTTAAAAGAGTAATGCAAACGGTTCTATCCTTGGGAAATGCGCTAAACCAAGGAACTGCTAGAGgtaaggcctgtgctggggaacttga---gctaactatatgttgagctaacattccag-------------------------------------------
upper sequence: LOC_Os08g17820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ15040 (Selaginella moellendorffii), 5'ss of exon 11
ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaat-tgtagaagtattagttgtccaa-gagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt
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GTGAAAGAGTCTCCTAAGCTTAAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaagaagagtgcccgggagcttgagctaagtaacaagtgtggctgttgttccag-----------------------------------------------
upper sequence: LOC_Os08g17820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ14916 (Selaginella moellendorffii), 5'ss of exon 7
ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaattgtagaagtattagttgtccaagagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt
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------------------CTTGAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGTGTTAAACCAAGGAACTGCTAGAGgtaagaagagtgccagggagcttga--gctaagtagcaagtgtggctgttgttccag-------------------------------------------
upper sequence: LOC_Os08g17820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ38303 (Selaginella moellendorffii), 5'ss of exon 4
ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaattgtagaagtattagttgtccaagagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt
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-------AGTCTCCTAAGCTTGAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaagaagagtgccagggagcttga--gctaagtagcaagtgtggctgttgttccag-------------------------------------------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|11442844|gb|BF430743.1|BF430743EST: GCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG GTTCTGCTGTTGGGTTCAGGTTGGATAGCTTACTCAAACTAAGT
genomic: GCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaa ... ttttctgcagGTTCTGCTGTTGGGTTCAGGTTGGATAGCTTACTCAAACTAAGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATAAGGGGTTCAGCTAAGCTGAAAAGGATTATGCAGACAATTCTTTCACTGGGAAATGCGTTAAACCAAGGAACTGCTAGAGgtaatgaaaattgtagaagtattagttgtccaagagaatatttggtgagcaaccaagtgctattcttatttttttcataaagactatttgaaaatcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA