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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattgataagatccagtagttctgctaaatcctagttgcataccccagacagatggctaaacatccaaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTAGAGGGTTTTGGCACTATCAAGGACTCTGAGTCCCTCTGCATGTTCCTCT

Basic information

species Oryza sativa
transcript LOC_Os01g65090.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65090.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G400604_T01 (Zea mays), 3'ss of exon 8
gtgagaattgataagatccagtagttctgctaaatcctagttgcataccccagacagatggctaaac----------atccaaa------------tttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTAGAGGGTTTTGGCACTATCAAGGACTCTGAGTCCCTCTGCATGTTCCTCT
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gtaaaagaagatatta--cgatggttcttctgaaacctagttccacacttgtataaaatggctaaatgataaagaaaatccaaacctaattatcaatttgcagGGTGCCTTTTATTTGTTCATTGACTTCAGCGCCTACTATGGGTCTGAAGTAGAGGGGTTTGGCACTATCAAGAATTCCGAGTCCCTTTGCATCTTCCTAT
















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|29686132|gb|CB682407.1|CB682407
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88244955|gb|CI244804.1|CI244804
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|89182862|gb|CI045620.1|CI045620
EST:     GTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: GTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88247987|gb|CI247836.1|CI247836
EST:     ATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCANGCTCCTACTATGGATCTGAAGT
genomic: ATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCA-GCTCCTACTATGGATCTGAAGT
EST: gi|86255317|gb|CI063806.1|CI063806
EST:     TAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|29644554|gb|CB649561.1|CB649561
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88993448|gb|CI110269.1|CI110269
EST:     TCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|86497677|gb|CI140310.1|CI140310
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|29644410|gb|CB649417.1|CB649417
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|86522863|gb|CI163069.1|CI163069
EST:     -TGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|396941455|gb|HO188664.1|HO188664
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88218668|gb|CI218517.1|CI218517
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|29683532|gb|CB679807.1|CB679807
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|87016653|gb|CI275655.1|CI275655
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88955871|gb|CI092159.1|CI092159
EST:     GGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCTTACTATGGATCTGAAGTA
genomic: GGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88968509|gb|CI098751.1|CI098751
EST:     GGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: GGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88248836|gb|CI247920.1|CI247920
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88243308|gb|CI244430.1|CI244430
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88973004|gb|CI019623.1|CI019623
EST:     GAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: GAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88248331|gb|CI248180.1|CI248180
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88246765|gb|CI246614.1|CI246614
EST:     AAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: AAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|29679352|gb|CB675627.1|CB675627
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|89166827|gb|CI104113.1|CI104113
EST:     TGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|86482986|gb|CI125619.1|CI125619
EST:     TAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
EST: gi|88228601|gb|CI228081.1|CI228081
EST:     TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAG                         GGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA
genomic: TTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 70 (downstream exon)
Score: 11

TGAAGCAGTCTCAACTATGGTCAAAGCATTCCAGGAACGTCGTGATTACCTTGTAAAAAGTTTCAAGGAACTGCCAGGTGTGAAGATATCAGAGCCTCAGgtgagaattg ... aaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTAGAGGGTTTTGGCACTATCAAGGACTCTGAGTCCCTCTGCATGTTCCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctaaatcctagttgcataccccagacagatggctaaacatccaaatttgtagGGTGCCTTTTATTTGTTCATCGACTTCAGCTCCTACTATGGATCTGAAGTAGAGGGTTTTGGCACTATCAAGGACTCTGAGTCCCTCTGCATGTTCCTCT
                                             aaatttgta  TA-rich tract