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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcttacttcattatagctacagttctgttgattcaggcctttgggcttttctaagggattccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAGTGGGTTGATCTTAAACAG

Basic information

species Oryza sativa
transcript LOC_Os09g10710.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g10710.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G049155_T03 (Zea mays), 3'ss of exon 5
gtttgttcttacttcattatagctacagttctgttgattcaggcctttgggcttttctaagggattccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAGTGGGTTGATCTTAAACAG
||  ||| |||||  | |   |      | ||  |  || | ||||   |   ||||| ||| | | |||||||||  || ||||   ||| ||||||||| ||||| || |||||| | ||||||||||||||||||||| ||
gtgcgtt-ttactatactggggtagt--tacttctcgtttaagcctccagctctttcttaggaaattcattgcagGGCCTTTATGTGCTGGTTTATGACATTAATACGGCAAATGAAACCTGGGAGTGGGTTGATCTTAAAGAG

upper sequence: LOC_Os09g10710.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G39100.1 (Glycine max), 3'ss of exon 4
gtttgttcttacttcattat-agctacagttctgttgattcaggcctttgggcttttctaagggattccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAGTGGGTTGATCTTAAACAG
|| ||||  || |  | ||| ||  || |     |  ||  |  |||||     ||||||      |   ||| |||  ||  |||| |||| |||||| || ||| |||| |||||| |||||||||||||| |||||||| ||
gtgtgtttatagtatactattagaaactgaggaatacatggactcctttaa-tatttctatttacatattttgtagGGACTACATGCTTTGGTTTATGATATGAATTCAGCAAATGAAACATGGGAGTGGGTTAATCTTAAAGAG
















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|29664515|gb|CB660790.1|CB660790
EST:     AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACG                         GATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
genomic: AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACGgtttgttctt ... tccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
EST: gi|218504904|gb|FG952258.1|FG952258
EST:     AGATAACAGTTTTTACGAAGCAACTATTACTGGATTATAATCCAGAAACG                         GATCTGTATGCATTGGCTTATGACATAAA
genomic: AGATAACAGTTTTTACGAAGCAACTATTACTG-ATTATAATCCAGAAACGgtttgttctt ... tccattgcagGATCTGTATGCATTGGCTTATGACATAAA
EST: gi|38477911|gb|CF962044.1|CF962044
EST:     AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACG                         GATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
genomic: AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACGgtttgttctt ... tccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
EST: gi|58675371|gb|CK064058.1|CK064058
EST:     AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACG                         GATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
genomic: AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACGgtttgttctt ... tccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
EST: gi|29642065|gb|CB647072.1|CB647072
EST:     AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACG                         GATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
genomic: AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACGgtttgttctt ... tccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
EST: gi|58683751|gb|CK072438.1|CK072438
EST:     AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACG                         GATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
genomic: AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACGgtttgttctt ... tccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
EST: gi|58655308|gb|CK043988.1|CK043988
EST:     AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACG                         GATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG
genomic: AAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACGgtttgttctt ... tccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAG

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: 64 (upstream exon), 75 (downstream exon)
Score: 22

ACTGCATATTAATCCATTAATTAATCGTAAAGTCATGAGCCGGTGGCCTGAAGATAACAGTTTTTACGAAGCAACTATTACTGATTATAATCCAGAAACGgtttgttctt ... tccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAGTGGGTTGATCTTAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctacagttctgttgattcaggcctttgggcttttctaagggattccattgcagGATCTGTATGCATTGGCTTATGACATAAATACAGCTAATGAATCATGGGAGTGGGTTGATCTTAAACAG
           tgttgat  putative branch site (score: 22)
                                            ttccatt  putative PPT
                                ttttctaa  TA-rich tract