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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacagacataagcaaactttcttctttgagtcctgacattacatcctggtcagaaaatttcagctcagaccacctaacgcctctgaatctcgccttgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g02410.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 6
gtaacagacataagcaaactttcttctttgagtcctgacattacatcctggtcagaaaatttcagctcagaccacctaacgcctctgaatctcgccttgtgg-tgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG
||||| |  |        || |  |   ||| | ||  ||||     |||  | | |    |  |     |  ||||      | ||            |   |  |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||    |||||| |  |||| |||||
gtaacggttactgct--cctctgctgcctgaattctc-cattgtcagctg--cggga----ttggtagtaatgacctgtttgttttgtcctgtaatccataaatacagGTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTCAACGGCATTGCGCCAGCTCCAAG

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 6
gtaacagacataagcaaactttcttctttgagtcctgacattacatcctggtcagaaaatttcagctcagaccacctaacgcctctgaatctcgccttgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG
       |   | ||  |   |  || |    ||    ||||     |||         |   |       |    |      |||   | |   |      |  |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||   |||||||||  |||| || ||
-----gtaaggacgcgcatcctgctcctgtcttctctgcattgtcagctgcgtgcttggtagtaatatgacctgtttgttttgtct---tgtgatccaaacatacagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTGGGCAAGTTCGACCTCAATGGCATTCCGTCAGCTCCGAG
















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|58605366|gb|CK033399.1|CK033399
EST:     CCCAGGTGTTCACCACCTACCAGGATCAGCAGACGACCGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagaca ... tgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
EST: gi|29655799|gb|CB652074.1|CB652074
EST:     CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagaca ... tgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
EST: gi|428460|gb|D24610.1|D24610
EST:     CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCA-NATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagaca ... tgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
EST: gi|58661511|gb|CK050191.1|CK050191
EST:     CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagaca ... tgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
EST: gi|55411112|gb|CV723488.1|CV723488
EST:     CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagaca ... tgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
EST: gi|5004223|gb|AU069372.1|AU069372
EST:     CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAN-ATGGACCAAGGACTGCCGTCTTCTCGGCAA
genomic: CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagaca ... tgtggtgtagGTCTTTGAGGGTGAGCGCAGCATG-ACCAAGGACTGCCGTCTTCTCGGCAA
EST: gi|29660696|gb|CB656971.1|CB656971
EST:     CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAG                         GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG
genomic: CCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagaca ... tgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAG

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: 75 (upstream exon), 72 (downstream exon)
Score: 302

AGTCATGACCAAGTTGATCCCCAGGAACACCGTCATCCCCACCAAGAAGTCCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagaca ... tgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaaaatttcagctcagaccacctaacgcctctgaatctcgccttgtggtgtagGTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG
                     acctaac  putative branch site (score: 302)
                                     tctcgcctt  putative PPT
     aatttca  TA-rich tract