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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaatttagacatggttatctgatctttgattttcatgtgcctctattggctattgagtgtcaactttgcatatgaggacatgtgatagttattgctatttaaccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAACTGAGAAGAATGTGCGTTCCAAATTCCTTAATGGTATTACTTCTGCGAA

Basic information

species Oryza sativa
transcript LOC_Os11g05930.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g05930.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G488465_T01 (Zea mays), 3'ss of exon 4
gtaaggaatttagacatggttatctgatctttgattttcatgtgcctctattggctat---tgagtgtcaactttgcatatgaggacatgtgatagttattgcta-tttaaccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAACTGAGAAGAATGTGCGTT-----CCAAATTCCTTAATGGTATTACTTCTGCGAA
|||||||||| |||| ||||||  | || ||   ||  | ||||| ||| ||| | ||   | |||||   |    |   || | |||||  ||||| ||| ||| ||| | |   || || ||||||||||||||    ||| |  ||  |||   | ||| ||| || ||| |       | |||        |  |     |||  | || | | |    || 
gtaaggaattgagacctggttacataattttatgttaacttgtgc-tctgttgtccatgagttagtgtgtgccactctattgtgcacatgcaatagtaatttctaatttcatcacatgcagGTGCTCCAAGTGGAA----GTGAGAAGAATGTGCGGTCCAAATGCCTT-AACGGTATTACTTCTGCAAAGGTGGCTGAGCAAATTATGGATAATGCCTTGAGGAT

upper sequence: LOC_Os11g05930.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G135446_T01 (Zea mays), 3'ss of exon 4
gtaaggaatttagacatggttatctgatctttgattttcatgtgcctctattggctattgagtgtcaactttgcatatgaggacatgtgatagttatt-gctatttaaccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAACTGAGAAGAATGTGC----GTTCCAAATTCCTTAATGG-TATTACTTCTGCGAA
             ||||| || | ||    || | ||  |||  |   |   ||  | | |||||   || | |   || | ||||||   ||| ||| | ||||| |     || || ||||||||||| ||    ||| |  ||  |||   | ||| ||| || ||  |       | |||    ||  |  |     |||||| || | | |    || 
------------cacatgattttatg----ttaactt--atgctctgttgccggtaagttagtgtgtgctattctattgtgcacatgtagcagtaatttgttatttcattgcatgcagGTGCTCCAAGTGAAA----GTGAGAAGAATGTGCGTTCCAAATGCCTT-AATGGTATTACTTCTGCAAAGGTGGCTGAGCAAATAATGGATAATGCCTTGAGGAT
















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|29630671|gb|CB635680.1|CB635680
EST:     TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATG                         ATGCTCCAAGTGGAAATGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
genomic: TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATGgtaaggaatt ... ccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
EST: gi|29661214|gb|CB657489.1|CB657489
EST:     TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATG                         ATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
genomic: TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATGgtaaggaatt ... ccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
EST: gi|29638597|gb|CB643606.1|CB643606
EST:     TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATG                         ATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
genomic: TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATGgtaaggaatt ... ccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
EST: gi|33678541|gb|CF306780.1|CF306780
EST:     TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGG--A-TG---                         ---CTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
genomic: TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATGgtaaggaatt ... ccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
EST: gi|5803459|gb|AI978429.1|AI978429
EST:     TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATG                         ATGCTCCAAGTGGAAATGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA
genomic: TTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATGgtaaggaatt ... ccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAA

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: 73 (upstream exon), 72 (downstream exon)
Score: 16

GTTGCAGATGGTGGGGCAGGCTCATCCAGAGAACATAAAATACAGAATGGTTTCATTGATGGAATGAACACAAAATCACATGCATTAAAGGGTAATGATGgtaaggaatt ... ccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAACTGAGAAGAATGTGCGTTCCAAATTCCTTAATGGTATTACTTCTGCGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcaactttgcatatgaggacatgtgatagttattgctatttaaccttttgtagATGCTCCAAGTGGAAACGCGTGTGGTGATAGTGAACTACAAGTGCTTTCAACTGAGAAGAATGTGCGTTCCAAATTCCTTAATGGTATTACTTCTGCGAA
                                       atttaac  putative branch site (score: 16)
                                             ccttttgt  CT-rich tract
                               ttattgctatttaa  TA-rich tract