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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatccagcaattggtgcaatctactatatttttatgtataacatatctatttccatgtaccatgcttgacatgttgttgctttgtgcagGTCTGCGTTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATATGATC

Basic information

species Oryza sativa
transcript LOC_Os02g54580.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G008242_T01 (Zea mays), 3'ss of exon 5
gtacatatccagcaattggtgcaatctactatatttttatgtataacatatctatttccatgtaccatgcttgacatgttgttgctttgtgcagGTCTGCGTTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATATGATC
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gtattggtccaataattgccaagtcatatca-gtctctataattcata-atcttgcttcaaaagtcctattt---acactgttaccttatgcagGTCTGCTTTGCGCTGTTTCAAGCGTCGTGTTGCCTATGCTAATGTAACATATGATC
















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|58695635|gb|CK084322.1|CK084322
EST:     CCCCCACTTCTCCTACGAATGGCTGAAGACTGTGATGATGGAAAATTCAT                         GTCTGCGCTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATA
genomic: CCCCCACTTCTCCTACGAATGGCTGAAGACTGTGATGATGGAAAATTCATgtacatatcc ... ctttgtgcagGTCTGCGTTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATA
EST: gi|29672624|gb|CB668899.1|CB668899
EST:     CCCCCACTTCTCCTACGAATGGCTGAAGACTGTGATGATGGAAAATTCAT                         GTCTGCGTTGCGCTCTTTTAAGCGCCGTGGTGCCTATGCGAATGTAACATA
genomic: CCCCCACTTCTCCTACGAATGGCTGAAGACTGTGATGATGGAAAATTCATgtacatatcc ... ctttgtgcagGTCTGCGTTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATA
EST: gi|29629784|gb|CB634793.1|CB634793
EST:     CCCCCACTTCTCCTACGAATGGCTGAAGACTGTGATGATGGAAAATTCAT                         GTCTGCGCTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATA
genomic: CCCCCACTTCTCCTACGAATGGCTGAAGACTGTGATGATGGAAAATTCATgtacatatcc ... ctttgtgcagGTCTGCGTTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATA

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: 54 (upstream exon), 56 (downstream exon)
Score: 11

TTGGGAGAACAGGGAAACATTTATTCCTTACAGACTCAGATGATGGGAAGCCCCCACTTCTCCTACGAATGGCTGAAGACTGTGATGATGGAAAATTCATgtacatatcc ... ctttgtgcagGTCTGCGTTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATATGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtataacatatctatttccatgtaccatgcttgacatgttgttgctttgtgcagGTCTGCGTTGCGCTCTTTTAAGCGCCGTGTTGCCTATGCGAATGTAACATATGATC
                                          ttgcttt  CT-rich tract
        atatctattt  TA-rich tract