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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttcctttcctgctgtagacaactatctaaagtaggttgtagcctatgacattccacaggcctaagatttcttctttactaaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG

Basic information

species Oryza sativa
transcript LOC_Os07g30790.1
intron # 5
splice site 3'
intron type U2

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|66930704|gb|CX117552.1|CX117552
EST:     GAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAG                         GCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
genomic: GAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAGgcaagttcct ... taaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
EST: gi|58601816|gb|CK012344.1|CK012344
EST:     CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAG                         GCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
genomic: CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAGgcaagttcct ... taaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
EST: gi|88539583|gb|CI469547.1|CI469547
EST:     CCCTGCTATCCAG                         GCATGGGCACGGTACACTCGGAGGGGAGGCAACTTGCCTATCACTGACAG
genomic: CCCTGCTATCCAGgcaagttcct ... taaattgcagGCATTGGCACGGTACACTCGGA-GGGAGGCAACTTGCCTATCACTGACAG
EST: gi|58695091|gb|CK083778.1|CK083778
EST:     CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAG                         GCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
genomic: CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAGgcaagttcct ... taaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
EST: gi|88472230|gb|CI409501.1|CI409501
EST:     CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAG                         GCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
genomic: CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAGgcaagttcct ... taaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
EST: gi|58595057|gb|CF993365.1|CF993365
EST:     CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAG                         GCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
genomic: CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAGgcaagttcct ... taaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
EST: gi|88201000|gb|CI201355.1|CI201355
EST:     CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAG                         GCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
genomic: CCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAGgcaagttcct ... taaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG

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: 52 (upstream exon), 47 (downstream exon)
Score: 14

GAATGTGTATGCCGACGAAGGTTCAGAGGCTATGGATGCAGCAGCTGTCCCTGCTATCCAGgcaagttcct ... taaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgtagcctatgacattccacaggcctaagatttcttctttactaaattgcagGCATTGGCACGGTACACTCGGAGGGAGGCAACTTGCCTATCACTGACAG
                                          tactaaa  putative branch site (score: 14)
                                 tttcttctttact  CT-rich tract
                                     ttctttactaaatt  TA-rich tract