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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCTTGGTAACCATTTGATGAGTAAGGGCTACAAATTGGTTACTGACGGAACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgagcaagtttaatggcatcttatgttgttttctctgagtccatgtgaactaactcaaatgttggtctgccttag

Basic information

species Oryza sativa
transcript LOC_Os12g22030.1
intron # 2
splice site 5'
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|29661231|gb|CB657506.1|CB657506
EST:     AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTG                         GTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
genomic: AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
EST: gi|88731473|gb|CI755086.1|CI755086
EST:     AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTG                         GTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
genomic: AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
EST: gi|86521243|gb|CI161449.1|CI161449
EST:     TGGGATCTGCGCCCTCTTGGCTTGACTG                         GTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
genomic: TGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
EST: gi|86520924|gb|CI161130.1|CI161130
EST:     AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGGCTG                         GTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACCAAA
genomic: AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
EST: gi|86514112|gb|CI156745.1|CI156745
EST:     TGGCTTGGCTG                         GTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
genomic: TGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
EST: gi|87027893|gb|CI276249.1|CI276249
EST:     AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTG                         GTAACTAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACTAAA
genomic: AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
EST: gi|58683023|gb|CK071710.1|CK071710
EST:     AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTG                         GTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
genomic: AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
EST: gi|58589560|gb|CF987868.1|CF987868
EST:     AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTG                         GTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
genomic: AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA
EST: gi|218489698|gb|FG969212.1|FG969212
EST:     AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTG                         GTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAATAAAA
genomic: AACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAA

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), 62 (downstream exon)
Score: 41

GCCCTTGGTAACCATTTGATGAGTAAGGGCTACAAATTGGTTACTGACGGAACAGAGAACCATCTTGTTCTCTGGGATCTGCGCCCTCTTGGCTTGACTGgtatgctgag ... tctgccttagGTAACAAAGTTGAGAAGGTCTGTGATTTGTGCAGCATTACACTGAACAAAAATGCTGTCTTTGGGGATAGCAGTGCAATGTCACCTGGTGGTGTCCGCAT




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