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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcgtaataagaccttttttttatgtttttgtttcccaaattttgctgtctggaaataatttcttgaaagggttggctttgatcgtttgctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAGCGCGTGGCGGTGAAGTACTACAGCGATGACTGGCCCTCTTTGTCCTCGA

Basic information

species Oryza sativa
transcript LOC_Os01g62150.1
intron # 1
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|33688268|gb|CF316507.1|CF316507
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|58686756|gb|CK075443.1|CK075443
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|88729722|gb|CI753232.1|CI753232
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|88390456|gb|CI607492.1|CI607492
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|33656563|gb|CF279177.1|CF279177
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|33657559|gb|CF280173.1|CF280173
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
EST: gi|88386053|gb|CI570688.1|CI570688
EST:     GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATG                         GAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG
genomic: GCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAG

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: 43 (upstream exon), 70 (downstream exon)
Score: 8

CATCGCCTCGCTCGCGCAGCAATCCGCGACAAATCCACCAGCCAATCGCGGCATCGCGCCCATCCCTTCCCCTATACTGCAAATCCGCTTCCCCGAGATGgtaatttcct ... gctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAGCGCGTGGCGGTGAAGTACTACAGCGATGACTGGCCCTCTTTGTCCTCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgtctggaaataatttcttgaaagggttggctttgatcgtttgctcgtgcagGAATCCTGTCCTTCGGTGAAGAACATTCTTGTGCTGGATTCCGAAGGGAAGCGCGTGGCGGTGAAGTACTACAGCGATGACTGGCCCTCTTTGTCCTCGA
                                 ctttgat  putative branch site (score: 8)
                                          tttgctc  putative PPT
          aaataatttcttgaaa  TA-rich tract