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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggtgggggtgctttgggcttcgggaatggtggtttagggtttggatcggggtttttgcgtgtgtgctgattgagatctaacactttctggaacgcgttggatcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG

Basic information

species Oryza sativa
transcript LOC_Os12g06020.1
intron # 2
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|29684686|gb|CB680961.1|CB680961
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|29676701|gb|CB672976.1|CB672976
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|33793549|gb|CF322657.1|CF322657
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|58686519|gb|CK075206.1|CK075206
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|29639082|gb|CB644091.1|CB644091
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|29669200|gb|CB665475.1|CB665475
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|33793116|gb|CF322439.1|CF322439
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|88727764|gb|CI749566.1|CI749566
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAG
EST: gi|88433452|gb|CI594266.1|CI594266
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|58685061|gb|CK073748.1|CK073748
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|58694565|gb|CK083252.1|CK083252
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|29639128|gb|CB644137.1|CB644137
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|58660010|gb|CK048690.1|CK048690
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|88357134|gb|CI616021.1|CI616021
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
EST: gi|87008879|gb|CI304822.1|CI304822
EST:     AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAG                         GAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACC
genomic: AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACC

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: 41 (upstream exon), 50 (downstream exon)
Score: 29

AGCCGGAAGGACGTCGAGGGATCGCTGTTCGTGGTGAAGAGgtgaggtggg ... tcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtgtgtgctgattgagatctaacactttctggaacgcgttggatcgcgtgtagGAACAAGCAGCCGAGGTTCCAGTTCATCGTCATGAACAGGCGTAACACCG
                  atctaac  putative branch site (score: 29)