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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTGGGCCGCCGGGGCCCCTCCGGCTTCTCCTGGAGTTCCACCGCCGACCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtacttattccccaacatttcttcttccttcttcatagtatttattattagtaatccag

Basic information

species Zea mays
transcript GRMZM2G009940_T02
intron # 1
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|76280839|gb|DV020407.1|DV020407
EST:     CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCG----T-                         --C-A---C-T---GGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
genomic: CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
EST: gi|31909769|gb|CD651085.1|CD651085
EST:     CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTG                         CCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGCAGACGGCGCGAA
genomic: CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
EST: gi|78106300|gb|DV524718.1|DV524718
EST:     CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCG----T-                         --C-A---C-T---GGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
genomic: CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
EST: gi|78084860|gb|DV513253.1|DV513253
EST:     CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCG----T-                         --C-A---C-T---GGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
genomic: CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
EST: gi|149082933|gb|EE172168.2|EE172168
EST:     CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCG----T-                         --C-A---C-T---GGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
genomic: CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
EST: gi|71438305|gb|DR819355.1|DR819355
EST:     CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCG----T-                         --C-A---C-T---GGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
genomic: CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
EST: gi|78105169|gb|DV523587.1|DV523587
EST:     CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCG----T-                         --C-A---C-T---GGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA
genomic: CCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAA

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 2 RNA-Seq libraries.


Block sizes: 15 (upstream exon), 49 (downstream exon)
Score: 2

CTTCTGGGCCGCCGGGGCCCCTCCGGCTTCTCCTGGAGTTCCACCGCCGACCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAACGCTGGCGCTGCGCGGGGCCCACGTCATCATGGCCGTCAGGAGCCTTCC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 7

CTTCTGGGCCGCCGGGGCCCCTCCGGCTTCTCCTGGAGTTCCACCGCCGACCAAGTCACGCAGGGCATCTCCGCCGCCGGCCTCACCGCCATCGTCACTGgtccgtactt ... agtaatccagCCCAATCCCATCCAGGGGCGTCCAGCGGCATCGGCGCGGAGACGGCGCGAACGCTGGCGCTGCGCGGGGCCCACGTCATCATGGCCGTCAGGAGCCTTCC




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