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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaatatttttctatctgtggacacaattccacttttactttgcatttgcctctgaaatattgtcacaattcatctgtgttttccaagacctcaagtcatgctcacactgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCATGGGAAGTAGAACCCCTTGATCGAACAAATCCACAGCCACCTCAACCTC

Basic information

species Zea mays
transcript GRMZM2G702026_T01
intron # 10
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|211284606|gb|FL307740.1|FL307740
EST:     CAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG                         GTCCAATGGGACGAGCCTTCTGCTATTCTGCGTCCAGATAGAGTTTCACCA
genomic: CAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAGgtaatcaata ... ctgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCA
EST: gi|31358117|gb|CD442474.1|CD442474
EST:     CAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG                         GTCCAATGGGACGAGCCTTCTGCTATTCTGCGTCCAGATAGAGTTTCACCA
genomic: CAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAGgtaatcaata ... ctgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCA
EST: gi|211531197|gb|FL317039.1|FL317039
EST:     CAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG                         GTCCAATGGGACGAGCCTTCTGCTATTCTGCGTCCAGATAGAGTTTCACCA
genomic: CAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAGgtaatcaata ... ctgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCA
EST: gi|211498503|gb|FL359837.1|FL359837
EST:     CAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAG                         GTCCAATGGGACGAGCCTTCTGCTATTCTGCGTCCAGATAGAGTTTCACCA
genomic: CAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAGgtaatcaata ... ctgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCA

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 450

ATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAGgtaatcaata ... ctgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCATGGGAAGTAGAACCCCTTGATCGAACAAATCCACAGCCACCTCAACCTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 368

ATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAGgtaatcaata ... ctgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCATGGGAAGTAGAACCCCTTGATCGAACAAATCCACAGCCACCTCAACCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 332

ATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAGgtaatcaata ... ctgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCATGGGAAGTAGAACCCCTTGATCGAACAAATCCACAGCCACCTCAACCTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 291

ATTCAGTGGGACAATTATTGGTATGGGATGCATGCCAGCTAACTCAACATCTCCATGGGCTAACTCTGAATGGAGATCATTGAAGgtaatcaata ... ctgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCATGGGAAGTAGAACCCCTTGATCGAACAAATCCACAGCCACCTCAACCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcacaattcatctgtgttttccaagacctcaagtcatgctcacactgctgacagGTCCAATGGGACGAGCCTTCCGCTATTCTGCGTCCAGATAGAGTTTCACCATGGGAAGTAGAACCCCTTGATCGAACAAATCCACAGCCACCTCAACCTC
                                     tgctcac  putative branch site (score: 291)
     aattcat  TA-rich tract