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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGGTGTTCTCATCACGGTAAGCGCCGCCGGCAGAATCGGCGGTCCGAATCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatctgaatcgacctgtgagatgtttcgatgcatcgttgtttggatcttgtatgtagcgtccgtcgtgtgagatttgtgtttaatgtcttcattt...

Basic information

species Zea mays
transcript GRMZM2G080060_T01
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|32871119|gb|CF010801.1|CF010801
EST:     TCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAG                         ATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
genomic: TCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
EST: gi|211375369|gb|FL214346.1|FL214346
EST:     TCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAG                         ATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
genomic: TCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
EST: gi|50323469|gb|CO518595.1|CO518595
EST:     TCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAG                         ATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
genomic: TCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
EST: gi|161590045|gb|EY962037.1|EY962037
EST:     CGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAG                         ATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
genomic: CGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
EST: gi|211375370|gb|FL214347.1|FL214347
EST:     TCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAG                         ATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG
genomic: TCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAG

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: 22 (upstream exon), 47 (downstream exon)
Score: 13

GGGGGTGTTCTCATCACGGTAAGCGCCGCCGGCAGAATCGGCGGTCCGAATCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAGATGAACTCGGTCGAGGTTAGGCAGACGGTTGGTCATCCTACCAACTCAT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 4

GGGGGTGTTCTCATCACGGTAAGCGCCGCCGGCAGAATCGGCGGTCCGAATCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAGATGAACTCGGTCGAGGTTAGGCAGACGGTTGGTCATCCTACCAACTCAT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 12

GGGGGTGTTCTCATCACGGTAAGCGCCGCCGGCAGAATCGGCGGTCCGAATCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAGATGAACTCGGTCGAGGTTAGGCAGACGGTTGGTCATCCTACCAACTCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 19

GGGGGTGTTCTCATCACGGTAAGCGCCGCCGGCAGAATCGGCGGTCCGAATCTCCAGGAACCGGCGATTCCACCTCAACGACTCCCACATCTGTGCGAAGgtatgcatct ... tgtcctgcagATGGCGTACACTCCTTTGGATACCCTCAAATGGGTTGTAAAGGAAATGGAGATGAACTCGGTCGAGGTTAGGCAGACGGTTGGTCATCCTACCAACTCAT