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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagctcaaaatagaaaatacatcatctgattatgatatatgatagatatgtacaagttccttttttttttgcttgtatgtctaagtttaagttttagctcttatttatcaaattgtcatgatatttctgtag

Basic information

species Zea mays
transcript GRMZM2G107731_T01
intron # 7
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|211002685|gb|FL029004.1|FL029004
EST:     GACAGAACATGCGTACGGAAATG-CTGGAAAATTTGATCATGCCATAAAG                         G-TGTCAGTGCCAAACTGGAGGA-CAGAGAGTTGAGCGCATTTC-CACCTA
genomic: GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
EST: gi|71436912|gb|DR817962.1|DR817962
EST:     GACAGAACATGCGTACGGAAATGTCTGAAAAATTTGATCATGCCATAAAG                         GGTGTCAGTGCCAAACTTGAG
genomic: GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAG
EST: gi|31354731|gb|CD439088.1|CD439088
EST:     GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG                         GGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
genomic: GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
EST: gi|60358220|gb|DN225193.1|DN225193
EST:     GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG                         GGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
genomic: GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
EST: gi|91055771|gb|EB166189.1|EB166189
EST:     GACAGAACATGCGTACGGAATTGTCTGAAAAATT-GATCATGCCATAA-G                         GGTGTCAGTGCCAAACTTGA
genomic: GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGA
EST: gi|213169996|gb|FM189145.1|FM189145
EST:     GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG                         GGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
genomic: GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
EST: gi|149081200|gb|EE170309.2|EE170309
EST:     GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG                         GGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
genomic: GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
EST: gi|32931571|gb|CF036383.1|CF036383
EST:     GTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG                         GGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
genomic: GTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
EST: gi|149027108|gb|EE046399.2|EE046399
EST:     GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAG                         GGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA
genomic: GACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTA

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), 49 (downstream exon)
Score: 292

GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 267

GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 230

GAAGAGTGCCAAAGGGTATCGACAGAGGGACAGAACATGCGTACGGAATTGTCTGAAAAATTTGATCATGCCATAAAGgttgacagct ... atttctgtagGGTGTCAGTGCCAAACTTGAGGAGCAGAGAGTTGAGCGCATTTCTCAGCTAGAAGAGAACAATAC