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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtctatggttcaacagtacctggatttcattaatcttattatagtttattacttacatttgtttgtaactcgaaatggtacattgtaattattatgtttctaggggttccttttaattgtttgatttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG

Basic information

species Zea mays
transcript GRMZM2G170843_T02
intron # 5
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|60347883|gb|DN214856.1|DN214856
EST:     TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCA                         GGGCGGGAACAATGCAGGCAGTGCCACAG
genomic: TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG
EST: gi|32837431|gb|CD977109.1|CD977109
EST:     TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCA                         GGGCGGGAACAATGCAGGCAGTGCCACAGGT
genomic: TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAGGT
EST: gi|60341162|gb|DN208135.1|DN208135
EST:     TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCA                         GGGCGGGAACAATGCAGGCAGTGCCACAG
genomic: TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG
EST: gi|32837421|gb|CD977099.1|CD977099
EST:     TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCA                         GGGCGGGAACAATGCAGGCAGTGCCACAGGT
genomic: TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAGGT
EST: gi|211529714|gb|FL481421.1|FL481421
EST:     TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCA                         GGGCGGGAACAATGCAGGCAGTGCCACAG
genomic: TCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG

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: 48 (upstream exon), 29 (downstream exon)
Score: 92

CAATTACTCTCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG


Block sizes: 48 (upstream exon), 29 (downstream exon)
Score: 109

CAATTACTCTCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 144

CAATTACTCTCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG


Block sizes: 49 (upstream exon), 29 (downstream exon)
Score: 102

CAATTACTCTCATTTCAGCAGACTTTATTAGGACAGCTTGGTCAACATCAACCTAGCCAgtgagtgtct ... tttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgtaattattatgtttctaggggttccttttaattgtttgatttgattcagGGGCGGGAACAATGCAGGCAGTGCCACAG
                               ttttaattgtttgatt  TA-rich tract