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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctggttactttttttctaatgtttttttcttcacttggatcagtatattgctatgtcaggttgttgagttgcccttttgtgctgctttatttg...

Basic information

species Zea mays
transcript GRMZM2G170843_T02
intron # 6
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|87151815|gb|DY396604.1|DY396604
EST:     CGGGAACAATGCAGGCAGTGCCACAG                         GTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
genomic: CGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
EST: gi|60347883|gb|DN214856.1|DN214856
EST:     GGGCGGGAACAATGCAGGCAGTGCCACAG                         GTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
genomic: GGGCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
EST: gi|60341162|gb|DN208135.1|DN208135
EST:     GGGCGGGAACAATGCAGGCAGTGCCACAG                         GTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
genomic: GGGCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
EST: gi|22490843|gb|BU050766.1|BU050766
EST:     GCGGGAACAATGCAGGCAGTGCCACAG                         GTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
genomic: GCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
EST: gi|211529714|gb|FL481421.1|FL481421
EST:     GGGCGGGAACAATGCAGGCAGTGCCACAG                         GTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC
genomic: GGGCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGC

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: 29 (upstream exon), 49 (downstream exon)
Score: 138

GGGCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGCTTGGTTCGGGAGGTGGTCTAGGTGTTCCAAATACCTCCAGCG


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 172

GGGCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGCTTGGTTCGGGAGGTGGTCTAGGTGTTCCAAATACCTCCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

GGGCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGCTTGGTTCGGGAGGTGGTCTAGGTGTTCCAAATACCTCCAGCG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 170

GGGCGGGAACAATGCAGGCAGTGCCACAGgtaaatcctg ... atatgtgcagGTACACGGGGAAACCCTAGCCTTGACACCTTGATGAGCATGCTCAGCGGGCTTGGTTCGGGAGGTGGTCTAGGTGTTCCAAATACCTCCAGCG