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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgctttcacgttcagcttttccaggtttttgctctgctctagatattgtcagttggaactaacagaaatatgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG

Basic information

species Zea mays
transcript GRMZM2G149520_T02
intron # 11
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|18655143|gb|BM499948.1|BM499948
EST:     CCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTT                         GGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTAC
genomic: CCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTTgtaagttgct ... tgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTAC
EST: gi|31353684|gb|CD438041.1|CD438041
EST:     CCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTT                         GGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTAC
genomic: CCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTTgtaagttgct ... tgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTAC
EST: gi|24766670|gb|CA401817.1|CA401817
EST:     CCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTT                         GGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTAC
genomic: CCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTTgtaagttgct ... tgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTAC

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: 345

TGTTATTCCTATCTTCAGGCAGCAAGCAGAGCAGTTGCTAAGCTCTTCCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTTgtaagttgct ... tgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

TGTTATTCCTATCTTCAGGCAGCAAGCAGAGCAGTTGCTAAGCTCTTCCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTTgtaagttgct ... tgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 243

TGTTATTCCTATCTTCAGGCAGCAAGCAGAGCAGTTGCTAAGCTCTTCCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTTgtaagttgct ... tgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

TGTTATTCCTATCTTCAGGCAGCAAGCAGAGCAGTTGCTAAGCTCTTCCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTTgtaagttgct ... tgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgctctgctctagatattgtcagttggaactaacagaaatatgtgtcttagGGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG
                               aactaac  putative branch site (score: 206)
              tagatatt  TA-rich tract