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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgatttcaaacaagcccctttgttgcaactatccagagcctgtctgtatagtaacatgtcctttcatattttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCAGTTACTTATCAGGTTTCTAAACGAAGGGGCATGTCAATTACGAGAAACC

Basic information

species Zea mays
transcript GRMZM2G033592_T01
intron # 15
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|91873217|gb|EB403174.1|EB403174
EST:     CTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCG                         GACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
genomic: CTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
EST: gi|7216726|gb|AW562848.1|AW562848
EST:     CTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCG                         GACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
genomic: CTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
EST: gi|26559626|gb|CA831861.1|CA831861
EST:     ATATACAATTGCACTGATGGGATTGCG                         GACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
genomic: ATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
EST: gi|26456384|gb|CA827967.1|CA827967
EST:     CTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCG                         GACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
genomic: CTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
EST: gi|22818916|gb|BU499006.1|BU499006
EST:     TACAATATACAATTGCACTGATGGGATTGCG                         GACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
genomic: TACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
EST: gi|87157223|gb|DY402012.1|DY402012
EST:     CTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCG                         GACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA
genomic: CTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCA

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: 90

AACATACTCCTGTAGGAGATATGGTCAAGCAAATGCTGACATAGAGAAAGCTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCAGTTACTTATCAGGTTTCTAAACGAAGGGGCATGTCAATTACGAGAAACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 90

AACATACTCCTGTAGGAGATATGGTCAAGCAAATGCTGACATAGAGAAAGCTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCAGTTACTTATCAGGTTTCTAAACGAAGGGGCATGTCAATTACGAGAAACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

AACATACTCCTGTAGGAGATATGGTCAAGCAAATGCTGACATAGAGAAAGCTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCAGTTACTTATCAGGTTTCTAAACGAAGGGGCATGTCAATTACGAGAAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

AACATACTCCTGTAGGAGATATGGTCAAGCAAATGCTGACATAGAGAAAGCTTGGAGATATTTGTATCATACAATATACAATTGCACTGATGGGATTGCGgtgtgatttc ... ttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCAGTTACTTATCAGGTTTCTAAACGAAGGGGCATGTCAATTACGAGAAACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactatccagagcctgtctgtatagtaacatgtcctttcatattttggttgcagGACCATAATAAAGACTATATAGTTGAATTTCCAGACATAAGTCCCAGCTCAGTTACTTATCAGGTTTCTAAACGAAGGGGCATGTCAATTACGAGAAACC
                       tagtaac  putative branch site (score: 75)
                                 tcctttcatatttt  putative PPT
                                    tttcatatttt  TA-rich tract