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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGGAGAGACTAGTTTCTGGTTCTGATGATTTTACAATGTTTCTTTGGGAACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctccagacaaaaatgtttcttttcttaggctgtgtaactaattaattgtttggttatatgcaactgtaggtgatgatttgtttgtttctttttgcag

Basic information

species Zea mays
transcript GRMZM2G157034_T02
intron # 11
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|211305745|gb|FK970548.1|FK970548
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
EST: gi|111433430|gb|EE297747.1|EE297747
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
EST: gi|148969157|gb|EE019898.2|EE019898
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
EST: gi|32939016|gb|CF043835.1|CF043835
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATG
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATG
EST: gi|33095385|gb|CF055379.1|CF055379
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCACATGACTGGTCATCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
EST: gi|33092990|gb|CF052984.1|CF052984
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
EST: gi|110202220|gb|EC884117.1|EC884117
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCTTCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
EST: gi|148960782|gb|EE011442.2|EE011442
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
EST: gi|32928456|gb|CF033268.1|CF033268
EST:     AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAG                         CTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA
genomic: AACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCA

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: 46 (upstream exon), 49 (downstream exon)
Score: 119

TCCGGAGAGACTAGTTTCTGGTTCTGATGATTTTACAATGTTTCTTTGGGAACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 151

TCCGGAGAGACTAGTTTCTGGTTCTGATGATTTTACAATGTTTCTTTGGGAACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 156

TCCGGAGAGACTAGTTTCTGGTTCTGATGATTTTACAATGTTTCTTTGGGAACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 108

TCCGGAGAGACTAGTTTCTGGTTCTGATGATTTTACAATGTTTCTTTGGGAACCAACAATTAGTAAACAACCTAAAGCTCGCATGACTGGTCATCAGAAGgtattgcctc ... ctttttgcagCTTGTAAACCATGTTTACTTTTCCCCTGATGGACAATGGTTGGCAAGTGCATCCTTTGATAAATCTGTCAAGTTGTGGAATGGTATCACAGGTAAATTTG