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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggttccacctttttcaatttcaatcatgtgtgtacttcagttaattaacactattcgataatttggtttgtttgtagCTTCCTCCTTTACTGTAGACTGTGGGAGTAGTAGATCTGTATTTGCTTCAGATAATTCCATGTATCAACCTGATGATGCCAATCTTGGTGTTGCATCATA

Basic information

species Zea mays
transcript GRMZM2G126858_T01
intron # 14
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|31558038|gb|CD527250.1|CD527250
EST:     TTCAGCGAAACACGTCATGCTTTCTTGGCTCTCCACAAT                         CTTCCTCCTTTACTGTAGACTGTGGGAGTAGTAGATCTGTATTTGCTTCAG
genomic: TTCAGCGAAACACGTCATGCTTTCTTGGCTCTCCACAATgtgaggttcc ... ttgtttgtagCTTCCTCCTTTACTGTAGACTGTGGGAGTAGTAGATCTGTATTTGCTTCAG




















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), 48 (downstream exon)
Score: 27

TGTCTTACCTGCGGGGCTGGAGTGCCTTCAGCGAAACACGTCATGCTTTCTTGGCTCTCCACAATgtgaggttcc ... ttgtttgtagCTTCCTCCTTTACTGTAGACTGTGGGAGTAGTAGATCTGTATTTGCTTCAGATAATTCCATGTATCAACCTGATGATGCCAATCTTGGTGTTGCATCATA


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 22

TGTCTTACCTGCGGGGCTGGAGTGCCTTCAGCGAAACACGTCATGCTTTCTTGGCTCTCCACAATgtgaggttcc ... ttgtttgtagCTTCCTCCTTTACTGTAGACTGTGGGAGTAGTAGATCTGTATTTGCTTCAGATAATTCCATGTATCAACCTGATGATGCCAATCTTGGTGTTGCATCATA


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 14

TGTCTTACCTGCGGGGCTGGAGTGCCTTCAGCGAAACACGTCATGCTTTCTTGGCTCTCCACAATgtgaggttcc ... ttgtttgtagCTTCCTCCTTTACTGTAGACTGTGGGAGTAGTAGATCTGTATTTGCTTCAGATAATTCCATGTATCAACCTGATGATGCCAATCTTGGTGTTGCATCATA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 24

TGTCTTACCTGCGGGGCTGGAGTGCCTTCAGCGAAACACGTCATGCTTTCTTGGCTCTCCACAATgtgaggttcc ... ttgtttgtagCTTCCTCCTTTACTGTAGACTGTGGGAGTAGTAGATCTGTATTTGCTTCAGATAATTCCATGTATCAACCTGATGATGCCAATCTTGGTGTTGCATCATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatgtgtgtacttcagttaattaacactattcgataatttggtttgtttgtagCTTCCTCCTTTACTGTAGACTGTGGGAGTAGTAGATCTGTATTTGCTTCAGATAATTCCATGTATCAACCTGATGATGCCAATCTTGGTGTTGCATCATA
                    aattaac  putative branch site (score: 24)
 tttgttt  putative PPT
 ttaattaacactatt  TA-rich tract