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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaactaacaatgccggtgcatgaaacaatttgttgatcattcaacaagaacatgaccaaatcatttctgttgcagTCATTGAGACTATATCCACAGCCGCCGGTTTTAATTCGTAGGTCACTTGAGGACGATATCCTGGGAGGGTACCCAATTGGCCG

Basic information

species Zea mays
transcript GRMZM5G837869_T01
intron # 10
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|211191075|gb|FL114972.1|FL114972
EST:     CAATTGAGGATGTGAAGAAACTAAAGTACACGACTCGGGTTATTAATGAA                         TCATTGAGACTATATCCACAGCCGCCGGTTTTAATTCGTAGGTCACTTGAG
genomic: CAATTGAGGATGTGAAGAAACTAAAGTACACGACTCGGGTTATTAATGAAgtaagaaact ... tctgttgcagTCATTGAGACTATATCCACAGCCGCCGGTTTTAATTCGTAGGTCACTTGAG




















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

GCTGATAGTGTTCTAGGTGATGGTTTGCCAACAATTGAGGATGTGAAGAAACTAAAGTACACGACTCGGGTTATTAATGAAgtaagaaact ... tctgttgcagTCATTGAGACTATATCCACAGCCGCCGGTTTTAATTCGTAGGTCACTTGAGGACGATATCCTGGGAGGGTACCCAATTGGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

GCTGATAGTGTTCTAGGTGATGGTTTGCCAACAATTGAGGATGTGAAGAAACTAAAGTACACGACTCGGGTTATTAATGAAgtaagaaact ... tctgttgcagTCATTGAGACTATATCCACAGCCGCCGGTTTTAATTCGTAGGTCACTTGAGGACGATATCCTGGGAGGGTACCCAATTGGCCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 71

GCTGATAGTGTTCTAGGTGATGGTTTGCCAACAATTGAGGATGTGAAGAAACTAAAGTACACGACTCGGGTTATTAATGAAgtaagaaact ... tctgttgcagTCATTGAGACTATATCCACAGCCGCCGGTTTTAATTCGTAGGTCACTTGAGGACGATATCCTGGGAGGGTACCCAATTGGCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 102

GCTGATAGTGTTCTAGGTGATGGTTTGCCAACAATTGAGGATGTGAAGAAACTAAAGTACACGACTCGGGTTATTAATGAAgtaagaaact ... tctgttgcagTCATTGAGACTATATCCACAGCCGCCGGTTTTAATTCGTAGGTCACTTGAGGACGATATCCTGGGAGGGTACCCAATTGGCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaacaatttgttgatcattcaacaagaacatgaccaaatcatttctgttgcagTCATTGAGACTATATCCACAGCCGCCGGTTTTAATTCGTAGGTCACTTGAGGACGATATCCTGGGAGGGTACCCAATTGGCCG
          tgttgat  putative branch site (score: 102)
                                        tcatttct  putative PPT
                                     aaatcattt  TA-rich tract