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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGGATAGCTGAAGGAGTTGATTGCATTGCTCTATCATTTGTAAATGATGCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGAgtgagtagatagcttccacttacttcctaatgctctaaaatatccatagttatttgttgcttgagagctgcttaaaatatacataaggactgtagaatgt...

Basic information

species Zea mays
transcript GRMZM2G177947_T02
intron # 4
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|149106831|gb|EE188728.2|EE188728
EST:     GCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGA                         GCACATCAAAG
genomic: GCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGAgtgagtagat ... tgtataacagGCACATCAAAG
EST: gi|9732862|gb|BE511614.1|BE511614
EST:     GCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGA                         GCACATCAAAGTATTTGCAAAGATTGAGAGTCTAGAATCTCTCAAGAACCT
genomic: GCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGAgtgagtagat ... tgtataacagGCACATCAAAGTATTTGCAAAGATTGAGAGTCTAGAATCTCTCAAGAACCT
EST: gi|76012665|gb|DT939835.1|DT939835
EST:     GCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGA                         GCACATCAAAGTATTTG
genomic: GCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGAgtgagtagat ... tgtataacagGCACATCAAAGTATTTG

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: 77

TTGGGATAGCTGAAGGAGTTGATTGCATTGCTCTATCATTTGTAAATGATGCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGAgtgagtagat ... tgtataacagGCACATCAAAGTATTTGCAAAGATTGAGAGTCTAGAATCTCTCAAGAACCTGAAAGACATCATAGAGGCATCTGATGGAGTTATGGTAGCACGAGGGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

TTGGGATAGCTGAAGGAGTTGATTGCATTGCTCTATCATTTGTAAATGATGCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGAgtgagtagat ... tgtataacagGCACATCAAAGTATTTGCAAAGATTGAGAGTCTAGAATCTCTCAAGAACCTGAAAGACATCATAGAGGCATCTGATGGAGTTATGGTAGCACGAGGGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 28

TTGGGATAGCTGAAGGAGTTGATTGCATTGCTCTATCATTTGTAAATGATGCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGAgtgagtagat ... tgtataacagGCACATCAAAGTATTTGCAAAGATTGAGAGTCTAGAATCTCTCAAGAACCTGAAAGACATCATAGAGGCATCTGATGGAGTTATGGTAGCACGAGGGGAT


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

TTGGGATAGCTGAAGGAGTTGATTGCATTGCTCTATCATTTGTAAATGATGCTAATGATATAAAGCAGTTGAAAGCTTACCTCTCTAGAAGATCGTTAGAgtgagtagat ... tgtataacagGCACATCAAAGTATTTGCAAAGATTGAGAGTCTAGAATCTCTCAAGAACCTGAAAGACATCATAGAGGCATCTGATGGAGTTATGGTAGCACGAGGGGAT