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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGTTATCCCAAAAATATGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCAGATTCAGgtttctgttataactgagttattattatgatattagaaagggtctatcttctattgttatcactcttttgaattgaaaacctctttggttcattctgttt...

Basic information

species Zea mays
transcript GRMZM2G168913_T01
intron # 6
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|78118889|gb|DV537273.1|DV537273
EST:     TGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCATATTCAG                         GCATCCGGAGGACAGTTACTTGGAAGGCCTGCGCCATCACCTGAAACCACA
genomic: TGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCAGATTCAGgtttctgtta ... ctacttgcagGCATCCGGAGGACAGTTACTTGGAAGGCCTGCGCCATCACCTGGAACCACA
EST: gi|76287277|gb|DV026845.1|DV026845
EST:     TGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCAGATTCAG                         GCATCCGGAGGACAGTTACTTGGAAGGCC
genomic: TGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCAGATTCAGgtttctgtta ... ctacttgcagGCATCCGGAGGACAGTTACTTGGAAGGCC

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: 47 (upstream exon), 49 (downstream exon)
Score: 316

GTAGTTATCCCAAAAATATGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCAGATTCAGgtttctgtta ... ctacttgcagGCATCCGGAGGACAGTTACTTGGAAGGCCTGCGCCATCACCTGGAACCACAGGAACCCCTAATTTCGAGAATGTGTCCACTCCTCCAATGCCATATGCTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 127

GTAGTTATCCCAAAAATATGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCAGATTCAGgtttctgtta ... ctacttgcagGCATCCGGAGGACAGTTACTTGGAAGGCCTGCGCCATCACCTGGAACCACAGGAACCCCTAATTTCGAGAATGTGTCCACTCCTCCAATGCCATATGCTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 166

GTAGTTATCCCAAAAATATGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCAGATTCAGgtttctgtta ... ctacttgcagGCATCCGGAGGACAGTTACTTGGAAGGCCTGCGCCATCACCTGGAACCACAGGAACCCCTAATTTCGAGAATGTGTCCACTCCTCCAATGCCATATGCTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 144

GTAGTTATCCCAAAAATATGTCAACATTTGCACCTAATAGTGTCAACAGCCAGGGAAATCAGATTCAGgtttctgtta ... ctacttgcagGCATCCGGAGGACAGTTACTTGGAAGGCCTGCGCCATCACCTGGAACCACAGGAACCCCTAATTTCGAGAATGTGTCCACTCCTCCAATGCCATATGCTA