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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcggtggcacccagttccagccacctcctcatgctatctcctcagcgattgccgctcgtctcacagctgcttcatggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATCTGAAT

Basic information

species Zea mays
transcript GRMZM2G042981_T01
intron # 1
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|71442985|gb|DR824035.1|DR824035
EST:     GCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACG                         AATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATC
genomic: GCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACGgtacgtcggt ... atggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATC
EST: gi|78080011|gb|DV508423.1|DV508423
EST:     GCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACG                         AATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATC
genomic: GCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACGgtacgtcggt ... atggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATC
EST: gi|211054708|gb|FL185984.1|FL185984
EST:     GCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACG                         AATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATC
genomic: GCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACGgtacgtcggt ... atggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATC

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: 73

GGCGGCGTGCCCTGGAACCGGGTGGAACTTACGCTGCTCGTACTCTACGCGCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACGgtacgtcggt ... atggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATCTGAAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 28

GGCGGCGTGCCCTGGAACCGGGTGGAACTTACGCTGCTCGTACTCTACGCGCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACGgtacgtcggt ... atggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATCTGAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 35

GGCGGCGTGCCCTGGAACCGGGTGGAACTTACGCTGCTCGTACTCTACGCGCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACGgtacgtcggt ... atggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATCTGAAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 38

GGCGGCGTGCCCTGGAACCGGGTGGAACTTACGCTGCTCGTACTCTACGCGCTGGGCTTCTACCTCGTCGTGATCTGGAGGTCGCTTCGCCTCTCGCACGgtacgtcggt ... atggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATCTGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgctatctcctcagcgattgccgctcgtctcacagctgcttcatggttgcagAATATTCCGGGAGGCTCTACGGACTACGCGTGGGATCACTTGCGGGTCATCTGAAT
                             gtctcac  putative branch site (score: 38)