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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGATGGAGTGAATATTTCAGCCAATGCAGTTCATCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTGgtatttcctcaagtcttgcaatcagttttatttatcatatgagtagcagaatagggaagggtttgtagcttctgaaaaacatttacatggatctcaagttaaaatatcataggtaactgttatccctaccttgcag

Basic information

species Zea mays
transcript GRMZM2G464885_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|71448014|gb|DR829064.1|DR829064
EST:     TCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTG                         CTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG
genomic: TCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTGgtatttcctc ... taccttgcagCTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG
EST: gi|71433931|gb|DR814981.1|DR814981
EST:     TCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTTTG                         CTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG
genomic: TCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTGgtatttcctc ... taccttgcagCTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG
EST: gi|60341574|gb|DN208547.1|DN208547
EST:     TCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTG                         CTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG
genomic: TCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTGgtatttcctc ... taccttgcagCTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG
EST: gi|71433932|gb|DR814982.1|DR814982
EST:     TCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTG                         CTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG
genomic: TCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTGgtatttcctc ... taccttgcagCTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 24 (downstream exon)
Score: 9

GAGGATGGAGTGAATATTTCAGCCAATGCAGTTCATCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTGgtatttcctc ... taccttgcagCTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG


Block sizes: 38 (upstream exon), 31 (downstream exon)
Score: 9

GAGGATGGAGTGAATATTTCAGCCAATGCAGTTCATCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTGgtatttcctc ... taccttgcagCTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG


Block sizes: 41 (upstream exon), 42 (downstream exon)
Score: 9

GAGGATGGAGTGAATATTTCAGCCAATGCAGTTCATCCTGGTGTCATCATGACTAACCTTTTTAGGAACAGGACTATTGTCTCTGgtatttcctc ... taccttgcagCTTTACTGAACTCCATTGGAAGAATCATATGTAGAACAGTTGAGCAG