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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaatgttctatttactatatcttccaaagttgaaacatgtagtggtagactatttcaatgggggtgtgagggtgtctatttatttctaactagt...

Basic information

species Zea mays
transcript GRMZM2G043056_T01
intron # 13
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|60358393|gb|DN225366.1|DN225366
EST:     CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC                         GCAACAAGGTTTGGGATACCTCCAGCCAAACANNNNNNNACCTTCATACGG
genomic: CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGG
EST: gi|60357017|gb|DN223990.1|DN223990
EST:     CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC                         GCAACAAGGTTTGGGATACCTCCAGCCAAACACCCC---ACCTTCATACGG
genomic: CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGG
EST: gi|60355844|gb|DN222817.1|DN222817
EST:     CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC                         GCAACAAGGTTTGGGATACCTCCAGCCAAACANNNNNNNACCTTCATACGG
genomic: CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGG
EST: gi|60338909|gb|DN205882.1|DN205882
EST:     CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC                         GCAACAAGGTTTGGGATACCTCCAGCCAAACACCCC---ACCTTCATACGG
genomic: CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGG
EST: gi|78115032|gb|DV533420.1|DV533420
EST:     CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC                         GCAACAAGGTTTGGGATACCTCCAGCCAAACANNNNNNNACCTTCATACGG
genomic: CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGG
EST: gi|211019067|gb|FL469808.1|FL469808
EST:     CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC                         GCAACAAGGTTTGGGATACCTCCAGCCAAACACCCC---ACCTTCATACGG
genomic: CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGG
EST: gi|31361667|gb|CD446024.1|CD446024
EST:     CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC                         GCAACAAGGTTTGGGATACCTCCAGCCAAACACCCC---ACCTTCATACGG
genomic: CCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGG

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: 264

GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGGCTCCGTTGGGGGTAGTAATCCATTCGGGTAAAAGAAGTGTGGGAACACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGGCTCCGTTGGGGGTAGTAATCCATTCGGGTAAAAGAAGTGTGGGAACACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGGCTCCGTTGGGGGTAGTAATCCATTCGGGTAAAAGAAGTGTGGGAACACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 108

GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAACgtgagtaaat ... gacatcgcagGCAACAAGGTTTGGGATACCTCCAGCCAAACACCCCCCCACCTTCATACGGCTCCGTTGGGGGTAGTAATCCATTCGGGTAAAAGAAGTGTGGGAACACC