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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTCATCGACGACCGCTGGCCACCCCCTCGATCTCTTGACCCGGAGGCGAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgcccgattttgctctcagtctcagatccagtcattttccttcccatttattagtatttgggtagcctcgtggtggggtagaaaccttgattagt...

Basic information

species Zea mays
transcript GRMZM2G160316_T02
intron # 1
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|91056386|gb|EB166804.1|EB166804
EST:     CAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: CAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|78106644|gb|DV525062.1|DV525062
EST:     CAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: CAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|32850992|gb|CD990673.1|CD990673
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAA
EST: gi|9733695|gb|BE512447.1|BE512447
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|6626308|gb|AW257840.1|AW257840
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|32850990|gb|CD990671.1|CD990671
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|211363317|gb|FL163078.1|FL163078
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|5555318|gb|AI881269.1|AI881269
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|91877793|gb|EB407750.1|EB407750
EST:     CAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: CAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|31997958|gb|CD661849.1|CD661849
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|211365960|gb|FL163084.1|FL163084
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|211363315|gb|FL163076.1|FL163076
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|9794649|gb|BE552957.1|BE552957
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGTAGTCTGTCGCGGCTCTTATGGACTCG
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGG-AGTCTGTCGCGGCTCTTATGGACTCG
EST: gi|78082750|gb|DV511143.1|DV511143
EST:     CAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: CAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|211363320|gb|FL163081.1|FL163081
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|76282459|gb|DV022027.1|DV022027
EST:     CAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: CAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|211365961|gb|FL163085.1|FL163085
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|211363319|gb|FL163080.1|FL163080
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|211365959|gb|FL163083.1|FL163083
EST:     GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
EST: gi|211363316|gb|FL163077.1|FL163077
EST:     GAGGACGGGGGCCAGCAGCGGCSGGCAGCGCCTGCCCGTCTTGTTATAGG                         GAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA
genomic: GAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 724

TCTTTCATCGACGACCGCTGGCCACCCCCTCGATCTCTTGACCCGGAGGCGAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGACAAGCTCCAAGATACAACAGCTTCAGGAGGCATTCGCTGAGCTTGAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 224

TCTTTCATCGACGACCGCTGGCCACCCCCTCGATCTCTTGACCCGGAGGCGAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGACAAGCTCCAAGATACAACAGCTTCAGGAGGCATTCGCTGAGCTTGAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 391

TCTTTCATCGACGACCGCTGGCCACCCCCTCGATCTCTTGACCCGGAGGCGAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGACAAGCTCCAAGATACAACAGCTTCAGGAGGCATTCGCTGAGCTTGAGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 223

TCTTTCATCGACGACCGCTGGCCACCCCCTCGATCTCTTGACCCGGAGGCGAGGACGGGGGCCAGCAGCGGCCGCCAGCGCCTGCCCGTCTTGTTATAGGgtgagtgccc ... tttcttgcagGAGCGTTCGCCATGTCTGAAATGGAGTCTGTCGCGGCTCTTATGGACTCGACAAGCTCCAAGATACAACAGCTTCAGGAGGCATTCGCTGAGCTTGAGAG