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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattcagccttggagataacattgacgtttaactgcttattatcgttgccacactgacattaagacttgctatctgttgcag

Basic information

species Zea mays
transcript GRMZM2G329306_T01
intron # 9
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|71329028|gb|DR801213.1|DR801213
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTTTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|211484888|gb|FL049377.1|FL049377
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|32930877|gb|CF035689.1|CF035689
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|113703884|gb|EE681388.1|EE681388
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|211517927|gb|FL479799.1|FL479799
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|149051834|gb|EE155961.2|EE155961
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|78124365|gb|DV542749.1|DV542749
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTTTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|71443878|gb|DR824928.1|DR824928
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|60350322|gb|DN217295.1|DN217295
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|32930670|gb|CF035482.1|CF035482
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|76017867|gb|DT945037.1|DT945037
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|88756258|gb|DY540399.1|DY540399
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTTTGTTTTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|32930642|gb|CF035454.1|CF035454
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|149012518|gb|EE042586.2|EE042586
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATTTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTTTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG
EST: gi|211145441|gb|FL467393.1|FL467393
EST:     TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG                         GAGTCTCATGGGAGTCTGCTCTGCNNNNNNNCGCAGATTACTGATCTTTAG
genomic: TCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAG

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), 48 (downstream exon)
Score: 65

GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAGATAGAAGGAAACATAGTGGGGGGAAAGGAAGCTTTTGTTTTCTTGTACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAGATAGAAGGAAACATAGTGGGGGGAAAGGAAGCTTTTGTTTTCTTGTACT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 56

GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAGATAGAAGGAAACATAGTGGGGGGAAAGGAAGCTTTTGTTTTCTTGTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAGgtctgattca ... tctgttgcagGAGTCTCATGGGAGTCTGCTCTGCAAAAAAACGCAGATTACTGATCTTTAGATAGAAGGAAACATAGTGGGGGGAAAGGAAGCTTTTGTTTTCTTGTACT