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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagtgctaaatttacagcagctacaactgtctcagtgagctggaatgcatgtgcctgacttgcggcggcatggttttgaaattctcag

Basic information

species Zea mays
transcript GRMZM2G027115_T01
intron # 11
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|32921306|gb|CF026118.1|CF026118
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|211114268|gb|FL244779.1|FL244779
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|76018985|gb|DT946155.1|DT946155
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGA
EST: gi|18169104|gb|BM338944.1|BM338944
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGATGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|15499363|gb|BI595876.1|BI595876
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|18169085|gb|BM338925.1|BM338925
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAT                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAG
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAG
EST: gi|15426986|gb|BI542808.1|BI542808
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
EST: gi|71447208|gb|DR828258.1|DR828258
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGA
EST: gi|211114263|gb|FL244774.1|FL244774
EST:     TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAG                         GCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA
genomic: TCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGA

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), 48 (downstream exon)
Score: 149

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 69

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 54

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagt ... aaattctcagGCCAACTTTCCTTCGCTCGAGAGCTTGATAGAGAGAATTCACGAGGATGGAAGAGTAGCAGAGAAGGCACTAGACCTGCCAATGTATGCCAAGTACAAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACCTTGGCTGCTTCATAATTTCGGCGAGGACTTCTATGGCGAGGAGGTGCGCCTTGCCATCGTTGGCTACATAAGACCTGAGgtaattgagtgctaaatttacagcagctacaactgtctcagtgagctggaatgcatgtgcctgacttgcggcggcatggttttgaaattctcag

- - - - - - - - - - - - - - - - - - - - - GAGGAG