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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttggcatagttgatgtagttattttcgtatttcgctagtgttcttcttcggggttgcaatgtagaagtacttgtgttgtaaaaatgaattgca...

Basic information

species Zea mays
transcript GRMZM2G035417_T01
intron # 3
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|60356802|gb|DN223775.1|DN223775
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|211524990|gb|FL195258.1|FL195258
EST:     CGTCGAGTGGAGCTTCTACCACTACTGCTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGCCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|29130299|gb|CB381003.1|CB381003
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAG
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAG
EST: gi|71448259|gb|DR829309.1|DR829309
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|78121958|gb|DV540342.1|DV540342
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|211521980|gb|FL195242.1|FL195242
EST:     CGTCGAGTGGAGCTTCTACCACTACTGCTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGCCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|78107573|gb|DV525991.1|DV525991
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|9825075|gb|BE575292.1|BE575292
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|5566780|gb|AI881646.1|AI881646
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|94472331|gb|EB701289.1|EB701289
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAAACACC
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAA-CACC
EST: gi|20803264|gb|BQ294314.1|BQ294314
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|91876714|gb|EB406671.1|EB406671
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|211524983|gb|FL195251.1|FL195251
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAWCACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|74244160|gb|DT652074.1|DT652074
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|76908411|gb|DV162927.1|DV162927
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
EST: gi|89763929|gb|DY690917.1|DY690917
EST:     CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTG                         GGCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA
genomic: CATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCA

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: 530

GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 629

GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 415

GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 866

GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttg ... tttgcaatagGCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAAGGCATCATCGAGTGGAGCTTCTACCGCTACTACTGCAAAAGCTCCTGCAACTCTGgttagttttggcatagttgatgtagttattttcgtatttcgctagtgttcttcttcggggttgcaatgtagaagtacttgtgttgtaaaaatgaattgca

- - - - - - -  AGTGGA
- - - - - - - - GTGGAG
- - - - - - - - - GGAGCT
- - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatgaa