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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatttattttctttctacatatggagcagtcataaactgtagcaatttctcaaaacgtcaaacagtcatctgctatgtttgcctgttatctttatgcttgccatgtactgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGACCTGAAAGAACTTGTTTCGAAGTTCATTCCAGAAGTTATTGGTAAGGAGA

Basic information

species Zea mays
transcript GRMZM2G145258_T01
intron # 4
splice site 3'
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|211215691|gb|FL434867.1|FL434867
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|149105848|gb|EE291447.2|EE291447
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|17921801|gb|BM259452.1|BM259452
EST:     CAANCCAAGTCAAGAGANCCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|24767178|gb|CA402322.1|CA402322
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGAAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|213178623|gb|FM189778.1|FM189778
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTACGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|31360389|gb|CD444746.1|CD444746
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGAAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|84977073|gb|DW475495.1|DW475495
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|19770034|gb|BQ034755.1|BQ034755
EST:     CCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|16377119|gb|BI991771.1|BI991771
EST:     TGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: TGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|12971869|gb|BG267698.1|BG267698
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|18384904|gb|BM418103.1|BM418103
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCGTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|5005674|gb|AI711736.1|AI711736
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|31359742|gb|CD444099.1|CD444099
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGAAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|18168263|gb|BM338103.1|BM338103
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|31357009|gb|CD441366.1|CD441366
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGAAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|37376013|gb|CF624502.1|CF624502
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGACATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|83279071|gb|DV943079.1|DV943079
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|67018238|gb|CO446987.1|CO446987
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|213183157|gb|FM184569.1|FM184569
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|84351598|gb|DW246003.1|DW246003
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|67042647|gb|CO468902.1|CO468902
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|67013865|gb|CO442614.1|CO442614
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|4837583|gb|AI670673.1|AI670673
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCCCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTGTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|84977492|gb|DW475914.1|DW475914
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCAT-CCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|13490883|gb|BG517647.1|BG517647
EST:     TGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: TGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|95107896|gb|EB740125.1|EB740125
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
EST: gi|4647336|gb|AI622411.1|AI622411
EST:     CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAG                         ATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACCATGTGA
genomic: CAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTA-CATGTGA
EST: gi|5871099|gb|AW017540.1|AW017540
EST:     TGCTCAGGCATCCCAGATCCGTCAG                         ATCCCCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC
genomic: TGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGAC

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: 2276

CGACAACTACATGTTGCGTTTGTTCTGCATCGGCTTCACCAAGAGGCGCCCAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGACCTGAAAGAACTTGTTTCGAAGTTCATTCCAGAAGTTATTGGTAAGGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1861

CGACAACTACATGTTGCGTTTGTTCTGCATCGGCTTCACCAAGAGGCGCCCAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGACCTGAAAGAACTTGTTTCGAAGTTCATTCCAGAAGTTATTGGTAAGGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1869

CGACAACTACATGTTGCGTTTGTTCTGCATCGGCTTCACCAAGAGGCGCCCAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGACCTGAAAGAACTTGTTTCGAAGTTCATTCCAGAAGTTATTGGTAAGGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1120

CGACAACTACATGTTGCGTTTGTTCTGCATCGGCTTCACCAAGAGGCGCCCAAACCAAGTCAAGAGAACCTGCTATGCTCAGGCATCCCAGATCCGTCAGgtaacattta ... ctgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGACCTGAAAGAACTTGTTTCGAAGTTCATTCCAGAAGTTATTGGTAAGGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtcatctgctatgtttgcctgttatctttatgcttgccatgtactgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGACCTGAAAGAACTTGTTTCGAAGTTCATTCCAGAAGTTATTGGTAAGGAGA
                       ttatctttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatttattttctttctacatatggagcagtcataaactgtagcaatttctcaaaacgtcaaacagtcatctgctatgtttgcctgttatctttatgcttgccatgtactgtgtgcagATCCGCCGTAAGATGGTTGAGATTATGATCAACCAGGCTTCTACATGTGACCTGAAAGAACTTGTTTCGAAGTTCATTCCAGAAGTTATTGGTAAGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA