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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAGCCGGGCGGACGGATTGATCCCGGGACGAGGTGTCTCAGCTCTTGATCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccgctcttttgatcccgcaaagttttttctttcgtttttgcaaatataatttgttattaggccggtgaatgatctttagtctttaccctggtc...

Basic information

species Zea mays
transcript GRMZM2G180720_T01
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|211337284|gb|FL086335.1|FL086335
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|32910888|gb|CF015700.1|CF015700
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|71764560|gb|DR962497.1|DR962497
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|14244707|gb|BG842645.2|BG842645
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|60355224|gb|DN222197.1|DN222197
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|211337287|gb|FL086338.1|FL086338
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|76923753|gb|DV169644.1|DV169644
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|211337285|gb|FL086336.1|FL086336
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|101390817|gb|EB817343.1|EB817343
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAA
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|37418356|gb|CF646846.1|CF646846
EST:     CTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCCGA-G                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCA
genomic: CTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGC-GAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCA
EST: gi|32863719|gb|CF003401.1|CF003401
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|32920066|gb|CF024878.1|CF024878
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|30031984|gb|CB833835.1|CB833835
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|71440960|gb|DR822010.1|DR822010
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|211459513|gb|FL086339.1|FL086339
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|60355230|gb|DN222203.1|DN222203
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|211337286|gb|FL086337.1|FL086337
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|32915160|gb|CF019972.1|CF019972
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
EST: gi|91868372|gb|EB400012.1|EB400012
EST:     TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: TCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG

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: 268

TTGAGCCGGGCGGACGGATTGATCCCGGGACGAGGTGTCTCAGCTCTTGATCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 499

TTGAGCCGGGCGGACGGATTGATCCCGGGACGAGGTGTCTCAGCTCTTGATCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 564

TTGAGCCGGGCGGACGGATTGATCCCGGGACGAGGTGTCTCAGCTCTTGATCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 566

TTGAGCCGGGCGGACGGATTGATCCCGGGACGAGGTGTCTCAGCTCTTGATCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccg ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAGCCGGGCGGACGGATTGATCCCGGGACGAGGTGTCTCAGCTCTTGATCTTGATCCTGATCCTGGGAGGCGTTCCTGGTTTATTGGTGGGAGCGAAGgtgagatccgctcttttgatcccgcaaagttttttctttcgtttttgcaaatataatttgttattaggccggtgaatgatctttagtctttaccctggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG