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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaacatgattgtcagttataaaacttgcctgactggttatataactttatcgaatctgctatgatcgttgacatctgaaaatgttcatcgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAACATCAATAAGATCGCATACCCGGACTTATTGCCTTCGACCTCTGTTATTG

Basic information

species Zea mays
transcript GRMZM2G056078_T01
intron # 3
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|211523857|gb|FL149373.1|FL149373
EST:     TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
genomic: TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
EST: gi|211523863|gb|FL149379.1|FL149379
EST:     TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGTGGCTCCATCTGATATCACCTCATATGA
genomic: TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGA
EST: gi|116820025|gb|EC863204.1|EC863204
EST:     TCCTTCCTAAGCGTAAACCTCTGACTGAGGAAGAGATTGAGGCTATTATG                         CTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
genomic: TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
EST: gi|44681853|gb|CK786901.1|CK786901
EST:     TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
genomic: TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
EST: gi|211523849|gb|FL149365.1|FL149365
EST:     TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
genomic: TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
EST: gi|211526858|gb|FL149380.1|FL149380
EST:     TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAA
genomic: TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAA
EST: gi|211523854|gb|FL149370.1|FL149370
EST:     TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
genomic: TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
EST: gi|5499310|gb|AI855177.1|AI855177
EST:     TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATG                         CTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC
genomic: TCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAAC

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: 461

AGATGTGCCTTCCCCACCGTCGCATACTGCTGTAGGAGGTCAAGCTTCACTCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAACATCAATAAGATCGCATACCCGGACTTATTGCCTTCGACCTCTGTTATTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 352

AGATGTGCCTTCCCCACCGTCGCATACTGCTGTAGGAGGTCAAGCTTCACTCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAACATCAATAAGATCGCATACCCGGACTTATTGCCTTCGACCTCTGTTATTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 270

AGATGTGCCTTCCCCACCGTCGCATACTGCTGTAGGAGGTCAAGCTTCACTCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAACATCAATAAGATCGCATACCCGGACTTATTGCCTTCGACCTCTGTTATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 553

AGATGTGCCTTCCCCACCGTCGCATACTGCTGTAGGAGGTCAAGCTTCACTCCTTCCTAAGCGTAAACCTCTGACTGAAGAAGAGATTGAGGCTATTATGgtatgccttt ... cgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAACATCAATAAGATCGCATACCCGGACTTATTGCCTTCGACCTCTGTTATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttatcgaatctgctatgatcgttgacatctgaaaatgttcatcgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAACATCAATAAGATCGCATACCCGGACTTATTGCCTTCGACCTCTGTTATTG
                                  aaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggaacatgattgtcagttataaaacttgcctgactggttatataactttatcgaatctgctatgatcgttgacatctgaaaatgttcatcgcattgcagCTGGGTGGCTCCATCTGATATCACCTCATATGAATTGGAATTTCTAGGAACATCAATAAGATCGCATACCCGGACTTATTGCCTTCGACCTCTGTTATTG

- - -catgatt
- - - - - - - - - - - - - -tgcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctatg