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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtcatgcagaatatcactttatgccattgagaactaaatttttttggacataacaacctaagagtgattaatcttcgctgtcattttatattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG

Basic information

species Zea mays
transcript GRMZM2G107575_T01
intron # 2
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|86466680|gb|DY233050.1|DY233050
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|86468277|gb|DY234647.1|DY234647
EST:     TGTTCAAGAACATAAGTGGTTCGGAGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|149079633|gb|EE168627.2|EE168627
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|101388735|gb|EB816351.1|EB816351
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|91053272|gb|EB163690.1|EB163690
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|32799975|gb|CD952211.1|CD952211
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTA
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTA
EST: gi|78085933|gb|DV514326.1|DV514326
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|32804727|gb|CD956963.1|CD956963
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTA
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTA
EST: gi|211199934|gb|FL305445.1|FL305445
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|149016909|gb|EE045638.2|EE045638
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|211202489|gb|FL305452.1|FL305452
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|76018012|gb|DT945182.1|DT945182
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|71427887|gb|DR808937.1|DR808937
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|32799514|gb|CD951750.1|CD951750
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTA
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTA
EST: gi|20208081|gb|BQ134170.1|BQ134170
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|32809691|gb|CD961925.1|CD961925
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTA
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTA
EST: gi|211199933|gb|FL305444.1|FL305444
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGWATTCCAGCTAGCACTATTNTAAGAATCAGAGGAAAGAAAATCCTTT
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATT-TAAGAATCAGAGGAAAGAAAATC-TTT
EST: gi|211199938|gb|FL305449.1|FL305449
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|26456204|gb|CA827787.1|CA827787
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|91052665|gb|EB163083.1|EB163083
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
EST: gi|71317611|gb|DR795553.1|DR795553
EST:     TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAG                         GAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC
genomic: TGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTC

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: 191

TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 122

TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

TCAGCGTTAGTGAGGTTGAGGCTCTATTCGAGCTGTTCAAGAGCATAAGTGGTTCGGTGATTGATGATGGCCTGATCAACAAGgtatattcta ... tattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggacataacaacctaagagtgattaatcttcgctgtcattttatattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG
                      gattaat  putative branch site (score: 222)
                                   tgtcattttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtcatgcagaatatcactttatgccattgagaactaaatttttttggacataacaacctaagagtgattaatcttcgctgtcattttatattgcgtagGAAGAATTCCAGCTAGCACTATTTAAGAATCAGAGGAAAGAAAATCTTTTCGCCAATCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- -tcatgca
- - - - - - - - - - - -tgccatt
- - - - - - - - - - - - - - - - -aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -aacaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtca