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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttcttactcaagaatgaattagcaaaataccctacaggattcagaagcactgatccttgtttctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 12
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|211174464|gb|FL381682.1|FL381682
EST:     GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|67027757|gb|CO456506.1|CO456506
EST:     GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|32935034|gb|CF039846.1|CF039846
EST:     GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|211459151|gb|FL411539.1|FL411539
EST:     ACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: ACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|211215524|gb|FL427999.1|FL427999
EST:     GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|32844417|gb|CD984098.1|CD984098
EST:     GTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|67019408|gb|CO448157.1|CO448157
EST:     GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|211214717|gb|FL394674.1|FL394674
EST:     GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|67037452|gb|CO464268.1|CO464268
EST:     GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
EST: gi|67010832|gb|CO439581.1|CO439581
EST:     GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCA                         GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT
genomic: GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCT

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: 628

GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 735

GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 623

GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1301

GAACACTGTTGATAGAGCCTAAACCACAGGAACCTACAAAACACCAgtaagcttct ... tctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattagcaaaataccctacaggattcagaagcactgatccttgtttctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG
                               cactgat  putative branch site (score: 1301)
                                     tccttgtttctctcgc  CT-rich tract
       aaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttcttactcaagaatgaattagcaaaataccctacaggattcagaagcactgatccttgtttctctcgcagGTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT