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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattttgggtgatcgacgctgcagacaaatttgtgcagattttggtgctttgcgataccgctatttgacggcttgtaatgttgatctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCACGAG

Basic information

species Zea mays
transcript GRMZM2G082664_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|211015453|gb|FL446495.1|FL446495
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|71433814|gb|DR814864.1|DR814864
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|211035970|gb|FL104470.1|FL104470
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGGCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTT
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTT
EST: gi|76924992|gb|DV170232.1|DV170232
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|148945041|gb|EC890225.2|EC890225
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|149003162|gb|EE038900.2|EE038900
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|211035971|gb|FL104471.1|FL104471
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCACGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|211038407|gb|FL104474.1|FL104474
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|149028361|gb|EE286119.2|EE286119
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|88758154|gb|DY542295.1|DY542295
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|211038406|gb|FL104473.1|FL104473
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|116827363|gb|EC871258.1|EC871258
EST:     GCGGAGGTTTGGCCTGTGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAATGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
EST: gi|211038408|gb|FL104475.1|FL104475
EST:     GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGG                         CTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC
genomic: GCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCAC

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: 117

GGATCATTTGGCGCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

GGATCATTTGGCGCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GGATCATTTGGCGCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

GGATCATTTGGCGCGGAGGTTTGGCCTGGGAAAATGGCAAACATACGTGCACTTCTGGTCGGgtaagatttt ... tctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtgctttgcgataccgctatttgacggcttgtaatgttgatctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCACGAG
                                       tgttgat  putative branch site (score: 212)
                                             tctcccac  CT-rich tract
                      tatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattttgggtgatcgacgctgcagacaaatttgtgcagattttggtgctttgcgataccgctatttgacggcttgtaatgttgatctcccacagCTTATCGCGGGCAAGGGGATCCTTAGCAGAGGCTGGACGATGTGCTTCCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA