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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatgcacagaattgcatgttattgttatttggaagctggttacttttgagtgtttttgttattgattatgcacgtgtaaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 5
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|148941319|gb|EC886225.2|EC886225
EST:     AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG                         GTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
genomic: AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
EST: gi|22472411|gb|BU036891.1|BU036891
EST:     AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG                         GTTGCAAAGGTGGTAGATGAGCTAGTAGAG
genomic: AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAG
EST: gi|21809491|gb|BQ667809.1|BQ667809
EST:     AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG                         GTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
genomic: AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
EST: gi|22541992|gb|BU092430.1|BU092430
EST:     AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG                         GTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGGG
genomic: AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGGG
EST: gi|211095653|gb|FK967022.1|FK967022
EST:     TATGGTATTTTTGGCCTTTGGAA-CAGGCAATACGAACATTTTAAATA-G                         GTTGCAAAGGTGGTAGATGAGCTAGTAGAAGAGCAGG
genomic: TATGGTATTTTTGGCCTT-GGAAACAGGCAATACGAACATTTTAA-TAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
EST: gi|211098118|gb|FK967027.1|FK967027
EST:     TATGGTATTTTTGGCCTTTGGAA-CAGGCAATACGAACATTTTAAATA-G                         GTTGCAAAGGTGGTAGATGAGCTAGTAGAAGAGCAGG
genomic: TATGGTATTTTTGGCCTT-GGAAACAGGCAATACGAACATTTTAA-TAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
EST: gi|148940766|gb|EC885587.2|EC885587
EST:     AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG                         GTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
genomic: AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
EST: gi|148970820|gb|EE021584.2|EE021584
EST:     AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG                         GTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
genomic: AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
EST: gi|19437265|gb|BM953675.1|BM953675
EST:     AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAG                         GTTGCAAAGGTGGTA
genomic: AATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTA

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), 37 (downstream exon)
Score: 520

GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 869

GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 802

GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 1485

GGAAAAGAGAAGGAAGTTTGGTTGAAGGATCTTAAATATGGTATTTTTGGCCTTGGAAACAGGCAATACGAACATTTTAATAAGgttaatgcac ... taaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagctggttacttttgagtgtttttgttattgattatgcacgtgtaaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG
                            tattgat  putative branch site (score: 1485)
                     tttttgttattgatta  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatgcacagaattgcatgttattgttatttggaagctggttacttttgagtgtttttgttattgattatgcacgtgtaaaatgcagGTTGCAAAGGTGGTAGATGAGCTAGTAGAGGAGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG