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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgctatgttagctgcttcagaatgatatagctgatcattgttttgctagtaggagtagtgcttaatgtttttccattgttaattgcattcttttgagcagCCGAGAAGAGG

Basic information

species Zea mays
transcript GRMZM2G161969_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|20301579|gb|BQ164522.1|BQ164522
EST:     CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGGG
genomic: CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGA-GG
EST: gi|71329666|gb|DR801555.1|DR801555
EST:     CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGGG
genomic: CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGA-GG
EST: gi|113659135|gb|DW816431.1|DW816431
EST:     CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGG
genomic: CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGAGG
EST: gi|21809699|gb|BQ668017.1|BQ668017
EST:     CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGGG
genomic: CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGA-GG
EST: gi|5439400|gb|AI820321.1|AI820321
EST:     CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGGG
genomic: CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGA-GG
EST: gi|20208397|gb|BQ134486.1|BQ134486
EST:     CCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGGG
genomic: CCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGA-GG
EST: gi|5343148|gb|AI795333.1|AI795333
EST:     CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGG
genomic: CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGAGG
EST: gi|148935652|gb|EC879696.2|EC879696
EST:     CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGGG
genomic: CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGA-GG
EST: gi|4776441|gb|AI665444.1|AI665444
EST:     CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTG                         CCGAGAAGAGGG
genomic: CTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGA-GG

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), 47 (downstream exon)
Score: 180

GGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

GGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

GGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 463

GGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTTCTGgtaatgagtt ... ttttgagcagCCGAGAAGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagtaggagtagtgcttaatgtttttccattgttaattgcattcttttgagcagCCGAGAAGAGG
                               tgttaat  putative branch site (score: 463)
                                        cattctttt  putative PPT
                ttaatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgctatgttagctgcttcagaatgatatagctgatcattgttttgctagtaggagtagtgcttaatgtttttccattgttaattgcattcttttgagcagCCGAGAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - gctgctt
- - - - - - - - - - - - - - -gctgatc
- - - - - - - - - - - - - - - - - - - - ttttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattc