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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgttatcattacacatctatttacatcctttaaataaatacatccattaaactttgataaatgtatttgaaaacctgcag

Basic information

species Zea mays
transcript GRMZM2G059381_T01
intron # 17
splice site 5'
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|33090935|gb|CF050929.1|CF050929
EST:     GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAAC                         AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
EST: gi|87153602|gb|DY398391.1|DY398391
EST:     GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAAC                         AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
EST: gi|19350747|gb|BM895279.1|BM895279
EST:     GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAAC                         AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
EST: gi|60395514|gb|DN228384.1|DN228384
EST:     GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAAC                         AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
EST: gi|58030032|gb|CX725459.1|CX725459
EST:     GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAAC                         AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
EST: gi|93283329|gb|EB675593.1|EB675593
EST:     GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAAC                         AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
EST: gi|32847207|gb|CD986888.1|CD986888
EST:     GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAAC                         AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
EST: gi|211308069|gb|FL216534.1|FL216534
EST:     GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAAC                         AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTT

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: 61

AAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

AAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

AAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

AAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgtt ... aaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGGTTACTATAAAGATGAAGTCCAAACgtaacttgttatcattacacatctatttacatcctttaaataaatacatccattaaactttgataaatgtatttgaaaacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG