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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGAAGCAGCTGAGAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatgtctaaccctctatgcttgtgtctttaaactacctttttccaattcttactgcaagatagcatgcttcatgttgtgccgatttttaaggat...

Basic information

species Zea mays
transcript GRMZM2G343688_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G343688_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g37630.1 (Oryza sativa), 5'ss of exon 3
CCAAGAAGCAGCTGAGAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatgtctaaccctctatgcttgtgtctttaaactacctttttccaattcttactgcaagatagcatgctt-catgttgtgccgatttttaaggat-------
|||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||| ||||||||| ||||||      | ||  ||| ||    | |   | | | |||| ||   |  ||||| |  | ||||   ||||  || |||    | |  |||    |        
CCAAGAAGCAGCTGAGAAAGAAGCCGCTCTTGCAAGGAGGAGACAAGAGAAGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgt------tcacattctttgtccatcttccttatcaacctgttatga--tcttattctaggataatgtgctgacaagttacaaccacatttgtctacttttgat
















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|211061442|gb|FL105773.1|FL105773
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCANAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|9953320|gb|BE639903.1|BE639903
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|78083899|gb|DV512292.1|DV512292
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTTTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTTTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|211470731|gb|FL464832.1|FL464832
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|76288092|gb|DV027660.1|DV027660
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|89246999|gb|DY618785.1|DY618785
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTTTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|148946845|gb|EC892122.2|EC892122
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|9961361|gb|BE644254.1|BE644254
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|148958551|gb|EC904794.2|EC904794
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|78111230|gb|DV529627.1|DV529627
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|211329018|gb|FL455397.1|FL455397
EST:     AGACCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCACCTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|23357488|gb|BU645137.1|BU645137
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|9461590|gb|BE453807.1|BE453807
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|149075103|gb|EE163593.2|EE163593
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTTTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|211329017|gb|FL455396.1|FL455396
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|14245022|gb|BG842960.2|BG842960
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|149104942|gb|EE290413.2|EE290413
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTTTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTTTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|211061441|gb|FL105772.1|FL105772
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|50336583|gb|CO531709.1|CO531709
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
EST: gi|14203011|gb|BG836688.1|BG836688
EST:     AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGG                         GTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT
genomic: AGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGT

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: 47 (upstream exon), 47 (downstream exon)
Score: 180

CCAAGAAGCAGCTGAGAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGTTCTGCAACCGTCGCTTCCCTCTATGACTATGTCGATTCTCTAGACTGCA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 220

CCAAGAAGCAGCTGAGAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGTTCTGCAACCGTCGCTTCCCTCTATGACTATGTCGATTCTCTAGACTGCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 235

CCAAGAAGCAGCTGAGAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGTTCTGCAACCGTCGCTTCCCTCTATGACTATGTCGATTCTCTAGACTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 263

CCAAGAAGCAGCTGAGAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatg ... gacttggcagGTTCTCATAAGATTCCCAACTGGAGAGCGCAGAGAGCGGAGATTCTACAGTTCTGCAACCGTCGCTTCCCTCTATGACTATGTCGATTCTCTAGACTGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGAAGCAGCTGAGAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatgtctaaccctctatgcttgtgtctttaaactacctttttccaattcttactgcaagatagcatgcttcatgttgtgccgatttttaaggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA