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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctcttgtacccattccgccattccgtgaaattaacggttttatgtcattgttgattatcgctaaatgctaatgacatgatgagattgtttggcg...

Basic information

species Zea mays
transcript GRMZM2G080722_T02
intron # 2
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|6587608|gb|AW244926.1|AW244926
EST:     CCACCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211138214|gb|FL122277.1|FL122277
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGAC
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGAC
EST: gi|211393122|gb|FK956090.1|FK956090
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395750|gb|FK956107.1|FK956107
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395748|gb|FK956105.1|FK956105
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211393118|gb|FK956086.1|FK956086
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211393127|gb|FK956095.1|FK956095
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|32908833|gb|CF013646.1|CF013646
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|116818678|gb|EC861726.1|EC861726
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395745|gb|FK956102.1|FK956102
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211393125|gb|FK956093.1|FK956093
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211393120|gb|FK956088.1|FK956088
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395747|gb|FK956104.1|FK956104
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211137287|gb|FL122274.1|FL122274
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211138215|gb|FL122278.1|FL122278
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395746|gb|FK956103.1|FK956103
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211393121|gb|FK956089.1|FK956089
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395743|gb|FK956100.1|FK956100
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211393123|gb|FK956091.1|FK956091
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211138212|gb|FL122275.1|FL122275
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395741|gb|FK956098.1|FK956098
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTWATCCAGCAGTTTATGAACTATTCATCAGGTCT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCT-ATCCAGCAGTTTATGAACTATTCATCAGGTCT
EST: gi|211215605|gb|FL316840.1|FL316840
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211138213|gb|FL122276.1|FL122276
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395742|gb|FK956099.1|FK956099
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACTAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211138217|gb|FL122280.1|FL122280
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTA
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTA
EST: gi|211395740|gb|FK956097.1|FK956097
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211138218|gb|FL122281.1|FL122281
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395752|gb|FK956109.1|FK956109
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211395751|gb|FK956108.1|FK956108
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|32908771|gb|CF013584.1|CF013584
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|32908664|gb|CF013477.1|CF013477
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211138219|gb|FL122282.1|FL122282
EST:     CCGCCCTCATGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|149051827|gb|EE155954.2|EE155954
EST:     CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
EST: gi|211138216|gb|FL122279.1|FL122279
EST:     CSGCCCTCATGAGGGRACTTATGAGATCGTCCCGTGCATCGACATCAGCT                         GCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT
genomic: CCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTT

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), 48 (downstream exon)
Score: 152

GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTTAGTGGCACTCCTAATGCAAATGGGGACTCAGTGACAACACGAGTAGCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 159

GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTTAGTGGCACTCCTAATGCAAATGGGGACTCAGTGACAACACGAGTAGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 85

GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTTAGTGGCACTCCTAATGCAAATGGGGACTCAGTGACAACACGAGTAGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 180

GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctct ... ttttgcgcagGCTGTGTCACGACCAGCTATCCAGCAGTTTATGAACTATTCATCAGGTCTTAGTGGCACTCCTAATGCAAATGGGGACTCAGTGACAACACGAGTAGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTACCATGGCAAGATCACTCTCCACCGCCCTCGTGAGGGGACTTATGAGATCGTCCCGTGCATCGACATCAGCTgtaaggctcttgtacccattccgccattccgtgaaattaacggttttatgtcattgttgattatcgctaaatgctaatgacatgatgagattgtttggcg

- - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT