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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtcttcgatccggcgtcttctcctcccccgattgtcccgggatctttttccgacctaagtttgggcggttgctccaaaccctagtctctccctctgctaggctagccagtggtgtgctggggcgctggagcagccttggatctgcgggttttgattggtgtctcctcgcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA

Basic information

species Zea mays
transcript GRMZM2G114513_T02
intron # 1
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|211095367|gb|FL067776.1|FL067776
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211097837|gb|FL067788.1|FL067788
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211079577|gb|FL056323.1|FL056323
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211097840|gb|FL067791.1|FL067791
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|21760018|gb|BQ635559.1|BQ635559
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211095370|gb|FL067779.1|FL067779
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211095362|gb|FL067771.1|FL067771
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCAATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211095368|gb|FL067777.1|FL067777
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211092897|gb|FL067767.1|FL067767
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211097835|gb|FL067786.1|FL067786
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211095373|gb|FL067782.1|FL067782
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211095375|gb|FL067784.1|FL067784
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|9254928|gb|BE345396.1|BE345396
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211097834|gb|FL067785.1|FL067785
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211095371|gb|FL067780.1|FL067780
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211092899|gb|FL067769.1|FL067769
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211095369|gb|FL067778.1|FL067778
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
EST: gi|211095366|gb|FL067775.1|FL067775
EST:     TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAG                         GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC
genomic: TCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCC

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: 209

CGCCCAGGAAATGGCGTCGATGCAGAGCTGGCGCAAGGCCTACGGCGCCATCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA


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

CGCCCAGGAAATGGCGTCGATGCAGAGCTGGCGCAAGGCCTACGGCGCCATCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

CGCCCAGGAAATGGCGTCGATGCAGAGCTGGCGCAAGGCCTACGGCGCCATCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

CGCCCAGGAAATGGCGTCGATGCAGAGCTGGCGCAAGGCCTACGGCGCCATCAAGGACACCACAACCGTTAGCCTCGCCAACCTCAACTCGGACTTCAAGgtgtgtcttc ... gcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctggagcagccttggatctgcgggttttgattggtgtctcctcgcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA
                          ttttgat  putative branch site (score: 198)
                                    tgtctcctcgctttt  putative PPT
                          ttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtcttcgatccggcgtcttctcctcccccgattgtcccgggatctttttccgacctaagtttgggcggttgctccaaaccctagtctctccctctgctaggctagccagtggtgtgctggggcgctggagcagccttggatctgcgggttttgattggtgtctcctcgcttttgtagGATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG