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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGTGACTATGGCCACGGCGGGGGGCAGATGCGGGGCAACCCGGACTCCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccaccgatcccctcgtctcccctgctaaaccctaaccctagctgcctgattcgtctctgatccgtggtttggtttcacctcgctcgcag

Basic information

species Zea mays
transcript GRMZM2G113592_T02
intron # 1
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|148969418|gb|EE020215.2|EE020215
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|148978947|gb|EE026414.2|EE026414
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCCCCCGACGGGGCTCACGCCCCACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|211227314|gb|FL251475.1|FL251475
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|211227313|gb|FL251474.1|FL251474
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGANGGGGCTCACGCCCAACCTRCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|149078708|gb|EE167506.2|EE167506
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|71312602|gb|DR792823.1|DR792823
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|91873232|gb|EB403189.1|EB403189
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|89759256|gb|DY688127.1|DY688127
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|31358158|gb|CD442515.1|CD442515
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|91052321|gb|EB162739.1|EB162739
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|148967855|gb|EE019150.2|EE019150
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|149072504|gb|EE160783.2|EE160783
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|211227312|gb|FL251473.1|FL251473
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|211227315|gb|FL251476.1|FL251476
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|71310643|gb|DR791619.1|DR791619
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|91051679|gb|EB162097.1|EB162097
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
EST: gi|211227311|gb|FL251472.1|FL251472
EST:     CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTC                         ATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC
genomic: CCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTC

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: 877

GATGGGTGACTATGGCCACGGCGGGGGGCAGATGCGGGGCAACCCGGACTCCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTCGAACCGCGTCCACCGCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 516

GATGGGTGACTATGGCCACGGCGGGGGGCAGATGCGGGGCAACCCGGACTCCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTCGAACCGCGTCCACCGCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 557

GATGGGTGACTATGGCCACGGCGGGGGGCAGATGCGGGGCAACCCGGACTCCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTCGAACCGCGTCCACCGCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 704

GATGGGTGACTATGGCCACGGCGGGGGGCAGATGCGGGGCAACCCGGACTCCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccacc ... tcgctcgcagATGGGGCAGATCCACCCGACGGGGCTCACGCCCAACCTGCTTAAGCTCTTCGAACCGCGTCCACCGCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGTGACTATGGCCACGGCGGGGGGCAGATGCGGGGCAACCCGGACTCCCGCCCCAGGGGCCAGGGCCAGCGCCCTAACGTCCAGCAGCTCAAGCTCgtaagccaccgatcccctcgtctcccctgctaaaccctaaccctagctgcctgattcgtctctgatccgtggtttggtttcacctcgctcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT