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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accatcgaaatgtaaagaatattgtttgaccccgcgccatggcgaccttgattatttttttttttgcatgaactgacccaagatttttcttgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGTACTTAAAAACACCTGTGATGGCTACAATGCGGCCTGTCTGATGTTCCTAAC

Basic information

species Zea mays
transcript GRMZM5G837018_T01
intron # 15
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|32929791|gb|CF034603.1|CF034603
EST:     AAGACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAG                         GATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
genomic: AACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
EST: gi|32928858|gb|CF033670.1|CF033670
EST:     AAGACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAG                         GATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
genomic: AACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
EST: gi|32929234|gb|CF034046.1|CF034046
EST:     AAGACAAAAAAGAACATTCTGGCAGCCACGATTTCAGTCTGCACAGAAAG                         GATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
genomic: AACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
EST: gi|32929010|gb|CF033822.1|CF033822
EST:     AAGACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAG                         GATCTGTGGTCCACGGAAAGGAAATGACAGGCCTCGAGATCCTTCTGGT
genomic: AACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
EST: gi|32929217|gb|CF034029.1|CF034029
EST:     AAGACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAG                         GATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
genomic: AACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
EST: gi|32928591|gb|CF033403.1|CF033403
EST:     AAGACAACAAGGAACATTCTGGCAGCCACGATTTCAGTCTGCACAGAAAG                         GATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT
genomic: AACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGT

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), 47 (downstream exon)
Score: 91

ACCTACGGCATTCTTTTCTACTCCAGAAAAACCTAAGGAGGCTCAGTCCCAACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGTACTTAAAAACACCTGTGATGGCTACAATGCGGCCTGTCTGATGTTCCTAAC


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 13

ACCTACGGCATTCTTTTCTACTCCAGAAAAACCTAAGGAGGCTCAGTCCCAACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGTACTTAAAAACACCTGTGATGGCTACAATGCGGCCTGTCTGATGTTCCTAAC


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 16

ACCTACGGCATTCTTTTCTACTCCAGAAAAACCTAAGGAGGCTCAGTCCCAACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGTACTTAAAAACACCTGTGATGGCTACAATGCGGCCTGTCTGATGTTCCTAAC


Block sizes: 46 (upstream exon), 36 (downstream exon)
Score: 14

ACCTACGGCATTCTTTTCTACTCCAGAAAAACCTAAGGAGGCTCAGTCCCAACACAACAAGGAACATTCTGGCAGCCATGATTTCAGTCTGCACAGAAAGgtaaactgtt ... tgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGTACTTAAAAACACCTGTGATGGCTACAATGCGGCCTGTCTGATGTTCCTAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgattatttttttttttgcatgaactgacccaagatttttcttgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGTACTTAAAAACACCTGTGATGGCTACAATGCGGCCTGTCTGATGTTCCTAAC
                         aactgac  putative branch site (score: 14)
                                      tttttcttgcc  putative PPT
     attatttttttttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accatcgaaatgtaaagaatattgtttgaccccgcgccatggcgaccttgattatttttttttttgcatgaactgacccaagatttttcttgccgtgcagGATCTGTGGTCCACGGAAAGGAAATGACGGGCCTCGAGATCCTTCTGGTACTTAAAAACACCTGTGATGGCTACAATGCGGCCTGTCTGATGTTCCTAAC

- - - - - - -aaagaata
- - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - -gccatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaactg