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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgtcatcaactttcatctgttcttttgcttcattatctgctttcgtcttctttttctggaagctaaatttattctgtatcttttcattttttggcagTTGATCATGTGTTCTTCAAG

Basic information

species Zea mays
transcript GRMZM2G130351_T01
intron # 6
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|78118655|gb|DV537039.1|DV537039
EST:     GAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATG                         TTGATCATGTGTTCTTCAAG
genomic: GAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATGgtatgcatca ... tttttggcagTTGATCATGTGTTCTTCAAG
EST: gi|149081470|gb|EE170604.2|EE170604
EST:     GAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATG                         TTGATCATGTGTTCTTCAAG
genomic: GAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATGgtatgcatca ... tttttggcagTTGATCATGTGTTCTTCAAG
EST: gi|148953215|gb|EE152697.2|EE152697
EST:     GAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATG                         TTGATCATGTGTTCTTCAAG
genomic: GAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATGgtatgcatca ... tttttggcagTTGATCATGTGTTCTTCAAG
EST: gi|76021633|gb|DT948803.1|DT948803
EST:     GAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATG                         TTGATCATGTGTTCTTCAAG
genomic: GAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATGgtatgcatca ... tttttggcagTTGATCATGTGTTCTTCAAG

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), 20 (downstream exon)
Score: 69

GCTGTGAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATGgtatgcatca ... tttttggcagTTGATCATGTGTTCTTCAAG


Block sizes: 47 (upstream exon), 20 (downstream exon)
Score: 16

GCTGTGAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATGgtatgcatca ... tttttggcagTTGATCATGTGTTCTTCAAG


Block sizes: 46 (upstream exon), 20 (downstream exon)
Score: 13

GCTGTGAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATGgtatgcatca ... tttttggcagTTGATCATGTGTTCTTCAAG


Block sizes: 46 (upstream exon), 16 (downstream exon)
Score: 7

GCTGTGAAAGACAAGTTGAGCCAAGTTGCACGTTCCATCGGTCAATCTGCAAATGgtatgcatca ... tttttggcagTTGATCATGTGTTCTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtcttctttttctggaagctaaatttattctgtatcttttcattttttggcagTTGATCATGTGTTCTTCAAG
                  agctaaa  putative branch site (score: 7)
                             ttctgtatcttttcat  putative PPT
                     taaatttattctgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgtcatcaactttcatctgttcttttgcttcattatctgctttcgtcttctttttctggaagctaaatttattctgtatcttttcattttttggcagTTGATCATGTGTTCTTCAAG

- - - - - - ctttcat
- - - - - - - - - - - - -ttttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtatc