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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacacacacacacacaggcttgttaactgttattgtattcacaacactcgcttgtttttctgttctgcttaacgtctgtctcggtttggtctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGTTCCTGTTCACTACGGCCGAATGGCTGGAGACCAGGGCGAGCCACAAG

Basic information

species Zea mays
transcript GRMZM2G099191_T01
intron # 2
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|89754996|gb|DY685578.1|DY685578
EST:     GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAG                         TTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
genomic: GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
EST: gi|149004834|gb|EE039339.2|EE039339
EST:     GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAG                         TTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
genomic: GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
EST: gi|149070628|gb|EE159039.2|EE159039
EST:     GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAG                         TTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
genomic: GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
EST: gi|24765848|gb|CA401007.1|CA401007
EST:     TCAACATACTCATGCTCATCGCAG                         TTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGAGT
genomic: TCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
EST: gi|148934257|gb|EC878279.2|EC878279
EST:     GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAG                         TTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
genomic: GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
EST: gi|149079488|gb|EE168465.2|EE168465
EST:     GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAG                         TTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
genomic: GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
EST: gi|149103749|gb|EE289155.2|EE289155
EST:     GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCAT--C--                         TTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT
genomic: GCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGT

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: 242

CTGGCGGCGGCGGCCGCCGGCCTGCCGCCGATCGCCCTCAGGAGCTTCGCGGCCGCGCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGTTCCTGTTCACTACGGCCGAATGGCTGGAGACCAGGGCGAGCCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

CTGGCGGCGGCGGCCGCCGGCCTGCCGCCGATCGCCCTCAGGAGCTTCGCGGCCGCGCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGTTCCTGTTCACTACGGCCGAATGGCTGGAGACCAGGGCGAGCCACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 393

CTGGCGGCGGCGGCCGCCGGCCTGCCGCCGATCGCCCTCAGGAGCTTCGCGGCCGCGCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGTTCCTGTTCACTACGGCCGAATGGCTGGAGACCAGGGCGAGCCACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 328

CTGGCGGCGGCGGCCGCCGGCCTGCCGCCGATCGCCCTCAGGAGCTTCGCGGCCGCGCGGAGGCTCACCCTCGACGTCAACATACTCATGCTCATCGCAGgtaaacacaa ... ctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGTTCCTGTTCACTACGGCCGAATGGCTGGAGACCAGGGCGAGCCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcgcttgtttttctgttctgcttaacgtctgtctcggtttggtctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGTTCCTGTTCACTACGGCCGAATGGCTGGAGACCAGGGCGAGCCACAAG
                     gcttaac  putative branch site (score: 328)
                                            tctgctt  putative PPT
      ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacacacacacacacaggcttgttaactgttattgtattcacaacactcgcttgtttttctgttctgcttaacgtctgtctcggtttggtctgcttgcagTTTCCGGGGCGATAGCTCTCAAGGACTACTCCGAGGCTGGGTTCATCGTGTTCCTGTTCACTACGGCCGAATGGCTGGAGACCAGGGCGAGCCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
-acacaca
- - - - - - cacaggc
- - - - - - - - - - - - - - - - - - - -cacaaca