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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttacttatgtttactgaccatgaaaacttttttttttaaacacagtgatgactaatgaggaagtgaggcagatatatcttggtgatgtattttgattgaagtcaactttgtagaggaggagcttatacaatgtatatttgcagAAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAATGGATGCATCCAGCTTTGACGCCTTGGCCACGGGTGCAGTATTCGGTGA

Basic information

species Zea mays
transcript GRMZM2G158162_T03
intron # 11
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|148956308|gb|EC902110.2|EC902110
EST:     TGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAG                         AAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAGA
genomic: TGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAGgtaagattta ... atatttgcagAAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAA
EST: gi|60397624|gb|DN230440.1|DN230440
EST:     TGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAG                         AAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAA
genomic: TGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAGgtaagattta ... atatttgcagAAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAA

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: 109

CTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAGgtaagattta ... atatttgcagAAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAATGGATGCATCCAGCTTTGACGCCTTGGCCACGGGTGCAGTATTCGGTGA


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 84

CTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAGgtaagattta ... atatttgcagAAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAATGGATGCATCCAGCTTTGACGCCTTGGCCACGGGTGCAGTATTCGGTGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 79

CTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAGgtaagattta ... atatttgcagAAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAATGGATGCATCCAGCTTTGACGCCTTGGCCACGGGTGCAGTATTCGGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

CTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAGgtaagattta ... atatttgcagAAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAATGGATGCATCCAGCTTTGACGCCTTGGCCACGGGTGCAGTATTCGGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgattgaagtcaactttgtagaggaggagcttatacaatgtatatttgcagAAATGAGGAGGCGAAAGGGCAGCTATGGTCTGAAGCTGAATGTCGCTGAAATGGATGCATCCAGCTTTGACGCCTTGGCCACGGGTGCAGTATTCGGTGA
 ttttgat  putative branch site (score: 243)
                                  ttatacaatgtatatt  TA-rich tract