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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttgcgagatttagtatactgaacaatatcattgggtcaacattcttttttcagagtgataacattctggacaattgtgtttttttgtgcagAAAGGCGATCAACAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGGCACAG

Basic information

species Zea mays
transcript GRMZM2G014577_T01
intron # 13
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|74234427|gb|DT642341.1|DT642341
EST:     TCAGCAAGGCAATATCTTCAGCAAAAACCGAAGAGGAAAAAACTAAAATT                         AAAGGCGATCAACAAACTTCAACAAGGACAATGAGGTCATATAACAATATA
genomic: TCAGCAAGGCAATATCTTCAGCAAAAACCGAAGAGGAAAAAACTAAAATTgtgagttttt ... ttttgtgcagAAAGGCGATCAACAAACTTCAACAAGGACAATGAGGTCATATAACAATATA




















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), 47 (downstream exon)
Score: 137

AGAGACGGTAAGAGCAGCCTCAAAGCGACTAACTCAGGGAATGGCAGATTTCAGCAAGGCAATATCTTCAGCAAAAACCGAAGAGGAAAAAACTAAAATTgtgagttttt ... ttttgtgcagAAAGGCGATCAACAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGGCACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

AGAGACGGTAAGAGCAGCCTCAAAGCGACTAACTCAGGGAATGGCAGATTTCAGCAAGGCAATATCTTCAGCAAAAACCGAAGAGGAAAAAACTAAAATTgtgagttttt ... ttttgtgcagAAAGGCGATCAACAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGGCACAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 128

AGAGACGGTAAGAGCAGCCTCAAAGCGACTAACTCAGGGAATGGCAGATTTCAGCAAGGCAATATCTTCAGCAAAAACCGAAGAGGAAAAAACTAAAATTgtgagttttt ... ttttgtgcagAAAGGCGATCAACAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGGCACAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 74

AGAGACGGTAAGAGCAGCCTCAAAGCGACTAACTCAGGGAATGGCAGATTTCAGCAAGGCAATATCTTCAGCAAAAACCGAAGAGGAAAAAACTAAAATTgtgagttttt ... ttttgtgcagAAAGGCGATCAACAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGGCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacattcttttttcagagtgataacattctggacaattgtgtttttttgtgcagAAAGGCGATCAACAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGGCACAG
                   tgataac  putative branch site (score: 74)
                                        tgttttttt  putative PPT
                                   aattgtgttttttt  TA-rich tract