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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcttgatttatttttcttttctcaccctttcccccatttcttgtagtttacactttcatggtttcctcttctgcagGAATTCCTCATTAATCAAAAGCGTCCAAAGACAACGAGGGTAACTCAAGTGATTCAAGGTTATGAGAGTCATGCTTTCAAGTCCAAGTTTGAATCGTGGC

Basic information

species Zea mays
transcript GRMZM2G047310_T02
intron # 8
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|76284001|gb|DV023569.1|DV023569
EST:     GACGGGTAACACAAATGGAGGATAGAAAATCTGCCACTAAAGCAGTTGAT                         GAATTCCTCATTAATCAAAAGCGTCCAAAGACAACGAGGGTAACTCAAGTG
genomic: GACGGGTAACACAAATGGAGGATAGAAAATCTGCCACTAAAGCAGTTGATgtaaattctt ... tcttctgcagGAATTCCTCATTAATCAAAAGCGTCCAAAGACAACGAGGGTAACTCAAGTG




















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: 11 (upstream exon), 49 (downstream exon)
Score: 320

TACCAAATGTTTCTTACTTGACTGTGGGGCTGAAATATATGTATGGGTTGGACGGGTAACACAAATGGAGGATAGAAAATCTGCCACTAAAGCAGTTGATgtaaattctt ... tcttctgcagGAATTCCTCATTAATCAAAAGCGTCCAAAGACAACGAGGGTAACTCAAGTGATTCAAGGTTATGAGAGTCATGCTTTCAAGTCCAAGTTTGAATCGTGGC


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

TACCAAATGTTTCTTACTTGACTGTGGGGCTGAAATATATGTATGGGTTGGACGGGTAACACAAATGGAGGATAGAAAATCTGCCACTAAAGCAGTTGATgtaaattctt ... tcttctgcagGAATTCCTCATTAATCAAAAGCGTCCAAAGACAACGAGGGTAACTCAAGTGATTCAAGGTTATGAGAGTCATGCTTTCAAGTCCAAGTTTGAATCGTGGC


Block sizes: 11 (upstream exon), 49 (downstream exon)
Score: 223

TACCAAATGTTTCTTACTTGACTGTGGGGCTGAAATATATGTATGGGTTGGACGGGTAACACAAATGGAGGATAGAAAATCTGCCACTAAAGCAGTTGATgtaaattctt ... tcttctgcagGAATTCCTCATTAATCAAAAGCGTCCAAAGACAACGAGGGTAACTCAAGTGATTCAAGGTTATGAGAGTCATGCTTTCAAGTCCAAGTTTGAATCGTGGC


Block sizes: 11 (upstream exon), 49 (downstream exon)
Score: 278

TACCAAATGTTTCTTACTTGACTGTGGGGCTGAAATATATGTATGGGTTGGACGGGTAACACAAATGGAGGATAGAAAATCTGCCACTAAAGCAGTTGATgtaaattctt ... tcttctgcagGAATTCCTCATTAATCAAAAGCGTCCAAAGACAACGAGGGTAACTCAAGTGATTCAAGGTTATGAGAGTCATGCTTTCAAGTCCAAGTTTGAATCGTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaccctttcccccatttcttgtagtttacactttcatggtttcctcttctgcagGAATTCCTCATTAATCAAAAGCGTCCAAAGACAACGAGGGTAACTCAAGTGATTCAAGGTTATGAGAGTCATGCTTTCAAGTCCAAGTTTGAATCGTGGC
 ttctcac  putative branch site (score: 278)
                                        tttcctcttctgc  putative PPT
              atttctt  TA-rich tract