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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccactggtatagcatctcgatcctagtttccttttctgtttggttgaatgctatatgtatttttcatgtttgatcactgatataaaagcctttggtgcagCCAATTAGCAACTATGCTATCGCATACCCGCAACAGCCTGGAATGGTCGGCTTACCAACTGCTATTCCAGGTTCTCAATCAGACCTTACAGCATATGCTC

Basic information

species Physcomitrella patens
transcript PP1S12_239V6.1
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|162270407|gb|FC447107.1|FC447107
EST:     CAATGGGCTATGTAACGGCTCCTCCCCCTTACAATGGTTACCCTTACCAG                         CCAATTAGCAACTATGCTATCGCATACCCGCAACAGCCTGGAATGGTCGGC
genomic: CAATGGGCTATGTAACGGCTCCTCCCCCTTACAATGGTTACCCTTACCAGgtgataattt ... tttggtgcagCCAATTAGCAACTATGCTATCGCATACCCGCAACAGCCTGGAATGGTCGGC
EST: gi|208353532|gb|DC938725.1|DC938725
EST:     CAATGGGCTATGTAACGGCTCCTCCCCCTTACAATGGTTACCNT-ACCAG                         CCA-TTAGCA-CTATGCTATCGCATACC
genomic: CAATGGGCTATGTAACGGCTCCTCCCCCTTACAATGGTTACCCTTACCAGgtgataattt ... tttggtgcagCCAATTAGCAACTATGCTATCGCATACC

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 1 RNA-Seqlibrary.


Block sizes: 30 (upstream exon), 35 (downstream exon)
Score: 6

TTCTTCCCCTCCTATACCCGGTCAGCAACCATCTATTTTTGGTGCTGTACCAATGGGCTATGTAACGGCTCCTCCCCCTTACAATGGTTACCCTTACCAGgtgataattt ... tttggtgcagCCAATTAGCAACTATGCTATCGCATACCCGCAACAGCCTGGAATGGTCGGCTTACCAACTGCTATTCCAGGTTCTCAATCAGACCTTACAGCATATGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgctatatgtatttttcatgtttgatcactgatataaaagcctttggtgcagCCAATTAGCAACTATGCTATCGCATACCCGCAACAGCCTGGAATGGTCGGCTTACCAACTGCTATTCCAGGTTCTCAATCAGACCTTACAGCATATGCTC
                             cactgat  putative branch site (score: 6)
                                           ccttt  putative PPT
      tatatgtatttttcat  TA-rich tract