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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcagcttacaagttagccctgtaaaaggtgacgttgatatctttttgtgatttctattgacattattttgttgtttgtgcatgcttcttgtttggcagGTTGTGATGCCCTCACTTGCTCG

Basic information

species Physcomitrella patens
transcript PP1S68_234V6.1
intron # 5
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|18348518|gb|BJ180567.1|BJ180567
EST:     AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG                         GTTGTGATGCCCTCACTTGCTCG
genomic: AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatc ... tgtttggcagGTTGTGATGCCCTCACTTGCTCG
EST: gi|100391368|gb|BY971622.1|BY971622
EST:     AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG                         GTTGTGATGCCCTCACTTGCTCG
genomic: AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatc ... tgtttggcagGTTGTGATGCCCTCACTTGCTCG
EST: gi|208353776|gb|DC906464.1|DC906464
EST:     AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG                         GTTGTGATGCCCTCACTTGCTCG
genomic: AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatc ... tgtttggcagGTTGTGATGCCCTCACTTGCTCG
EST: gi|100441829|gb|BY981052.1|BY981052
EST:     AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG                         GTTGTGATGCCCTCACTTGCTCG
genomic: AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatc ... tgtttggcagGTTGTGATGCCCTCACTTGCTCG
EST: gi|208400731|gb|DC904909.1|DC904909
EST:     AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG                         GTTGTGATGCCCTCACTTGCTCG
genomic: AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatc ... tgtttggcagGTTGTGATGCCCTCACTTGCTCG
EST: gi|208365198|gb|DC931164.1|DC931164
EST:     AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG                         GTTGTGATGCCCTCACTTGCTCG
genomic: AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatc ... tgtttggcagGTTGTGATGCCCTCACTTGCTCG
EST: gi|100451564|gb|CJ974830.1|CJ974830
EST:     AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG                         GTTGTGATGCCCTCACTTGCTCG
genomic: AGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatc ... tgtttggcagGTTGTGATGCCCTCACTTGCTCG

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: 12 (upstream exon), 26 (downstream exon)
Score: 2

ACTTTTGATGCTGTTGATGGCAAGCAAGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatc ... tgtttggcagGTTGTGATGCCCTCACTTGCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgatttctattgacattattttgttgtttgtgcatgcttcttgtttggcagGTTGTGATGCCCTCACTTGCTCG
           tattgac  putative branch site (score: 2)
                                        cttcttgttt  putative PPT
           tattgacattatttt  TA-rich tract