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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaaagactcggcggcgcaggcaacacaacttcttattggactcccttgatggaaatggattcattttcttgatatgtgtacgtttgtgtatgtgacagTGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAGCATATCACCCGGACAGAATCGTATTCTATTACTTCCCACCTATACGAAG

Basic information

species Physcomitrella patens
transcript PP1S93_56V6.3
intron # 1
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|100424092|gb|BY976661.1|BY976661
EST:     CAAGTAGCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAG                         TGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAG
genomic: CAAGTAGCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAGgtatgcttgt ... tatgtgacagTGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAG
EST: gi|67718133|gb|BJ968392.1|BJ968392
EST:     AAGTATGCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAG                         TGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAG
genomic: AAGTA-GCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAGgtatgcttgt ... tatgtgacagTGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAG
EST: gi|67717017|gb|BJ967276.1|BJ967276
EST:     CAAGTAGCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAG                         TGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAG
genomic: CAAGTAGCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAGgtatgcttgt ... tatgtgacagTGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAG
EST: gi|100377463|gb|BY968534.1|BY968534
EST:     CAAGTAGCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAG                         TGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAG
genomic: CAAGTAGCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAGgtatgcttgt ... tatgtgacagTGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAG

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), 23 (downstream exon)
Score: 7

AATCCCCAACCTTCTGATGTTGCTTCGTTGATAGACTTTGTCCAGGAGCACAAGTAGCGTCGTTGGATAACCATTTTAAGCCACAGTCATGATGCCGAAGgtatgcttgt ... tatgtgacagTGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAGCATATCACCCGGACAGAATCGTATTCTATTACTTCCCACCTATACGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgatggaaatggattcattttcttgatatgtgtacgtttgtgtatgtgacagTGTTGAACTCCGAGACGACCCAGTTTTAAAAGAAAGGGGATGAGGCAGGAGCATATCACCCGGACAGAATCGTATTCTATTACTTCCCACCTATACGAAG
                       tcttgat  putative branch site (score: 7)
               attcatttt  TA-rich tract