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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaattctcgcaatgttatcatcaatgctgagaccttggcgttgtttcgatccgttaatattcaaatatactagtgtattattcttgattcaatgtgcacGCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGATGCCAGGCCCGACCATTTTTTGAATCTTATTCATTATGAG

Basic information

species Physcomitrella patens
transcript PP1S91_170V6.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

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|67691913|gb|BJ952146.1|BJ952146
EST:     AGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATAT                         GCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGAT
genomic: AGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATATatatcctcca ... caatgtgcacGCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGAT
EST: gi|15261388|gb|BI436698.1|BI436698
EST:     AGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATAT                         GCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGAT
genomic: AGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATATatatcctcca ... caatgtgcacGCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGAT
EST: gi|67508687|gb|BJ941548.1|BJ941548
EST:     AGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATAT                         GCTCGGGATCGTGGAGCGCACATGTACTGGCTT
genomic: AGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATATatatcctcca ... caatgtgcacGCTCGGGATCGTGGAGCGCACATGTACTGGCTT
EST: gi|208395303|gb|DC915945.1|DC915945
EST:     AGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATAT                         GCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGAT
genomic: AGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATATatatcctcca ... caatgtgcacGCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGAT

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: 28 (upstream exon), 35 (downstream exon)
Score: 10

AACTGAGAAAGGAACGAGCCCTCGTGGGGATAGATTGCTGAATGCGGAGGAGGAGGTTTTGAAGGTCGATGGAAACGTTGTACGATTGGCAGGCCTATATatatcctcca ... caatgtgcacGCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGATGCCAGGCCCGACCATTTTTTGAATCTTATTCATTATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgatccgttaatattcaaatatactagtgtattattcttgattcaatgtgcacGCTCGGGATCGTGGAGCGCACATGTACTGGCTTCAAAAAGGAACAGTAGATGCCAGGCCCGACCATTTTTTGAATCTTATTCATTATGAG
                                   attcttgat  putative branch site 
         ttaatattcaaatata  TA-rich tract