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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactccatcggtttatttgtgtgtttcattaatcatttttacaattgtccctgatctttgtttaactttatttatcatctgtctaacttcgattttgcagTGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTTCTGGGTTAGAGGTGATATTTTATTTAATATAGAACTTGGTTTCTCTATG

Basic information

species Physcomitrella patens
transcript PP1S87_139V6.2
intron # 12
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|37821905|gb|BJ579971.1|BJ579971
EST:     GATTTGGGGCGCCAGATATGAAGCCTGAGTTCACGAAGTTTGGTTCAGTG                         TGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTT
genomic: GATTTGGGGCGCCAGATATGAAGCCTGAGTTCACGAAGTTTGGTTCAGTGgtgcgtttcc ... gattttgcagTGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTT
EST: gi|208390866|gb|DC945897.1|DC945897
EST:     GATTTGGGGCGCCAGATATGAAGCCTGAGTTCACGAAGTTTGGTTCAGTG                         TGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTT
genomic: GATTTGGGGCGCCAGATATGAAGCCTGAGTTCACGAAGTTTGGTTCAGTGgtgcgtttcc ... gattttgcagTGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTT
EST: gi|22132216|gb|BQ827040.1|BQ827040
EST:     GATTTGGGGCGCCAGATATGAAGCCTGAGTTCACGAAGTTTGGTTCAGTG                         TGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTT
genomic: GATTTGGGGCGCCAGATATGAAGCCTGAGTTCACGAAGTTTGGTTCAGTGgtgcgtttcc ... gattttgcagTGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTT

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: 19 (upstream exon), 34 (downstream exon)
Score: 2

ATGGGTAATAAAGGAGCTTTTATCCGATTTGGGGCGCCAGATATGAAGCCTGAGTTCACGAAGTTTGGTTCAGTGgtgcgtttcc ... gattttgcagTGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTTCTGGGTTAGAGGTGATATTTTATTTAATATAGAACTTGGTTTCTCTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtccctgatctttgtttaactttatttatcatctgtctaacttcgattttgcagTGGCATCCAAACGTGAGACCTATGCAATATGCGAACAACTTTTTTAATTTTCTGGGTTAGAGGTGATATTTTATTTAATATAGAACTTGGTTTCTCTATG
                                   gtctaac  putative branch site (score: 2)
        atctttgtttaacttt  TA-rich tract