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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcatttcaatcctaaccagaacctacgaagtagtaaactgttcggatacttgaatatgactcgtatatgagccgcttctgacactactgcctggcagCAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTACAGCCGGTCGAGAAATTCTTTGTCCAAGGTCCATCAATTTCGCAGAATTC

Basic information

species Physcomitrella patens
transcript PP1S97_119V6.2
intron # 7
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|37828624|gb|BJ586636.1|BJ586636
EST:     TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAG                         CAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
genomic: TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAGgtagatatct ... tgcctggcagCAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
EST: gi|37836924|gb|BJ594932.1|BJ594932
EST:     TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAG                         CAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
genomic: TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAGgtagatatct ... tgcctggcagCAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
EST: gi|37823781|gb|BJ581847.1|BJ581847
EST:     TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAG                         CAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
genomic: TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAGgtagatatct ... tgcctggcagCAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
EST: gi|37830231|gb|BJ588243.1|BJ588243
EST:     TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAG                         CAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
genomic: TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAGgtagatatct ... tgcctggcagCAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
EST: gi|37834132|gb|BJ592144.1|BJ592144
EST:     TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAG                         CAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC
genomic: TTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAGgtagatatct ... tgcctggcagCAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTAC

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: 29 (upstream exon), 24 (downstream exon)
Score: 4

GAAGCCCAGGCCTATGCCAAAAGTAATGGCATGTTCTTTATTGAAACGTCAGCGAAGACTTCTGAGAACGTGAACCAATTATTTGAGgtagatatct ... tgcctggcagCAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTACAGCCGGTCGAGAAATTCTTTGTCCAAGGTCCATCAATTTCGCAGAATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggatacttgaatatgactcgtatatgagccgcttctgacactactgcctggcagCAATGCACTGAAGGCGATATTGCCAGGAAGCCCAAGCATCCAAGTCTGTACAGCCGGTCGAGAAATTCTTTGTCCAAGGTCCATCAATTTCGCAGAATTC
                                 ttctgac  putative branch site (score: 4)
       ttgaatat  TA-rich tract