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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattacacgtactcgtatcatgtttgtttagtcgattttgtagatgaagtttactttttacgatccttgatgagtattgtgtgcgacgagtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTATGCAGCCGGCAAATACTCGGAGGCCTTGGAATGCTACGCTAGTGCATTGG

Basic information

species Physcomitrella patens
transcript PP1S62_216V6.1
intron # 3
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|100391448|gb|BY971662.1|BY971662
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
EST: gi|18367329|gb|BJ199412.1|BJ199412
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCA
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCA
EST: gi|208379389|gb|DC922947.1|DC922947
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
EST: gi|208383738|gb|DC911462.1|DC911462
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
EST: gi|37847056|gb|BJ605064.1|BJ605064
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
EST: gi|208344970|gb|DC909081.1|DC909081
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
EST: gi|18366670|gb|BJ198749.1|BJ198749
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
EST: gi|100426583|gb|BY977301.1|BY977301
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
EST: gi|100387222|gb|BY970366.1|BY970366
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGGCAACA-TTTGTA
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGG-CAACAATTTGTA
EST: gi|208400047|gb|DC925259.1|DC925259
EST:     GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCG                         AAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT
genomic: GCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTAT

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: 35 (upstream exon), 30 (downstream exon)
Score: 5

AGAGAAGAACGCTTCAAGTTCGAACGAGAAATCAGCTACCACATCAGGAAGCACCGAAGATCATTTTGAGGATGCTTTGACTGAGGAGGAGCTCCGAGCGgtgtgtgaaa ... gtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTATGCAGCCGGCAAATACTCGGAGGCCTTGGAATGCTACGCTAGTGCATTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagtttactttttacgatccttgatgagtattgtgtgcgacgagtggacacagAAAGCCATATCTCTAGCAAATGCAGCGAAGTCTCAAGGCAACAATTTGTATGCAGCCGGCAAATACTCGGAGGCCTTGGAATGCTACGCTAGTGCATTGG
                    ccttgat  putative branch site (score: 5)
     tttacttttta  TA-rich tract