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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattgactgtcgtttagaatcattttatctccattttttttttgttagtcacacatctctagtctcttctctaattcatgactactggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAACCATTGCTCGCTACGAAACTCCTGCTCACATCAACATTGACAAG

Basic information

species Physcomitrella patens
transcript PP1S199_127V6.1
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|162180389|gb|FC355810.1|FC355810
EST:     AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCTGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
EST: gi|162195103|gb|FC371378.1|FC371378
EST:     AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCTGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
EST: gi|37846883|gb|BJ604891.1|BJ604891
EST:     AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
EST: gi|162150713|gb|FC327609.1|FC327609
EST:     AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCTGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
EST: gi|162192956|gb|FC371458.1|FC371458
EST:     AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCTGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
EST: gi|162192955|gb|FC371457.1|FC371457
EST:     AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCTGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
EST: gi|162224470|gb|FC399846.1|FC399846
EST:     AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCTGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
EST: gi|162194122|gb|FC369465.1|FC369465
EST:     TGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCTGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: TGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
EST: gi|37844425|gb|BJ602433.1|BJ602433
EST:     AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGG                         GAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC
genomic: AAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAAC

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: 20 (upstream exon), 29 (downstream exon)
Score: 3

GTAAACAAGGGCACAGCGAGTGCTAGTGAAATTCTAGCGGGTGCTCTTAAGGACAACAAACGAGCTGTTATTCTTGGAGAACCCACGTTTGGAAAAGGgttagtattg ... ggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAACCATTGCTCGCTACGAAACTCCTGCTCACATCAACATTGACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttagtcacacatctctagtctcttctctaattcatgactactggccgagcagGAGAATACAGTCCGTGTTTCAGTTGTCTGATGGTTCAGGCATGGCCGTAACCATTGCTCGCTACGAAACTCCTGCTCACATCAACATTGACAAG
                           ctctaat  putative branch site (score: 3)
                              taattcat  TA-rich tract