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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagctgggagaatgaggttgacatgagcggtgttaactctggtctgtaccctcgtaggataatgcattacgttaactcctgtaatgtgatggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG

Basic information

species Physcomitrella patens
transcript PP1S4_12V6.3
intron # 5
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|162178865|gb|FC354797.1|FC354797
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|208351568|gb|DC909998.1|DC909998
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|162159187|gb|FC334358.1|FC334358
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|100375450|gb|BY948872.1|BY948872
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAGTAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|162185024|gb|FC362470.1|FC362470
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|18348776|gb|BJ180825.1|BJ180825
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|67568839|gb|BJ941663.1|BJ941663
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|67571702|gb|BJ944526.1|BJ944526
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|100437911|gb|BY961558.1|BY961558
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|162257953|gb|FC433839.1|FC433839
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
EST: gi|162276463|gb|FC452466.1|FC452466
EST:     TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCAT                         GGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT
genomic: TTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGT

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), 35 (downstream exon)
Score: 61

TGCCGCAGCTAATGGCGTAAAGAGGGTCTGGGTGGGGCAGAACACTCTTCTTTCCACCCCTGCCGTGTCTGCAATCATCCGAGAGCGAGTGAATAGTCATgtaagtggag ... tggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaccctcgtaggataatgcattacgttaactcctgtaatgtgatggttttcagGGTGAAAAGGCGTACGGTGCATTCATTCTGACCGCCAGCCACAACCCCGGTGGTCCCGACGAG
                         cgttaac  putative branch site (score: 61)
                                                ttttc  putative PPT
              ataat  TA-rich tract