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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtactatttttgcgttgcggttattcatatttgtactctgtactacaatttcagtctgatttaactcgcatttaagcttattcaaattggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACCTTCGATGCCCTTCCTTCTGACAAAGTGAAAG

Basic information

species Physcomitrella patens
transcript PP1S4_12V6.3
intron # 2
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|208351568|gb|DC909998.1|DC909998
EST:     CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
EST: gi|162159187|gb|FC334358.1|FC334358
EST:     CCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
EST: gi|100375450|gb|BY948872.1|BY948872
EST:     CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
EST: gi|100434059|gb|BY978946.1|BY978946
EST:     CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
EST: gi|18348776|gb|BJ180825.1|BJ180825
EST:     CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
EST: gi|67568839|gb|BJ941663.1|BJ941663
EST:     CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
EST: gi|67571702|gb|BJ944526.1|BJ944526
EST:     CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
EST: gi|100437911|gb|BY961558.1|BY961558
EST:     CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
EST: gi|162257953|gb|FC433839.1|FC433839
EST:     CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAG                         GTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC
genomic: CTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACC

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: 36

AGCTTGAAGGATGGTGCTCTTTAAAGTTGTGAAGCAGGAGACTAAGGCGATCGATGGCCAAAAGCCTGGTACCTCTGGTTTGCGTAAGAAGgtgcatacga ... ggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACCTTCGATGCCCTTCCTTCTGACAAAGTGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaatttcagtctgatttaactcgcatttaagcttattcaaattggatccgcagGTGACAGTGTTTAAGCAGGACCATTACCTTGCCAACTTTGTGCAAGCCACCTTCGATGCCCTTCCTTCTGACAAAGTGAAAG
               atttaac  putative branch site (score: 36)
                                  ttattcaaatt  TA-rich tract