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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgacttgtaactactttttaaaaagaaaattttgatgcatgctgaagtgattgaattggtgatttcaatggttgaatgccacctaacgtggtcttgtcttagttgcagGAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGTACAATGGCAATGGCACGACAG

Basic information

species Physcomitrella patens
transcript PP1S149_77V6.1
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|37851023|gb|BJ609031.1|BJ609031
EST:     AGATCATGGTGGAGGGTCAGAAGCAGCCCATCTATGGTACTACTCTTGAG                         GAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGT
genomic: AGATCATGGTGGAGGGTCAGAAGCAGCCCATCTATGGTACTACTCTTGAGgtgaatgact ... ttagttgcagGAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGT
EST: gi|162232024|gb|FC409098.1|FC409098
EST:     AGATCATGGTGGAGGGTCAGAAGCAGCCCATCTATGGTACTACTCTTGAG                         GAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGT
genomic: AGATCATGGTGGAGGGTCAGAAGCAGCCCATCTATGGTACTACTCTTGAGgtgaatgact ... ttagttgcagGAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGT
EST: gi|162169392|gb|FC345748.1|FC345748
EST:     AGATCATGGTGGAGGGTCAGAAGCAGCCCATCTATGGTACTACTCTTGAG                         GAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGT
genomic: AGATCATGGTGGAGGGTCAGAAGCAGCCCATCTATGGTACTACTCTTGAGgtgaatgact ... ttagttgcagGAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGT

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: 34 (upstream exon), 35 (downstream exon)
Score: 8

TGAAGGGTTTGTGGACCCAGCTACAGGCCAAGTCCGGACTGTCCCATTGGAGATCATGGTGGAGGGTCAGAAGCAGCCCATCTATGGTACTACTCTTGAGgtgaatgact ... ttagttgcagGAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGTACAATGGCAATGGCACGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattggtgatttcaatggttgaatgccacctaacgtggtcttgtcttagttgcagGAGCTCGGCCTACCTAAGGCGAAAATAAAGTTGCCATTCAATGCATTTGGTACAATGGCAATGGCACGACAG
                           acctaac  putative branch site (score: 8)
                                      tcttgtctt  putative PPT
        atttcaat  TA-rich tract