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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaatgcattgattgcatttgggagctttgtcaacttgtagcgataattgtctcgcaaacgattcgggcttccacaatttccttgttgataattgaatcaagtcaactgcttctgaagcaaacaaccccttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGACCCATCCGCACAAGGCGGCGACATGATCATGCGTATGATGGCTCGCAACC

Basic information

species Physcomitrella patens
transcript PP1S9_115V6.2
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|162276899|gb|FC452581.1|FC452581
EST:     CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAG                         ATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
genomic: CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAGgtaagtgaat ... cttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
EST: gi|162273610|gb|FC449339.1|FC449339
EST:     CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAG                         ATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
genomic: CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAGgtaagtgaat ... cttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
EST: gi|162194019|gb|FC370194.1|FC370194
EST:     CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAG                         ATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
genomic: CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAGgtaagtgaat ... cttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
EST: gi|162199338|gb|FC374017.1|FC374017
EST:     CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAG                         ATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
genomic: CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAGgtaagtgaat ... cttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
EST: gi|100375562|gb|BY948913.1|BY948913
EST:     CCACTGGCGCTTCCAGTGATTTGCAGCAAGCCTCTTCCATGGCGAAGCAG                         ATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
genomic: CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAGgtaagtgaat ... cttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
EST: gi|162268413|gb|FC444182.1|FC444182
EST:     CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAG                         ATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC
genomic: CCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAGgtaagtgaat ... cttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGAC

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: 14 (upstream exon), 31 (downstream exon)
Score: 4

TCTGGGTGGGCGCGCTGCAGAAGAAGTTATTTTCGGTGACGCTGAAGTGACCACTGGCGCTTCCAGTGATTTGCAGCAAGTCTCTTCCATGGCGAAGCAGgtaagtgaat ... cttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGACCCATCCGCACAAGGCGGCGACATGATCATGCGTATGATGGCTCGCAACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgataattgaatcaagtcaactgcttctgaagcaaacaaccccttggaacagATGGTGACGGCCTACGGCATGTCTGACATCGGCCCGTGGGCACTGATGGACCCATCCGCACAAGGCGGCGACATGATCATGCGTATGATGGCTCGCAACC
 tgttgat  putative branch site (score: 4)
                                          cccctt  putative PPT
     ataattgaat  TA-rich tract