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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcaatgcttgtgaaggttctgctttggagttatgtcgtgtaccttcgccactgaggatttgaggctatttattactgcagagctttgaggattttacattttcatgtattgacgagtctactctcgaatctctttcaaacattttactgttttcaaggtctaaacgcgattgtttgcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAGCCTGACCCTGATGAAAACACTTCTAGCCCTCTAAATCATGCGCTCTTAC

Basic information

species Physcomitrella patens
transcript PP1S9_381V6.2
intron # 9
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|162185271|gb|FC361781.1|FC361781
EST:     TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAG                         AATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
genomic: TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAGgtaaattcaa ... gcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
EST: gi|162166462|gb|FC343159.1|FC343159
EST:     TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAG                         AATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
genomic: TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAGgtaaattcaa ... gcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
EST: gi|162164287|gb|FC342102.1|FC342102
EST:     TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAG                         AATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
genomic: TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAGgtaaattcaa ... gcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
EST: gi|162157674|gb|FC332996.1|FC332996
EST:     TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAG                         AATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
genomic: TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAGgtaaattcaa ... gcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
EST: gi|100413113|gb|BY992593.1|BY992593
EST:     TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAG                         AATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
genomic: TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAGgtaaattcaa ... gcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
EST: gi|162159143|gb|FC334314.1|FC334314
EST:     TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAG                         AATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
genomic: TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAGgtaaattcaa ... gcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
EST: gi|162245447|gb|FC421349.1|FC421349
EST:     TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAG                         AATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG
genomic: TAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAGgtaaattcaa ... gcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAG

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), 34 (downstream exon)
Score: 26

CTCTGTAGAAATATCTAACGAACCGGACCCAGATGAGATAGCAGGAGAGATAGTGGTTACTGCAGAGGGTCAAGCGACAGGAAGGGAGCTTAACGATCAGgtaaattcaa ... gcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAGCCTGACCCTGATGAAAACACTTCTAGCCCTCTAAATCATGCGCTCTTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttcaaacattttactgttttcaaggtctaaacgcgattgtttgcttgaatagAATGCAAGAATGGAGCCCGATCCAGACGACGCATTGCAACACAGTGAGGAGCCTGACCCTGATGAAAACACTTCTAGCCCTCTAAATCATGCGCTCTTAC
                           gtctaaa  putative branch site (score: 26)
                                          tttgctt  putative PPT
      aaacatttta  TA-rich tract