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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGAGGAGCTTAACCTTAATAAAGTGTATGTGCCTTTGCTTGTTGATGATTTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttatttcacccacctattatatattcattagagttttatggaccgtatgtgtcttggtactttccaatactgaaacccctagcttgtgcttcactatagagatgtataccttctcttccatccactttcattcttaacgccgatgccgctgatgcgaaatgtcactcatctcttttaagtggaacgctgcag

Basic information

species Physcomitrella patens
transcript PP1S47_18V6.1
intron # 5
splice site 5'
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|162229412|gb|FC405603.1|FC405603
EST:     TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAG                         CGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
genomic: TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
EST: gi|162169731|gb|FC345268.1|FC345268
EST:     TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAG                         CGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
genomic: TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
EST: gi|162214492|gb|FC391459.1|FC391459
EST:     TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAG                         CGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
genomic: TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
EST: gi|18327807|gb|BJ159811.1|BJ159811
EST:     TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAG                         CGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
genomic: TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
EST: gi|162159094|gb|FC334889.1|FC334889
EST:     TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAG                         CGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
genomic: TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
EST: gi|162158873|gb|FC335396.1|FC335396
EST:     TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAG                         CGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
genomic: TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
EST: gi|162173166|gb|FC349233.1|FC349233
EST:     TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAG                         CGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
genomic: TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
EST: gi|162209036|gb|FC385588.1|FC385588
EST:     TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAG                         CGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA
genomic: TTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGA

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), 22 (downstream exon)
Score: 7

TCGAGGAGCTTAACCTTAATAAAGTGTATGTGCCTTTGCTTGTTGATGATTTCAACAAATTCATGAACGTGTTTAACCGTCCCGATTTTCATGGTTTCAGgtacttattt ... aacgctgcagCGTTACGATACCATACAAGGAAGATGCACTGAAGCTGTGTGATAGGGTTGAAAATGCTGCAAAG




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