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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtctcaaaaacatgtcgaaccaatcagctggactatgatttacctgtggtagatgtgtattggcaagactaagcgagagggagagtttaccattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGAATGCACTCAACTACGCATGTGGCGTGGGAACAACGGACTGCTCCGCCAT

Basic information

species Physcomitrella patens
transcript PP1S6_62V6.1
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|37820960|gb|BJ579026.1|BJ579026
EST:     TCCTGCACTTCNTGCGGCACCAAGCACTAGCCCCCAAG                         GGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
genomic: TCCTGCACCTCCTGCGGCACCAAGCACTAGCCCCCAAGgtgccgattt ... accattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
EST: gi|208351441|gb|DC921608.1|DC921608
EST:     TGTCCCCAGCTCTCCTGCACCTCCTGCGGCACCAAGCACTAGCCCCCAAG                         GGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
genomic: TGTCCCCAGCTCTCCTGCACCTCCTGCGGCACCAAGCACTAGCCCCCAAGgtgccgattt ... accattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
EST: gi|37832439|gb|BJ590451.1|BJ590451
EST:     TCCTGCGGCACCAAGCACTAGCCCCCAAG                         GGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
genomic: TCCTGCGGCACCAAGCACTAGCCCCCAAGgtgccgattt ... accattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
EST: gi|18339860|gb|BJ171887.1|BJ171887
EST:     TGTCCCCAGCTCTCCTGCACCTCCTGCGGCACCAAGCACTAGCCCCCAAG                         GGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
genomic: TGTCCCCAGCTCTCCTGCACCTCCTGCGGCACCAAGCACTAGCCCCCAAGgtgccgattt ... accattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
EST: gi|37826365|gb|BJ584377.1|BJ584377
EST:     TGCGGCACCAAGCACTAGCCCCCAAG                         GGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
genomic: TGCGGCACCAAGCACTAGCCCCCAAGgtgccgattt ... accattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
EST: gi|37822412|gb|BJ580478.1|BJ580478
EST:     TCCTGCACCTCCTGCGGCACCAAGCACTAGCCCCCAAG                         GGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
genomic: TCCTGCACCTCCTGCGGCACCAAGCACTAGCCCCCAAGgtgccgattt ... accattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
EST: gi|37838569|gb|BJ596577.1|BJ596577
EST:     TCCTGCGGCANCAAGCACTAGCCCCCAAG                         GGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA
genomic: TCCTGCGGCACCAAGCACTAGCCCCCAAGgtgccgattt ... accattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGA

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: 22 (upstream exon), 35 (downstream exon)
Score: 9

CCCAACTCTCAGCCTTTGCCTCCTTTAGCGTCTGCCCCGCCTCCCCTATCTGTCCCCAGCTCTCCTGCACCTCCTGCGGCACCAAGCACTAGCCCCCAAGgtgccgattt ... accattgcagGGAAGACTTGGTGTGTAGCAAAGGCAGGAGCTCCAGAGCAGGACATGCTGAATGCACTCAACTACGCATGTGGCGTGGGAACAACGGACTGCTCCGCCAT




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