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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGACAATCACTGTGTACAGATGTGGTCCGCTTGTAGATCTATGTCGTGGTCCTCATATCCCAAGCACTTCTCACGTGAAGGCGTTTGCTTGCTTGAGGgttagtggtactgccacactgacgtagatgcatgttttgtgttttgtttccttatttgaatgaatttgtaagtcacgagaatgtaattgtggtgagaatattctttgtgcacttcag

Basic information

species Physcomitrella patens
transcript PP1S400_36V6.1
intron # 7
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|162162678|gb|FC338980.1|FC338980
EST:     ACTTCTCACGTGAAGGCGTTTGCTTGCTTGAGG                         GCTTCGGCCTCATACTGGAGAGGAAGAGCAGACCGGGAAAGCCTTCAGCGT
genomic: ACTTCTCACGTGAAGGCGTTTGCTTGCTTGAGGgttagtggta ... tgcacttcagGCTTCGGCCTCATACTGGAGAGGAAGAGCAGACCGGGAAAGCCTTCAGCGT
EST: gi|100385844|gb|BY951038.1|BY951038
EST:     GTCCTCATATCCCAAGCACTTCTCACGTGAAGGCGTTTGCTTGCTTGAGG                         GCTTCGGCCTCATACTGGAGAGGAAGAGCAGACCGGGAAAGCCTTCAGCGT
genomic: GTCCTCATATCCCAAGCACTTCTCACGTGAAGGCGTTTGCTTGCTTGAGGgttagtggta ... tgcacttcagGCTTCGGCCTCATACTGGAGAGGAAGAGCAGACCGGGAAAGCCTTCAGCGT
EST: gi|162185106|gb|FC362240.1|FC362240
EST:     GTCCTCATATCCCAAGCACTTCTCACGTGAAGGCGTTTGCTTGCTTGAGG                         GCTTCGGCCTCATACTGGAGAGGAAGAGCAGACCGGGAAAGCCTTCAGCGT
genomic: GTCCTCATATCCCAAGCACTTCTCACGTGAAGGCGTTTGCTTGCTTGAGGgttagtggta ... tgcacttcagGCTTCGGCCTCATACTGGAGAGGAAGAGCAGACCGGGAAAGCCTTCAGCGT

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: 16 (upstream exon), 21 (downstream exon)
Score: 3

TAAGACAATCACTGTGTACAGATGTGGTCCGCTTGTAGATCTATGTCGTGGTCCTCATATCCCAAGCACTTCTCACGTGAAGGCGTTTGCTTGCTTGAGGgttagtggta ... tgcacttcagGCTTCGGCCTCATACTGGAGAGGAAGAGCAGACCGGGAAAGCCTTCAGCGTGTTTACGGCATTTCCTATCCAGACAACAAGCTACTGAAG




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