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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGCAGGTCGCTGTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggtcactgattttgtgtgcatgaattgaggaacatgatcgtctgctgtagcgctcattgtagcggagaatcgaggaagttcgatcgcatggaa...

Basic information

species Physcomitrella patens
transcript PP1S385_43V6.1
intron # 1
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|100448600|gb|CJ972899.1|CJ972899
EST:     GTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAG                         AGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
genomic: GTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggt ... tgatgttcagAGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
EST: gi|100385375|gb|BY950967.1|BY950967
EST:     GCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAG                         AGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
genomic: GCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggt ... tgatgttcagAGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
EST: gi|100452183|gb|CJ975143.1|CJ975143
EST:     GCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAG                         AGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
genomic: GCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggt ... tgatgttcagAGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
EST: gi|100390324|gb|BY952732.1|BY952732
EST:     GTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAG                         AGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
genomic: GTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggt ... tgatgttcagAGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
EST: gi|100352580|gb|BY945343.1|BY945343
EST:     GTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAG                         AGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
genomic: GTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggt ... tgatgttcagAGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
EST: gi|100411169|gb|BY992231.1|BY992231
EST:     CTGACGCAGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAG                         AGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
genomic: CTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggt ... tgatgttcagAGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
EST: gi|18372082|gb|BJ203684.1|BJ203684
EST:     GTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAG                         AGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA
genomic: GTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggt ... tgatgttcagAGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCA

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: 29 (upstream exon), 31 (downstream exon)
Score: 6

AATGGCAGGTCGCTGTCTGACGCGGCGCTGAACTTCCTTTCTCGCGTTCACAATTGCCTCCGAGgtacgtcggt ... tgatgttcagAGGTGTTCGTCGTGAAGCTAGATCTGCGAAGTGAACTGGGAAGATCTCGCAGCCATGGACCACGCTGCGGATGCAATGAGGACTGACTTGATGACAATTA




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