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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaagaaaacgctccaatcctcttcatactccgcatgtcttgaatttttttccggcgaacatggtgtatttgtttcgcttaccaatcgccttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTGGTCACTACCGCTGGGAATTTGACATCTTGAATTCGAATCATAGTTTTGA

Basic information

species Physcomitrella patens
transcript PP1S91_16V6.1
intron # 1
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|18368114|gb|BJ200199.1|BJ200199
EST:     GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCG                         CTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
genomic: GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCGgtaagtcagg ... cttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
EST: gi|18325287|gb|BJ157283.1|BJ157283
EST:     GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCG                         CTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
genomic: GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCGgtaagtcagg ... cttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
EST: gi|100353373|gb|BY964774.1|BY964774
EST:     GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCG                         CTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
genomic: GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCGgtaagtcagg ... cttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
EST: gi|18330992|gb|BJ162998.1|BJ162998
EST:     GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCG                         CTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
genomic: GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCGgtaagtcagg ... cttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
EST: gi|18362417|gb|BJ194487.1|BJ194487
EST:     GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCG                         CTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
genomic: GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCGgtaagtcagg ... cttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
EST: gi|18356215|gb|BJ188274.1|BJ188274
EST:     GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCG                         CTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG
genomic: GTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCGgtaagtcagg ... cttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTG

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), 35 (downstream exon)
Score: 92

GATCGGATACAAACCATTCGGAAGGGTGACGCAATAGGAGCTGGAGGGGAGTTTCGGTTTCGAATTCATAAGAAGAATCCCAGTTGTGCACTCGGATCCGgtaagtcagg ... cttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTGGTCACTACCGCTGGGAATTTGACATCTTGAATTCGAATCATAGTTTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttccggcgaacatggtgtatttgtttcgcttaccaatcgccttcctgcagCTTGAATCAGGGTCAGCTAGGCTGGAACAAGATATCGTCTCGTCATTGCTGGTCACTACCGCTGGGAATTTGACATCTTGAATTCGAATCATAGTTTTGA
                               cgcttac  putative branch site (score: 92)
                                         tcgccttcct  putative PPT
                      tatttgttt  TA-rich tract