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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattcctggctgtccgaatttcgattgacattcgtgttcgattcacattccgggggctttctatacaagaatactgtacttattgccacattagatatattttctggattttgtgtgatttttgcttcaatgatgtcctgatctatcttatgactgaatacacagGCCAATTTGACTAATGCCAATCTAGAAGGAGCATCAGTCACTGGCAATACTTATCTCAAAGGATCCATTATTACTGGCGCGG

Basic information

species Physcomitrella patens
transcript PP1S61_208V6.1
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|162241098|gb|FC417743.1|FC417743
EST:     CTGATGCGGACCTTAGGGGAGCTGATCTTTCATTAGCAAGACTATCAAAG                         GCCAATTTGACTAATGCCAATCTAGAANGAGCATCAGTCACTGGCAATACT
genomic: CTGATGCGGACCTTAGGGGAGCTGATCTTTCATTAGCAAGACTATCAAAGgtatattcct ... gaatacacagGCCAATTTGACTAATGCCAATCTAGAAGGAGCATCAGTCACTGGCAATACT
EST: gi|162209806|gb|FC385740.1|FC385740
EST:     CTGATGCGGACCTTAGGGGAGCTGATCTTTCATTAGCAAGACTATCAAAG                         GCCAATTTGACTAATGCCAATCTAGAAGGAGCATCAGTCACTGGCAATACT
genomic: CTGATGCGGACCTTAGGGGAGCTGATCTTTCATTAGCAAGACTATCAAAGgtatattcct ... gaatacacagGCCAATTTGACTAATGCCAATCTAGAAGGAGCATCAGTCACTGGCAATACT
EST: gi|162190314|gb|FC365328.1|FC365328
EST:     CTGATGCGGACCTTAGGGGAGCTGATCTTTCATTAGCAAGACTATCAAAG                         GCCAATTTGACTAATGCCAATCTAGAAGGAGCATCAGTCACTGGCAATACT
genomic: CTGATGCGGACCTTAGGGGAGCTGATCTTTCATTAGCAAGACTATCAAAGgtatattcct ... gaatacacagGCCAATTTGACTAATGCCAATCTAGAAGGAGCATCAGTCACTGGCAATACT
EST: gi|162186363|gb|FC361671.1|FC361671
EST:     CTGATGCGGACCTTANGGGAGCTGATCTTTCATTAGCAAGACTATCANAG                         GCCAATTTGACT
genomic: CTGATGCGGACCTTAGGGGAGCTGATCTTTCATTAGCAAGACTATCAAAGgtatattcct ... gaatacacagGCCAATTTGACT
EST: gi|100370508|gb|BY985444.1|BY985444
EST:     TGATGCCGACCTTAGGGGAGCTGATCTTTCATTTAGCA-GACTATCAAAG                         GGCCA-TTTGACTA
genomic: TGATGCGGACCTTAGGGGAGCTGATCTTTCATT-AGCAAGACTATCAAAGgtatattcct ... gaatacacagG-CCAATTTGACTA

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: 33 (upstream exon), 34 (downstream exon)
Score: 18

GAGCTGACCTTACTGATGCGGACCTTAGGGGAGCTGATCTTTCATTAGCAAGACTATCAAAGgtatattcct ... gaatacacagGCCAATTTGACTAATGCCAATCTAGAAGGAGCATCAGTCACTGGCAATACTTATCTCAAAGGATCCATTATTACTGGCGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtgatttttgcttcaatgatgtcctgatctatcttatgactgaatacacagGCCAATTTGACTAATGCCAATCTAGAAGGAGCATCAGTCACTGGCAATACTTATCTCAAAGGATCCATTATTACTGGCGCGG
                         tcctgat  putative branch site (score: 18)
     tgattttt  TA-rich tract