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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcacgtccctgtttattaatcggtggaatgatgttaactctttcctgatgagtatttggttctcgttattctgattgttcttccgtcccttttccccagATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTCTTCAAGCATTTCAAGCAG

Basic information

species Physcomitrella patens
transcript PP1S83_28V6.1
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|162264424|gb|FC440590.1|FC440590
EST:     CTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAG                         ATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
genomic: CTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAGgtaaagtttc ... ttttccccagATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
EST: gi|18338935|gb|BJ170961.1|BJ170961
EST:     CTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAG                         ATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
genomic: CTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAGgtaaagtttc ... ttttccccagATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
EST: gi|18333942|gb|BJ165958.1|BJ165958
EST:     GGCCACTACGAAGAATGCGGCAAGGTTCACAAG                         ATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
genomic: GGCCACTACGAAGAATGCGGCAAGGTTCACAAGgtaaagtttc ... ttttccccagATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
EST: gi|162173421|gb|FC349800.1|FC349800
EST:     CTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAG                         ATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
genomic: CTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAGgtaaagtttc ... ttttccccagATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
EST: gi|37843731|gb|BJ601739.1|BJ601739
EST:     CTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAG                         ATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC
genomic: CTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAGgtaaagtttc ... ttttccccagATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTC

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: 34 (upstream exon), 23 (downstream exon)
Score: 4

TGATGATAATATTGAGACTATCCGCAAGAGGTTTAAGGTTTTCATTGATTCTAGCCTACCGGTTGTGGGCCACTACGAAGAATGCGGCAAGGTTCACAAGgtaaagtttc ... ttttccccagATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTCTTCAAGCATTTCAAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatgagtatttggttctcgttattctgattgttcttccgtcccttttccccagATTGATGCAACCAAAACCCCAAGTGAAGTGTTTGAATCGATTAAACCACTCTTCAAGCATTTCAAGCAG
                        ttctgat  putative branch site (score: 4)
                        ttctgattgttcttcc  CT-rich tract
      agtattt  TA-rich tract