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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctatgtttcagagttggttcttttctgtgatataaattgtcttttcagatactacgatttttttcaatacgaggattcaacgacattttttgtttatttatttattgatttttattttatttttatttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCGTCTATCAGTCCAG

Basic information

species Physcomitrella patens
transcript PP1S173_136V6.1
intron # 14
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|162195982|gb|FC372166.1|FC372166
EST:     GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAG                         CATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
genomic: GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAGgtatctatgt ... atttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
EST: gi|162195983|gb|FC372167.1|FC372167
EST:     GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAG                         CATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
genomic: GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAGgtatctatgt ... atttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
EST: gi|162190104|gb|FC365846.1|FC365846
EST:     AAAGCGTGAAAATTCTGTCTGGACAAAGCAG                         CATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
genomic: AAAGCGTGAAAATTCTGTCTGGACAAAGCAGgtatctatgt ... atttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
EST: gi|37834281|gb|BJ592293.1|BJ592293
EST:     GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAG                         CATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
genomic: GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAGgtatctatgt ... atttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
EST: gi|18341657|gb|BJ173692.1|BJ173692
EST:     GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAG                         CATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
genomic: GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAGgtatctatgt ... atttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
EST: gi|162241844|gb|FC418099.1|FC418099
EST:     GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAG                         CATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG
genomic: GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAGgtatctatgt ... atttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCG

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), 29 (downstream exon)
Score: 10

GAGTAAAGCGTGAAAATTCTGTCTGGACAAAGCAGgtatctatgt ... atttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCGTCTATCAGTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgacattttttgtttatttatttattgatttttattttatttttatttttccagCATGGGAATCCTATCTCAATGGGTAAAGTGAGGCCAGGTGTTAATCGATCGTCTATCAGTCCAG
                       tattgat  putative branch site (score: 10)
                             tttttattttattttt  CT-rich tract
             tttatttatttattga  TA-rich tract