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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggatggtcctctgacagcggttaatgtggagatcggataggggatgttactttgcggagtatacaagcctcacttttgtctgttgcctttgttgtcagGTGAACAAGTACTACGACCTTGTTAACAGCTTCTACGAGTATGGGTGGGGAGAGTCTTACCACTTTGCCAACAGGTGA

Basic information

species Physcomitrella patens
transcript PP1S505_2V6.2
intron # 3
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|18359833|gb|BJ191894.1|BJ191894
EST:     CTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATG                         GTGAACAAGTACTACGACCTTGTTAACAGCTTCTACGAGTATGGGTGGGGG
genomic: CTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATGgtgagctcgt ... ttgttgtcagGTGAACAAGTACTACGACCTTGTTAACAGCTTCTACGAGTATGGGTGGGG-
EST: gi|18374486|gb|BJ206064.1|BJ206064
EST:     CTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATG                         GTGAACAAGTACTACGACCTTGTTAACAGCTTCTACGAGTATGGGTGGGGA
genomic: CTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATGgtgagctcgt ... ttgttgtcagGTGAACAAGTACTACGACCTTGTTAACAGCTTCTACGAGTATGGGTGGGGA
EST: gi|18345127|gb|BJ177168.1|BJ177168
EST:     CTATGCACGGAGGCGACAAAGAAGCAANAAAGAGCAATTACACTGACATG                         GNGAACAAGTACTACGAC
genomic: CTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATGgtgagctcgt ... ttgttgtcagGTGAACAAGTACTACGAC

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), 27 (downstream exon)
Score: 10

GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATGgtgagctcgt ... ttgttgtcagGTGAACAAGTACTACGACCTTGTTAACAGCTTCTACGAGTATGGGTGGGGAGAGTCTTACCACTTTGCCAACAGGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttactttgcggagtatacaagcctcacttttgtctgttgcctttgttgtcagGTGAACAAGTACTACGACCTTGTTAACAGCTTCTACGAGTATGGGTGGGGAGAGTCTTACCACTTTGCCAACAGGTGA
                       gcctcac  putative branch site (score: 10)
                                       ttgccttt  putative PPT
                tatacaa  TA-rich tract