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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttgatttcagtttgaagtccactaaaagttgaaggtgtatgaaaacgtgtcgaatgcgacgttgtcgctgattactctcgcttttatattgggcagGTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACACAG

Basic information

species Physcomitrella patens
transcript PP1S100_33V6.1
intron # 16
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|162233863|gb|FC409713.1|FC409713
EST:     TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCAT                         GTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
genomic: TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCATgtgagtaact ... tattgggcagGTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
EST: gi|18339957|gb|BJ171985.1|BJ171985
EST:     TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCAT                         GTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
genomic: TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCATgtgagtaact ... tattgggcagGTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
EST: gi|208367792|gb|DC944038.1|DC944038
EST:     TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCAT                         GTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
genomic: TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCATgtgagtaact ... tattgggcagGTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
EST: gi|162152497|gb|FC328775.1|FC328775
EST:     TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCAT                         GTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
genomic: TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCATgtgagtaact ... tattgggcagGTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
EST: gi|37825957|gb|BJ584023.1|BJ584023
EST:     TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCAT                         GTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA
genomic: TTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCATgtgagtaact ... tattgggcagGTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACA

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-Seq library.


Block sizes: 15 (upstream exon), 21 (downstream exon)
Score: 1

GAGGAAAGGCATTATCGTAGGCAGCGACCAAGAGGGTGATGATGCAGTCGTTTTGGCTCATgtgagtaact ... tattgggcagGTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACACAG































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacgtgtcgaatgcgacgttgtcgctgattactctcgcttttatattgggcagGTACCGTTGAACAACATGTTTGGCTATTCAACTGGTTTGCGCTCCATGACACAG
                        cgctgat  putative branch site (score: 1)
                                       cttttat  putative PPT
                                        ttttatatt  TA-rich tract