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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatgattagtattgtcgaatgtaagagaagctaagcttatgttctatatcgttatcttggcggtctctgctgatatgcattgaatgtgtcttttgtagTGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTGTTTCACGAAGCATTCTCCACAGTACAGAGTGTTGATGTTGGGTCGAGTA

Basic information

species Physcomitrella patens
transcript PP1S44_143V6.1
intron # 2
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|162236254|gb|FC412010.1|FC412010
EST:     GGTTCCTCAATGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATA                         TGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTG
genomic: GGTTCCTCAATGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATAgtaagtattt ... tcttttgtagTGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTG
EST: gi|67508186|gb|BJ941057.1|BJ941057
EST:     GGTTCCTCAATGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATA                         TGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTG
genomic: GGTTCCTCAATGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATAgtaagtattt ... tcttttgtagTGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTG
EST: gi|162186751|gb|FC362787.1|FC362787
EST:     GTTTCCTCA-TGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATA                         TGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTG
genomic: GTT-CCTCAATGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATAgtaagtattt ... tcttttgtagTGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTG
EST: gi|18351372|gb|BJ183424.1|BJ183424
EST:     GGTTCCTCAATGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATA                         TGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTG
genomic: GGTTCCTCAATGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATAgtaagtattt ... tcttttgtagTGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTG

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

TCTATGGATATGACAAAGGTGACATTGGCAAGCTGTTTATTGCTGGATTTGGTTCCTCAATGCTTTTTGGAACCATTGTGGGATCACTTGCGGATAGATAgtaagtattt ... tcttttgtagTGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTGTTTCACGAAGCATTCTCCACAGTACAGAGTGTTGATGTTGGGTCGAGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatatcgttatcttggcggtctctgctgatatgcattgaatgtgtcttttgtagTGGACGCAAGAGGATGAGTGTCATCTACTGTATTACATACATGCTGAGCTGTTTCACGAAGCATTCTCCACAGTACAGAGTGTTGATGTTGGGTCGAGTA
                        tgctgat  putative branch site (score: 1)
                                           tgtctttt  putative PPT
        ttatctt  TA-rich tract