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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaaagcgcacattgtattcgaaaaatatggagcatctgaaattgccgattatttatacaggttatttttaatcgtccattgatttagttgttgttcacagagcataccttgagctgtaataacgtgttgcttttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTGGCTGGCCGCATGAGTTTTCATGTGTAAGATCTTTACCTGCTAGCGTTCA

Basic information

species Physcomitrella patens
transcript PP1S495_7V6.1
intron # 6
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|37841386|gb|BJ599394.1|BJ599394
EST:     AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
genomic: AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAGgtgagcaaag ... ttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
EST: gi|208397762|gb|DC912545.1|DC912545
EST:     AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
genomic: AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAGgtgagcaaag ... ttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
EST: gi|37835626|gb|BJ593638.1|BJ593638
EST:     AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
genomic: AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAGgtgagcaaag ... ttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
EST: gi|67696502|gb|BJ956735.1|BJ956735
EST:     AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
genomic: AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAGgtgagcaaag ... ttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
EST: gi|162273972|gb|FC450111.1|FC450111
EST:     AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
genomic: AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAGgtgagcaaag ... ttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
EST: gi|208351509|gb|DC926327.1|DC926327
EST:     AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAG                         ATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG
genomic: AACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAGgtgagcaaag ... ttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTG

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: 32 (upstream exon), 27 (downstream exon)
Score: 8

GAGGAACGGAGGGCAGCTTTGCGGAAATATCAAGTTCACGATGAAACAATGCAGgtgagcaaag ... ttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTGGCTGGCCGCATGAGTTTTCATGTGTAAGATCTTTACCTGCTAGCGTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgttcacagagcataccttgagctgtaataacgtgttgcttttgtttacagATGAGTTCTGTTGATGCTGCAATTGATAGGAGAATACTAGAAGGCAGGTTGGCTGGCCGCATGAGTTTTCATGTGTAAGATCTTTACCTGCTAGCGTTCA
                             taataac  putative branch site (score: 8)
                                          cttttgttt  putative PPT
                                           ttttgttta  TA-rich tract