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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCGGTCGCTCAGGCTCAACACCTGGCCCGTTCAACGGCCAGAAGAAGAGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgtttacctatctgttcaattatcttgtgattgacttttattttgagaagatcgtcacttctcttgcaatggataaatactgatgtcgttgctag...

Basic information

species Physcomitrella patens
transcript PP1S86_24V6.1
intron # 1
splice site 5'
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|100392285|gb|BY953287.1|BY953287
EST:     AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
EST: gi|18330771|gb|BJ162777.1|BJ162777
EST:     CGGCTTGGGAAACGGCGNCACGCTTNCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: CGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
EST: gi|18342907|gb|BJ174943.1|BJ174943
EST:     AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
EST: gi|100383782|gb|BY969311.1|BY969311
EST:     AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
EST: gi|18346829|gb|BJ178874.1|BJ178874
EST:     AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
EST: gi|100446857|gb|CJ971156.1|CJ971156
EST:     AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
EST: gi|18331556|gb|BJ163567.1|BJ163567
EST:     CGGCTTGGGAAACGGCGTCACGCTTNCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: CGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
EST: gi|162166444|gb|FC342426.1|FC342426
EST:     AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
EST: gi|100352242|gb|BY983110.1|BY983110
EST:     AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGT                         ACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC
genomic: AGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCAC

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), 35 (downstream exon)
Score: 24

AGAGCGGTCGCTCAGGCTCAACACCTGGCCCGTTCAACGGCCAGAAGAAGAGCGGCTTGGGAAACGGCGTCACGCTTCCCCGCAAACCTTCTCGATCTGTgtgcgtgttt ... tgattcacagACCGCCCGGAGAGCGGACAGTTAAACGTTTGAGGTTGTCGAAGGCTCTCACCATCCCCGATGGCAGTACTGTTGCCGATGCCTGTCGTCGAATGGCCACT




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