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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGTGAATCCACAGAAGTTGGTTGTTTGCTAGGGGTTTGGGGTGATTTGTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAGgtgagtcgtgagcccttgttgatgctttcaaacgctgggaactctttttgttagtggcgttggacttgatttctgtctgaatggcggagatttcgagaaa...

Basic information

species Physcomitrella patens
transcript PP1S55_90V6.1
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|208391565|gb|DC933814.1|DC933814
EST:     GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAG                         GCCACCGGATTGCAGNNNNNNNNCTCTGTAACGAGCTTTAGCAAAAATGAC
genomic: GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAGgtgagtcgtg ... ctgtggacagGCCACCGGATTGCAGTTTTTTTTCTCTGTAACGAGCTTTAGCAAAAATGAC
EST: gi|18364993|gb|BJ197067.1|BJ197067
EST:     GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAG                         GCCACCGGATTGCAGNNNNNNNNCTCTGTAACGAGCTTTAGCAAAAATGAC
genomic: GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAGgtgagtcgtg ... ctgtggacagGCCACCGGATTGCAGTTTTTTTTCTCTGTAACGAGCTTTAGCAAAAATGAC
EST: gi|100412645|gb|BY974837.1|BY974837
EST:     GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAG                         GCCACCGGATTGCAGNNNNNNNNCTCTGTAACGAGCTTTAGCAAAAATGAC
genomic: GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAGgtgagtcgtg ... ctgtggacagGCCACCGGATTGCAGTTTTTTTTCTCTGTAACGAGCTTTAGCAAAAATGAC
EST: gi|67718167|gb|BJ968426.1|BJ968426
EST:     GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAG                         GCCACCGGATTGCAGNNNNNNNNCTCTGTAACGAGCTTTAGCAAAAATGAC
genomic: GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAGgtgagtcgtg ... ctgtggacagGCCACCGGATTGCAGTTTTTTTTCTCTGTAACGAGCTTTAGCAAAAATGAC
EST: gi|208355506|gb|DC942626.1|DC942626
EST:     GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAG                         GCCACCGGATTGCAGNNNNNNNNCTCTGTAACGAGCTTTAGCAAAAATGAC
genomic: GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAGgtgagtcgtg ... ctgtggacagGCCACCGGATTGCAGTTTTTTTTCTCTGTAACGAGCTTTAGCAAAAATGAC
EST: gi|208388011|gb|DC941678.1|DC941678
EST:     GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAG                         GCCACCGGATTGCAGNNNNNNNNCTCTGTAACGAGCTTTAGCAAAAATGAC
genomic: GTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAGgtgagtcgtg ... ctgtggacagGCCACCGGATTGCAGTTTTTTTTCTCTGTAACGAGCTTTAGCAAAAATGAC

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: 23 (upstream exon), 31 (downstream exon)
Score: 7

TCATGTGAATCCACAGAAGTTGGTTGTTTGCTAGGGGTTTGGGGTGATTTGTAGCTGGGCCTTTCGCTCGGGTTTCTCCCTCGCGATTTGTCTCTTTGAGgtgagtcgtg ... ctgtggacagGCCACCGGATTGCAGTTTTTTTTCTCTGTAACGAGCTTTAGCAAAAATGACGCCCTTGTCGATTATCAGTCTCCTTTTAGTGGCGGGGGTAGCATGGTTT




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