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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtatatgtccttgctcgcgaaaccctgcaacgtgatcaaccctacaagctctatactttagagtccagagtttgcttttcatattgtttttgtgcagGGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCACAAATGGGTGCAAGGGTTGGCATCTTCGATGCCGACATATATGGTCCCA

Basic information

species Physcomitrella patens
transcript PP1S414_7V6.1
intron # 5
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|162190920|gb|FC368118.1|FC368118
EST:     CTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAG                         GGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
genomic: CTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAGgtgccctgaa ... ttttgtgcagGGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
EST: gi|162255253|gb|FC431563.1|FC431563
EST:     CTGCTGGTCTGAAGAAAGTCTCANACATTGTGGCGGTTTCAAGTTGCAAG                         GGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
genomic: CTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAGgtgccctgaa ... ttttgtgcagGGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
EST: gi|100363772|gb|BY947610.1|BY947610
EST:     TGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCNAGTTTGCA-G                         GNTGGAGTTGG-AAGGTCCACAGTGGCAGTAAACCTTGC
genomic: TGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTT-GCAAGgtgccctgaa ... ttttgtgcagGGTGGAGTTGGGAAG-TCCACAGTGGCAGTAAACCTTGC
EST: gi|162150260|gb|FC326345.1|FC326345
EST:     CTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAG                         GGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
genomic: CTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAGgtgccctgaa ... ttttgtgcagGGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
EST: gi|162258151|gb|FC433933.1|FC433933
EST:     CTGCTGGTCTGAAGAAAGTCTCANACATTGTGGCGGTTTCAAGTTGCAAG                         GGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
genomic: CTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAGgtgccctgaa ... ttttgtgcagGGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
EST: gi|162173761|gb|FC349937.1|FC349937
EST:     CTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAG                         GGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA
genomic: CTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAGgtgccctgaa ... ttttgtgcagGGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCA

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: 31 (upstream exon), 18 (downstream exon)
Score: 5

TGTAAAAATGACTGCACAACCTGCCAAGCCTCTTATCGCAGATGATGTCCCTGCTGGTCTGAAGAAAGTCTCAAACATTGTGGCGGTTTCAAGTTGCAAGgtgccctgaa ... ttttgtgcagGGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCACAAATGGGTGCAAGGGTTGGCATCTTCGATGCCGACATATATGGTCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaagctctatactttagagtccagagtttgcttttcatattgtttttgtgcagGGTGGAGTTGGGAAGTCCACAGTGGCAGTAAACCTTGCGTATTCACTGGCACAAATGGGTGCAAGGGTTGGCATCTTCGATGCCGACATATATGGTCCCA
                                         ttgttttt  CT-rich tract
                                 ttttcatattgttttt  TA-rich tract