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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctatctggttttgttgtaattactccttgttgtcggtttcttatcgtgaggaaaaaatcttacctggttttttcttccgtttgcatttcctattgcagTTCTTCCACCAACAGGTTGATCACTTCGAAGGATGTTGCTTCAGTTCAGTTGAATGTGGGCCATGTCGACGAGAACGGTGTTTACACCGGGCAGTTTACC

Basic information

species Physcomitrella patens
transcript PP1S287_34V6.1
intron # 1
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|7047433|gb|AW477327.1|AW477327
EST:     GCAGAACGAGGAGGGTGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCCACCAACAGGTTGATCACTTCAAAGGATGTTGCTTCAGTTCAGTT
genomic: GCAGAACGAGGAGGGTGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgcgtataa ... cctattgcagTTCTTCCACCAACAGGTTGATCACTTCGAAGGATGTTGCTTCAGTTCAGTT
EST: gi|162252941|gb|FC429002.1|FC429002
EST:     CGAGGAGGGTGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCCACCAACAGGTTGATCACTTCGAAGGATGTTGCTTCAGTTCAGTT
genomic: CGAGGAGGGTGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgcgtataa ... cctattgcagTTCTTCCACCAACAGGTTGATCACTTCGAAGGATGTTGCTTCAGTTCAGTT
EST: gi|162252940|gb|FC429001.1|FC429001
EST:     CGAGGAGGGTGACAATGTGGATCTCTACATCCCCAGGAAGTG                         TTCTTCCACCAACAGGTTGATCACTTCGAAGGATGTTGCTTCAGTTCAGTT
genomic: CGAGGAGGGTGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgcgtataa ... cctattgcagTTCTTCCACCAACAGGTTGATCACTTCGAAGGATGTTGCTTCAGTTCAGTT

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), 34 (downstream exon)
Score: 27

CTTTTCTCTCGATCTCTCTCTCTCTCTCTCTCTCTCGCTTATCTTGCACCATGCAGAACGAGGAGGGTGACAATGTGGATCTCTACATCCCCAGGAAGTGgtgcgtataa ... cctattgcagTTCTTCCACCAACAGGTTGATCACTTCGAAGGATGTTGCTTCAGTTCAGTTGAATGTGGGCCATGTCGACGAGAACGGTGTTTACACCGGGCAGTTTACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtgaggaaaaaatcttacctggttttttcttccgtttgcatttcctattgcagTTCTTCCACCAACAGGTTGATCACTTCGAAGGATGTTGCTTCAGTTCAGTTGAATGTGGGCCATGTCGACGAGAACGGTGTTTACACCGGGCAGTTTACC
             atcttac  putative branch site (score: 27)
                        ttttttcttccgtttg  putative PPT
        aaaaaatctta  TA-rich tract