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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttttcggcttgtacggcttggagagaacagtcttcgttggggttgtgtcgtttcttcttgcatctgttcagagccgtgatatgttgtgcactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACCGAGCAACAGCTATTTCAGCAGCGGCTAAAACATCAAAGTCTCGTGCAAG

Basic information

species Physcomitrella patens
transcript PP1S84_50V6.2
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|100358593|gb|BY965724.1|BY965724
EST:     CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAG                         GTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
genomic: CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAGgtcagtggct ... cactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
EST: gi|18362766|gb|BJ194837.1|BJ194837
EST:     CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAG                         GTCANAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
genomic: CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAGgtcagtggct ... cactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
EST: gi|18363170|gb|BJ195242.1|BJ195242
EST:     CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAG                         GTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
genomic: CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAGgtcagtggct ... cactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
EST: gi|100407206|gb|BY974055.1|BY974055
EST:     CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAG                         GTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
genomic: CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAGgtcagtggct ... cactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
EST: gi|18373540|gb|BJ205118.1|BJ205118
EST:     CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAG                         GTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
genomic: CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAGgtcagtggct ... cactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
EST: gi|18375107|gb|BJ206685.1|BJ206685
EST:     CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAG                         GTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
genomic: CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAGgtcagtggct ... cactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
EST: gi|100377715|gb|BY986366.1|BY986366
EST:     CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAG                         GTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC
genomic: CTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAGgtcagtggct ... cactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACC

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: 21 (upstream exon), 32 (downstream exon)
Score: 4

AACTTCGGTCTCTGCTTTGTCCTCCATTTCCCCCTTTGCAGCGATTGCAACTGCACCCACTTCCTCGTCTAGTCCGACCGCTGCCACCCCGATCACCGAGgtcagtggct ... cactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACCGAGCAACAGCTATTTCAGCAGCGGCTAAAACATCAAAGTCTCGTGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcgtttcttcttgcatctgttcagagccgtgatatgttgtgcactaattagGTCAGAAACGCCGAGCGTGTGTTTGCCAAAGCGCATACAATGCAGCAGACCGAGCAACAGCTATTTCAGCAGCGGCTAAAACATCAAAGTCTCGTGCAAG
                                              actaatta  TA-rich tract