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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgaatattcttctctattgtaattactgttaagatctagttaatattaactgaaaattaggataatcggcttatattatatgttatctgaggtgcagGCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTGCATTGTAAAATATCCGGTGTTTCGGACCACTTCGCTACTG

Basic information

species Physcomitrella patens
transcript PP1S47_126V6.2
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|162162730|gb|FC337784.1|FC337784
EST:     TCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAG                         GCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTG
genomic: TCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAGgtgactgaaa ... tgaggtgcagGCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTG
EST: gi|162180420|gb|FC355841.1|FC355841
EST:     TCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAG                         GCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTG
genomic: TCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAGgtgactgaaa ... tgaggtgcagGCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTG
EST: gi|162179961|gb|FC356032.1|FC356032
EST:     TCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAG                         GCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTG
genomic: TCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAGgtgactgaaa ... tgaggtgcagGCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTG
EST: gi|100370689|gb|BY948467.1|BY948467
EST:     TCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAG                         GCAGCAACTGGAGAGGAG
genomic: TCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAGgtgactgaaa ... tgaggtgcagGCAGCAACTGGAGAGGAG

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: 15 (upstream exon), 21 (downstream exon)
Score: 1

CTGTACCGCTGGGGGTGCGTATGTGCCAGCTATGGCTGATGAAAGCGTCATCGTCAAAGGAAATGGCACAATCTTTCTTGCTGGTCCACCCCTAGTCAAGgtgactgaaa ... tgaggtgcagGCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTGCATTGTAAAATATCCGGTGTTTCGGACCACTTCGCTACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattaactgaaaattaggataatcggcttatattatatgttatctgaggtgcagGCAGCAACTGGAGAGGAGGTTAGCGCCGAGGATCTAGGAGGTGCGGCACTGCATTGTAAAATATCCGGTGTTTCGGACCACTTCGCTACTG
 tattaac  putative branch site (score: 1)
                            ttatattatatgttat  TA-rich tract