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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagtcgtggtctcaatttaatgttatagttgtattgcgcaggtttctgcattttctgagcttatgagttaacgagtaaaattattacatctccgtatattttttgtgtttcttctgtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGCGACTCTGATGTTTATGAGTGCGCTTACGTCCAATCCGAG

Basic information

species Physcomitrella patens
transcript PP1S79_110V6.1
intron # 3
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|162170324|gb|FC346521.1|FC346521
EST:     CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATG                         GCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATTCGAGCCATGGATGGC
genomic: CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATGgtaagagtcg ... gtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
EST: gi|37840321|gb|BJ598329.1|BJ598329
EST:     CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATG                         GCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
genomic: CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATGgtaagagtcg ... gtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
EST: gi|162153053|gb|FC330083.1|FC330083
EST:     CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATG                         GCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
genomic: CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATGgtaagagtcg ... gtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
EST: gi|162168311|gb|FC344625.1|FC344625
EST:     CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATG                         GCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
genomic: CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATGgtaagagtcg ... gtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
EST: gi|162195924|gb|FC375657.1|FC375657
EST:     CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATG                         GCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
genomic: CTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATGgtaagagtcg ... gtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
EST: gi|7147878|gb|AW509800.1|AW509800
EST:     GGATCTGCTACTCTTTCAATG                         GCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC
genomic: GGATCTGCTACTCTTTCAATGgtaagagtcg ... gtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGC

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: 34 (upstream exon), 35 (downstream exon)
Score: 22

TACACCTGCGGAAGTGGAGGAGCTGACCGTGCGTATCCAGAATGCCGGTACTGAGGTTGTGGACGCTAAGGCCGGAGCTGGATCTGCTACTCTTTCAATGgtaagagtcg ... gtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGCGACTCTGATGTTTATGAGTGCGCTTACGTCCAATCCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgagtaaaattattacatctccgtatattttttgtgtttcttctgtgcatacagGCGTATGCTGCTGCCAGATTTGCTGAATCGTGCATGCGAGCAATGGATGGCGACTCTGATGTTTATGAGTGCGCTTACGTCCAATCCGAG
 agttaac  putative branch site (score: 22)
                                     tttcttctgt  putative PPT
     taaaattattacatct  TA-rich tract