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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcattgcttgcatcaaattaagtagtccctttcgaaaagagtttcgtgctgtttttgaaaaaagattattgctggttttttgacaaggtcattcaagCGGCTAGAGGACAAGGCGAGGCACTTCTTTTGACGCAACAGAAGAGGTTCATTTTGGACTTGTCAATGACGGATGTTTCCCACACAACTCGTGCAAGGAT

Basic information

species Physcomitrella patens
transcript PP1S96_156V6.2
intron # 16
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|37845932|gb|BJ603940.1|BJ603940
EST:     GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATG                         CGGCTAGAGGACAAGGCGAGGCACTTCTTTTGACGCAACAGAAGAGGTTCA
genomic: GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATGgttagtttaa ... gtcattcaagCGGCTAGAGGACAAGGCGAGGCACTTCTTTTGACGCAACAGAAGAGGTTCA
EST: gi|37844229|gb|BJ602237.1|BJ602237
EST:     GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATG                         G
genomic: GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATGgttagtttaa ... gtcattcaag-
EST: gi|37844229|gb|BJ602237.1|BJ602237
EST:     GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATG                         G
genomic: GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATGgttagtttaa ... gtcattcaag-
EST: gi|37844229|gb|BJ602237.1|BJ602237
EST:     GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATG                         G
genomic: GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATGgttagtttaa ... gtcattcaag-
EST: gi|37837723|gb|BJ595731.1|BJ595731
EST:     GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATG                         G
genomic: GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATGgttagtttaa ... gtcattcaag-
EST: gi|37837723|gb|BJ595731.1|BJ595731
EST:     GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATG                         G
genomic: GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATGgttagtttaa ... gtcattcaag-
EST: gi|37837723|gb|BJ595731.1|BJ595731
EST:     GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATG                         G
genomic: GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATGgttagtttaa ... gtcattcaag-

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), 35 (downstream exon)
Score: 2

GTTTCTTTGAGGGGTAACTACTCGTATGGGGAAGACAATTTACGCATGgttagtttaa ... gtcattcaagCGGCTAGAGGACAAGGCGAGGCACTTCTTTTGACGCAACAGAAGAGGTTCATTTTGGACTTGTCAATGACGGATGTTTCCCACACAACTCGTGCAAGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtgctgtttttgaaaaaagattattgctggttttttgacaaggtcattcaagCGGCTAGAGGACAAGGCGAGGCACTTCTTTTGACGCAACAGAAGAGGTTCATTTTGGACTTGTCAATGACGGATGTTTCCCACACAACTCGTGCAAGGAT
                                   ttttgac  putative branch site (score: 2)
       tgtttttgaaaaaaga  TA-rich tract