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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtctaaatgccgacagtctgttgcgtttactgaatagtttggataatactaaccttacaggtccaaatttgtgataagtcttgacagtctggttgggtgtatatgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTGCGGTATGTCACACGAACGACTGCACTAGAGTATGAGGACATTCGGGCTG

Basic information

species Physcomitrella patens
transcript PP1S96_37V6.2
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|18350871|gb|BJ182922.1|BJ182922
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|67574689|gb|BJ947513.1|BJ947513
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|208352205|gb|DC906308.1|DC906308
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|208392681|gb|DC934011.1|DC934011
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|100443744|gb|BY963841.1|BY963841
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNN
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTT-
EST: gi|100386432|gb|BY951228.1|BY951228
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18329568|gb|BJ161574.1|BJ161574
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18366519|gb|BJ198598.1|BJ198598
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18355429|gb|BJ187488.1|BJ187488
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18359159|gb|BJ191219.1|BJ191219
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18329388|gb|BJ161394.1|BJ161394
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|18343533|gb|BJ175571.1|BJ175571
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG
EST: gi|208376907|gb|DC906848.1|DC906848
EST:     CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAG                         GCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCNNNNNNNG
genomic: CTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTG

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: 28 (upstream exon), 32 (downstream exon)
Score: 14

AGCAGCTATCAAGGCGCTGACAGCTGTTATCAGACGCAGCCAGGCATCCACTATGATGGGTCTCGAGATTGAGCTCAAGAACGCCTCAGAGGCCCTCAAGgtgcgtctaa ... atgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTGCGGTATGTCACACGAACGACTGCACTAGAGTATGAGGACATTCGGGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggtccaaatttgtgataagtcttgacagtctggttgggtgtatatgtgatcagGCTTGGGATGAAACCTCTATACCACTCTCTGCAGGCTGCGACCTTTTTTTGCGGTATGTCACACGAACGACTGCACTAGAGTATGAGGACATTCGGGCTG
                     tcttgac  putative branch site (score: 14)
       aaatttgt  TA-rich tract