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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgagcacaccttagactgtctgagattcaaccgtccctgttcacaatccgtgtttctgttgatgtgctgagccaattatgcatgttgtttctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGCAATGCAGTAGCTGGTCTCCCATCCAGAAAAGGTCTTCATTCTGCCATGT

Basic information

species Physcomitrella patens
transcript PP1S7_406V6.1
intron # 10
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|208350585|gb|DC922114.1|DC922114
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|162154869|gb|FC331911.1|FC331911
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|162162643|gb|FC338945.1|FC338945
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|37847527|gb|BJ605535.1|BJ605535
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|162250069|gb|FC427378.1|FC427378
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|208376893|gb|DC918792.1|DC918792
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|162250070|gb|FC427379.1|FC427379
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|37850322|gb|BJ608330.1|BJ608330
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|208398626|gb|DC920521.1|DC920521
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|162161580|gb|FC338787.1|FC338787
EST:     CCCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|162195749|gb|FC371140.1|FC371140
EST:     ACCATAGTGAACTCCTGGAACACGAACTGNGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|162195748|gb|FC371139.1|FC371139
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|162171828|gb|FC348978.1|FC348978
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|208345947|gb|DC921104.1|DC921104
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
EST: gi|37843562|gb|BJ601570.1|BJ601570
EST:     ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAG                         GATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC
genomic: ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGC

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: 35 (upstream exon), 31 (downstream exon)
Score: 17

ACCATAGTGAACTCCTGGAACACGAACTGGGGAGAGgtacaccact ... tctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGCAATGCAGTAGCTGGTCTCCCATCCAGAAAAGGTCTTCATTCTGCCATGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatccgtgtttctgttgatgtgctgagccaattatgcatgttgtttctgctccagGATGGTCTCTTCCGTATTGTGAGAGGCAACGATGAGTGTGGCATTGAGAGCAATGCAGTAGCTGGTCTCCCATCCAGAAAAGGTCTTCATTCTGCCATGT
            tgttgat  putative branch site (score: 17)
                                           tttctgctcc  putative PPT
                             aattat  TA-rich tract