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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaacacactaacaacatagatcgatttgaaatatgaatatgtaacttaaagtttttggaattttgtaaaagcttgagcgatctcttgttgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG

Basic information

species Physcomitrella patens
transcript PP1S132_95V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S132_95V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 9
-----atgaacacactaacaacatagatcgatt-tgaaatatga---atatgtaacttaaagttt--ttgga-----attttg----taaaagcttgagc-gatctcttgttg-------ctgttcagGCGTC-TTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG
     ||  |     ||| ||      || |   |  ||  |||   ||||||     || |  |   | ||     |||  |    ||||||  || ||  |  |||| |||        | | |  | |   | ||| | |||||||| || ||| ||||||| ||||| ||| |||||||||||||| | |||||||| | ||| |||||| || |  |||
gtaacattgatgtcataataattctagtcaaccatagaaagtgagctatatgttgagaaaggcatgcctagaggcagattcagggaataaaagtgtgtgctaagttctttttgattatatttttactagTGCAATGTTCAATGAATGGACTGTGGAGCTGAAGGGCATGGCTGATAGGATTATTAGCATGAGGCAACAGCTTTTTGATGCTCTGAAAACGAGAG

upper sequence: PP1S132_95V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv04s0008g03770.t01 (Vitis vinifera), 3'ss of exon 9
----atgaacacactaacaacatagatcgatttgaaatatgaatatgtaacttaaagtttttggaattttgtaaaagcttgagcgatctcttgttgctgtt-cagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG
      |||  || | | | |  |||  |||  ||  |   |   | | |  || |    ||   |||  ||     ||| |      |  |  |     | ||||  | | | | | |||||||| || ||||||||||  ||||||||||| ||||| |||||||| || || |||| ||| ||| | |  ||  |||
tgatgcgaatgcattca-atcgcagaaggat--gatgtgatagcttcttaaatatacacgtttagattacgtccc--cttaaatttgtttgtactttgactgcagGGATATGTACAATGAATGGACTGTTGAGTTGAAGGCAATGGCAGATCGTATTATCAGCATGCGCCAGCAACTCTTTGATGCTTTACGGGCCAGAG
















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|208348540|gb|DC905819.1|DC905819
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|208385027|gb|DC919707.1|DC919707
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162173605|gb|FC349573.1|FC349573
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162182166|gb|FC358181.1|FC358181
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|67726923|gb|BJ977182.1|BJ977182
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|37831224|gb|BJ589236.1|BJ589236
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162196336|gb|FC375406.1|FC375406
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|37839276|gb|BJ597284.1|BJ597284
EST:     TGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: TGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|208400819|gb|DC925099.1|DC925099
EST:     AGCCCCCCGNCTCATGGNGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162267155|gb|FC443386.1|FC443386
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|208350485|gb|DC926452.1|DC926452
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162205457|gb|FC381555.1|FC381555
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162196335|gb|FC375405.1|FC375405
EST:     GCCCCCCGGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGTTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: GCCCCCC-GGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162173604|gb|FC349572.1|FC349572
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|208366377|gb|DC947573.1|DC947573
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162175651|gb|FC351238.1|FC351238
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162263808|gb|FC438427.1|FC438427
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|37842485|gb|BJ600493.1|BJ600493
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTNTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
EST: gi|162176138|gb|FC351087.1|FC351087
EST:     AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGG                         GCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT
genomic: AGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGAT

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), 34 (downstream exon)
Score: 15

CAAGTCGGGTAGACAGTCAGTTAAAACTGGTCATCCGCCCCATGTACTCTAGCCCCCCGGCTCATGGTGCAGCCATTGCAGCGACGATTCTAGCTGACGGgtattgcttt ... tgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttaaagtttttggaattttgtaaaagcttgagcgatctcttgttgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG
 atgtaac  putative branch site (score: 15)
                                     tctcttgtt  putative PPT
               aattttgtaaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaacacactaacaacatagatcgatttgaaatatgaatatgtaacttaaagtttttggaattttgtaaaagcttgagcgatctcttgttgctgttcagGCGTCTTTTCCAGGAATGGACGGTAGAGTTGAAGGGTATGGCAGATCGGATTATTAGCATGCGTCAACAGCTCTATGACGCTCTGCAAGCTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT