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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtggcttcgtatccattcagttctctgtaatattatgtagcagaattggtggagtaaataataactatgcaagattttcggttgggctggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGAACAAAAACTAGCAGACATGCCTGCAGATGAAGCTGCAGTATACTGCAAG

Basic information

species Physcomitrella patens
transcript PP1S207_28V6.1
intron # 7
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|162264592|gb|FC440888.1|FC440888
EST:     GGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTGAGCGGTGTGTTAGA
genomic: GGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37827125|gb|BJ585137.1|BJ585137
EST:     AAGGATTACCANCGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|162175834|gb|FC352136.1|FC352136
EST:     CGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTNAGCGGTGTGTTAGA
genomic: CGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|162217120|gb|FC392484.1|FC392484
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|162191631|gb|FC367676.1|FC367676
EST:     AACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|162263698|gb|FC439623.1|FC439623
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         NGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTG
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTG
EST: gi|37840412|gb|BJ598420.1|BJ598420
EST:     TAGCTAAGATTCATGCTNG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: TAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37826709|gb|BJ584721.1|BJ584721
EST:     AAGGATTACCANCGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37827937|gb|BJ585949.1|BJ585949
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37828408|gb|BJ586420.1|BJ586420
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|208374509|gb|DC944979.1|DC944979
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37839229|gb|BJ597237.1|BJ597237
EST:     TAAGATTCATGCTNG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: TAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|208352669|gb|DC921403.1|DC921403
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|67720060|gb|BJ970319.1|BJ970319
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|162217121|gb|FC392485.1|FC392485
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37837900|gb|BJ595908.1|BJ595908
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|162263697|gb|FC439622.1|FC439622
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37848687|gb|BJ606695.1|BJ606695
EST:     AGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|208353452|gb|DC946316.1|DC946316
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|67697251|gb|BJ957484.1|BJ957484
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|208378223|gb|DC918844.1|DC918844
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37845126|gb|BJ603134.1|BJ603134
EST:     AAGGATTACCANCGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTNAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37826854|gb|BJ584866.1|BJ584866
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|162175835|gb|FC352137.1|FC352137
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTC-ATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|162272680|gb|FC448306.1|FC448306
EST:     AAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37845996|gb|BJ604004.1|BJ604004
EST:     AAGGATTACCANCGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
EST: gi|37824831|gb|BJ582897.1|BJ582897
EST:     AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTG                         GGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA
genomic: AAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGA

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: 32 (upstream exon), 32 (downstream exon)
Score: 10

ATCAACATGACGGAGAAGGATTACCAACGGAAGAAAAACAAGTGGCTAGCTAAGATTCATGCTTGgtaatatcta ... ggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGAACAAAAACTAGCAGACATGCCTGCAGATGAAGCTGCAGTATACTGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattggtggagtaaataataactatgcaagattttcggttgggctggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGAACAAAAACTAGCAGACATGCCTGCAGATGAAGCTGCAGTATACTGCAAG
               taataac  putative branch site (score: 10)
                                               ttttcc  putative PPT
         agtaaataataactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtggcttcgtatccattcagttctctgtaatattatgtagcagaattggtggagtaaataataactatgcaagattttcggttgggctggttttccagGGTACAGGAACATGGAGGTGGTGTCTTAATTCCATTTAGCGGTGTGTTAGAACAAAAACTAGCAGACATGCCTGCAGATGAAGCTGCAGTATACTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG