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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgaaactcgttttgtggcgcaaatttcaccggaaaccaaaattagtgactataattgtttgtgttatttctgaagttgctgtattcttggtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG

Basic information

species Physcomitrella patens
transcript PP1S47_175V6.1
intron # 1
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|100446572|gb|CJ970871.1|CJ970871
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100448859|gb|CJ973158.1|CJ973158
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAN                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100375388|gb|BY948854.1|BY948854
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100416395|gb|BY975367.1|BY975367
EST:     AGATTGGAACTTTTCCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100448868|gb|CJ973167.1|CJ973167
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100379831|gb|BY949966.1|BY949966
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCGGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|67724008|gb|BJ974267.1|BJ974267
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208355833|gb|DC930196.1|DC930196
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100427879|gb|BY959171.1|BY959171
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTTATCGAAAGTGCAGAA
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATT-ATCGAAAGTGCAGAA
EST: gi|67569178|gb|BJ942002.1|BJ942002
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|18356169|gb|BJ188228.1|BJ188228
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208384047|gb|DC911225.1|DC911225
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208366345|gb|DC943863.1|DC943863
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208370373|gb|DC931785.1|DC931785
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAGAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100381026|gb|BY986852.1|BY986852
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208394403|gb|DC942563.1|DC942563
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208389723|gb|DC938299.1|DC938299
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208391012|gb|DC929331.1|DC929331
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|67716920|gb|BJ967179.1|BJ967179
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|67709929|gb|BJ965745.1|BJ965745
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100442587|gb|BY963281.1|BY963281
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|100364611|gb|BY947820.1|BY947820
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208385596|gb|DC937141.1|DC937141
EST:     AGATTGGAACTTTTTCAGCGCTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208380443|gb|DC914867.1|DC914867
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTACCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208354200|gb|DC957420.1|DC957420
EST:     GATTGGAACTTTTTCAGCGCTTTTGAGAACGACGGCTCTGGGGNCATCAG                         GAAATAAAAAAGNTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAA
genomic: GATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGG-CATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAA
EST: gi|67725438|gb|BJ975697.1|BJ975697
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTNTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208389767|gb|DC933641.1|DC933641
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208361102|gb|DC957553.1|DC957553
EST:     GATTGGAACTTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: GATTGGAAC-TTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|162272918|gb|FC448854.1|FC448854
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|162272917|gb|FC448853.1|FC448853
EST:     CAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: CAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208368823|gb|DC951347.1|DC951347
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
EST: gi|208387707|gb|DC937272.1|DC937272
EST:     AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAG                         GAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG
genomic: AGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAG

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

GAAGATCACGTTTCCGCTCGAACACTCGCTTGGTGATGGCAAGTTTGAACAGATTGGAACTTTTTCAGCACTTTTGAGAACGACGGCTCTGGGGCATCAGgtgcagtgcg ... gtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgactataattgtttgtgttatttctgaagttgctgtattcttggtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG
                                              tttctgc  CT-rich tract
     tataattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgaaactcgttttgtggcgcaaatttcaccggaaaccaaaattagtgactataattgtttgtgttatttctgaagttgctgtattcttggtttctgcagGAAATAAAAAAGCTACGACTCGAAAGGAACAAATTATCGAAAGTGCAGAAGCGGCAATTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgta