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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagcgacccattcaaacgttctcttgttacgcaacgtacttacagtgactcaggcttttggatctgatgcgttggtattttgaaatgtctcatattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCGGGGTGCTGATGCGGATGTTCCCCTTTCAGAACAG

Basic information

species Physcomitrella patens
transcript PP1S8_105V6.1
intron # 4
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|208382534|gb|DC919758.1|DC919758
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|162221832|gb|FC398399.1|FC398399
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|22491811|gb|BU051734.1|BU051734
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|18339333|gb|BJ171360.1|BJ171360
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|162222858|gb|FC399320.1|FC399320
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|208348631|gb|DC905868.1|DC905868
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|162221833|gb|FC398400.1|FC398400
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|22492703|gb|BU052626.1|BU052626
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|37840617|gb|BJ598625.1|BJ598625
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|37834059|gb|BJ592071.1|BJ592071
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|67579152|gb|BJ951303.1|BJ951303
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|162222859|gb|FC399321.1|FC399321
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|7286949|gb|AW599436.1|AW599436
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAG
EST: gi|67507871|gb|BJ940747.1|BJ940747
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|37835955|gb|BJ593967.1|BJ593967
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
EST: gi|22132772|gb|BQ827346.1|BQ827346
EST:     GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGG                         CATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG
genomic: GAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCG

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: 33 (upstream exon), 31 (downstream exon)
Score: 8

AAACAACGTCGACAAAAAGAGTGTGCTGGAAAACCTAGATCTCGTCCTTCTCTGCCTTGATGAGATCATAGATGGCGGgtatatcttc ... catattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCGGGGTGCTGATGCGGATGTTCCCCTTTCAGAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactcaggcttttggatctgatgcgttggtattttgaaatgtctcatattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCGGGGTGCTGATGCGGATGTTCCCCTTTCAGAACAG
                atctgat  putative branch site (score: 8)
                              tattttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagcgacccattcaaacgttctcttgttacgcaacgtacttacagtgactcaggcttttggatctgatgcgttggtattttgaaatgtctcatattgcagCATCATTCTAGAGACTGATGCCAACGTCATAGCCGGCAGAGTTTCAATGCGGGGTGCTGATGCGGATGTTCCCCTTTCAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT