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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagatttcacgatcaggtggtatatatcgagtttctttgatcatgcatggattcgcagattttttcattgttctgatgcatttggatggcaatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG

Basic information

species Physcomitrella patens
transcript PP1S90_13V6.1
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|162199311|gb|FC375147.1|FC375147
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|208352454|gb|DC910182.1|DC910182
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|100379542|gb|BY949821.1|BY949821
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|162190182|gb|FC365924.1|FC365924
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|100427225|gb|BY959038.1|BY959038
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCCAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|100440297|gb|BY962162.1|BY962162
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|208388191|gb|DC933227.1|DC933227
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|100377995|gb|BY949627.1|BY949627
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|100370769|gb|BY948507.1|BY948507
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
EST: gi|162186442|gb|FC362998.1|FC362998
EST:     GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGG                         TATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
genomic: GCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG

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), 35 (downstream exon)
Score: 39

GCACGATGGTGCGAGGTACGAGACCGAGCAACTCCAGAACCGCCTACTGCTGTCCTTTTGCATGGCATCTTGGGAGGACGTCGGAATTGGGgtaatctgtt ... caatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatggattcgcagattttttcattgttctgatgcatttggatggcaatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG
                          ttctgat  putative branch site (score: 39)
              attttttcattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagatttcacgatcaggtggtatatatcgagtttctttgatcatgcatggattcgcagattttttcattgttctgatgcatttggatggcaatgtgcagTATCCTTTGCCAAGAGGCTTGCTCAAGAGTTTCCAACCTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG