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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctggtgacctgaggcattgttcgtatacgtgtggtgggaactcagtactgtcaggttttgtactaaagtgtatttgtatatgtatttcgattttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGATTATCCCAGCAAGCCCCCCAAGTGCAAGTTTCCACAGGGTTTTTTCCACC

Basic information

species Physcomitrella patens
transcript PP1S101_152V6.1
intron # 2
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|162260100|gb|FC435819.1|FC435819
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|19789833|gb|BQ041539.1|BQ041539
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|67698345|gb|BJ958578.1|BJ958578
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|208359068|gb|DC957816.1|DC957816
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|162271913|gb|FC448123.1|FC448123
EST:     GATCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|37821663|gb|BJ579729.1|BJ579729
EST:     GAGCTCTAAATTTGATGGTTTGNCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|162212826|gb|FC388626.1|FC388626
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|67570281|gb|BJ943105.1|BJ943105
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|67574918|gb|BJ947742.1|BJ947742
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|162203152|gb|FC379249.1|FC379249
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|208361067|gb|DC957532.1|DC957532
EST:     GAGCTCTAAANTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
EST: gi|162231752|gb|FC408514.1|FC408514
EST:     GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGG                         ACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT
genomic: GAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGAT

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: 48

GGATTTGTAGCGAGGCCGGAGACAGGTGCAGATGGAGCTCTAAATTTGATGGTTTGGCAGTGCACTTTGCCTGGAAAAGTTGGGgtatgatttc ... attttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGATTATCCCAGCAAGCCCCCCAAGTGCAAGTTTCCACAGGGTTTTTTCCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactgtcaggttttgtactaaagtgtatttgtatatgtatttcgattttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGATTATCCCAGCAAGCCCCCCAAGTGCAAGTTTCCACAGGGTTTTTTCCACC
                tactaaa  putative branch site (score: 48)
                                              ttttgcc  putative PPT
                          tatttgtatatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctggtgacctgaggcattgttcgtatacgtgtggtgggaactcagtactgtcaggttttgtactaaagtgtatttgtatatgtatttcgattttgccagACGGACTGGGAAGGTGGATTTTACCCTGTAGCAATTCACTTCAGTGAGGATTATCCCAGCAAGCCCCCCAAGTGCAAGTTTCCACAGGGTTTTTTCCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG