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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatctactgaaagatgtgtaccctattgtcattttatttcgggaggtaatgtatatccaatattagagaatgtagtaaccatgccctggattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCGACTGGTGTAGACCCATCTCCAGAGAACTGGAAGGAGATTTCTGCATTTT

Basic information

species Physcomitrella patens
transcript PP1S223_31V6.1
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|67716236|gb|BJ966496.1|BJ966496
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAG                         AAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
EST: gi|162256780|gb|FC432674.1|FC432674
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAG                         AAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
EST: gi|19789721|gb|BQ041471.1|BQ041471
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAG                         AAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
EST: gi|208361604|gb|DC942847.1|DC942847
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGNATGTGAA-                         AAAGCTCCCAATG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATG
EST: gi|162274186|gb|FC449946.1|FC449946
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAG                         AAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
EST: gi|162257990|gb|FC434084.1|FC434084
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAG                         AAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
EST: gi|162192506|gb|FC371697.1|FC371697
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAG                         AAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
EST: gi|162198689|gb|FC373470.1|FC373470
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAG                         AAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
EST: gi|100446972|gb|CJ971271.1|CJ971271
EST:     ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAG                         AAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG
genomic: ACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCG

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: 31 (upstream exon), 35 (downstream exon)
Score: 13

CAACATCTGGAGGGATGCCAACGTTCCTCAGAACACTTTCCGTTACTATGACGCAGCTACCAAGGGCCTCGACTTCAAGGGCCTCATGGAGGATGTGAAGgttagtgcta ... gattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCGACTGGTGTAGACCCATCTCCAGAGAACTGGAAGGAGATTTCTGCATTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtaatgtatatccaatattagagaatgtagtaaccatgccctggattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCGACTGGTGTAGACCCATCTCCAGAGAACTGGAAGGAGATTTCTGCATTTT
                             tagtaac  putative branch site (score: 13)
        tatatccaatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatctactgaaagatgtgtaccctattgtcattttatttcgggaggtaatgtatatccaatattagagaatgtagtaaccatgccctggattttgcagAAAGCTCCCAATGGTTCAGTTTTCCTATTGCACGCTTGTGCACACAACCCGACTGGTGTAGACCCATCTCCAGAGAACTGGAAGGAGATTTCTGCATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT