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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgtcaagaagagctactatatagcagcgtttatggtgaggttggagagaatgtcggagttgtgggaggtaacagatgtgtctggcgtggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATG

Basic information

species Physcomitrella patens
transcript PP1S505_6V6.1
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|208348255|gb|DC905497.1|DC905497
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208350053|gb|DC910288.1|DC910288
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACNAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208372097|gb|DC940279.1|DC940279
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAGAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100352660|gb|BY945383.1|BY945383
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100419397|gb|BY957563.1|BY957563
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208353412|gb|DC938689.1|DC938689
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100401171|gb|BY990866.1|BY990866
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100422729|gb|BY957971.1|BY957971
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|18368307|gb|BJ200392.1|BJ200392
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208377072|gb|DC910846.1|DC910846
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100444750|gb|BY982579.1|BY982579
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100386024|gb|BY969963.1|BY969963
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGANAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100359507|gb|BY947022.1|BY947022
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100444882|gb|BY982710.1|BY982710
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100435518|gb|BY960952.1|BY960952
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100399512|gb|BY972756.1|BY972756
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208400164|gb|DC904812.1|DC904812
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208391832|gb|DC942352.1|DC942352
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|67719022|gb|BJ969281.1|BJ969281
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100440118|gb|BY980404.1|BY980404
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208376766|gb|DC902947.1|DC902947
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|18360513|gb|BJ192576.1|BJ192576
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208350009|gb|DC910244.1|DC910244
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|208362445|gb|DC930978.1|DC930978
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
EST: gi|100428843|gb|BY959461.1|BY959461
EST:     AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGA                         GTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG
genomic: AACATTGGCGGAGTTTTGCCGAAACATGAGGTCCTCAAGTCGACTGAAGAgtacgtttcg ... ggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagagaatgtcggagttgtgggaggtaacagatgtgtctggcgtggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATG
                       aggtaac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgtcaagaagagctactatatagcagcgtttatggtgaggttggagagaatgtcggagttgtgggaggtaacagatgtgtctggcgtggtgatgcagGTACGAGAAGTATCATGCTATGCACGGAGGCGACAAAGAAGCAAGAAAGAGCAATTACACTGACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA