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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcagctcaaaatgtatagattttttttctgctctaatcagtcatgtacagtgttagatttttttcgaatgaagtatcttaaccgtgagcgggtc...

Basic information

species Physcomitrella patens
transcript PP1S1_300V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_300V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 3
GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcagctcaaaatgtatagattttttttctgctctaatcagtcatgtacagtgttagatttttttcgaatgaagtatcttaaccgtgagcgggtc-----
|||||  | ||||||||||||||| | || |||||||||||||| |||||||||  ||  |   ||  ||  || | | || |     |||   |||| |    | ||   ||||| |    || |  |   |    |  | |||        
GCTGGTCTTGCTAAACTTATTGGACTCGCTGGAGAAACCAATGTTCAGgtaatta-agtgcttcataaattaatatatattat----caatttatcatattttttttttagtttttatttggtgtaacaaggttttagaaaacggcgtgcaag
















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|18325673|gb|BJ157670.1|BJ157670
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|100391045|gb|BY953055.1|BY953055
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|100404176|gb|BY955293.1|BY955293
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|100396704|gb|BY953785.1|BY953785
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|100445852|gb|CJ970151.1|CJ970151
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208373427|gb|DC931872.1|DC931872
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208393616|gb|DC904332.1|DC904332
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|100372971|gb|BY949374.1|BY949374
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|100352928|gb|BY945520.1|BY945520
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208391526|gb|DC937674.1|DC937674
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGCGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208352123|gb|DC906268.1|DC906268
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTCCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208378504|gb|DC927201.1|DC927201
EST:     GGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208384630|gb|DC907103.1|DC907103
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|100353087|gb|BY945599.1|BY945599
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|67570889|gb|BJ943713.1|BJ943713
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208380958|gb|DC903870.1|DC903870
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208350215|gb|DC901599.1|DC901599
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208376930|gb|DC910792.1|DC910792
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|208378151|gb|DC902624.1|DC902624
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|162193916|gb|FC371729.1|FC371729
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
EST: gi|67575305|gb|BJ948129.1|BJ948129
EST:     GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAG                         GGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC
genomic: GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcag ... gcaattgcagGGCGAGGAGCAGAAAAAGCTCGATGTCTTGTCGAATCATGTCTTCATCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGATTAGCTAAACTTATTGGATTGGCAGGAGAAACCAATGTGCAGgtaatttcagctcaaaatgtatagattttttttctgctctaatcagtcatgtacagtgttagatttttttcgaatgaagtatcttaaccgtgagcgggtc

- - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - GGAGAA