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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaggaaacagcttttatttttttattgttagtttttttaaaggagattcaacatctatggaaccagttatttatttatttatttatttatttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGCTTCGCGGACGGAGAAATCTACGTACAGCTACAAGAGAGTGTTCGTGGTT

Basic information

species Physcomitrella patens
transcript PP1S42_193V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ14005 (Selaginella moellendorffii), 3'ss of exon 1
aaaggaaacagcttttatttttttattgttagtttttttaaaggagattcaacatctatggaaccagttatttatttatttatttatttatttcttgt-agGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGCTTCGCGGACGGAGAAATCTACGTACAGCTACAAGAGAGTGTTCGTGGTT
  || | | |   ||| |||| || | |||   | | ||         | || | || |||  |   || ||  |   ||| | | |||  ||  | | |||||||||||| ||||||||| || ||  | ||||||||   ||| |||||||| || ||||| ||||||||||| |||||||| || || ||  | ||  
gtagaagaaaagctttcttttgttctcgttgtctctattg--------ttaa-aactttgg--ctgtttgttcctccctttgtctcttttgttgctatcagGAAATCGCGTGCTACATGGGCCTAGAACTTGGAAAGATTTGCATCAAGCGCTTTGCTGACGGTGAAATCTACGTCCAGCTACAGGAAAGCGTGAGAGGCA

upper sequence: PP1S42_193V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ12994 (Selaginella moellendorffii), 3'ss of exon 1
---aaaggaaacagcttttatttttttattgttagtttttttaaaggagattcaacatctatggaaccagttatttatttatttatttatt-tatttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGCTTCGCGGACGGAGAAATCTACGTACAGCTACAAGAGAGTGTTCGTGGTT
    |||||||    | || | || | |||||   | || ||||  ||  |||    | |           | ||  |   ||| | | || | || ||   |||||||||||| ||||||||| || ||  | ||||||||   ||| |||||||| || ||||| ||||||||||| |||||||| || || ||  | ||  
gtagaaggaaaactttcttttgttctcattgtctctattgttaa--gactttcgctgttt-----------tgttcctccctttgtctcttctgttgctatcagGAAATCGCGTGCTACATGGGCCTAGAACTTGGAAAGATTTGCATCAAGCGCTTTGCTGACGGTGAAATCTACGTCCAGCTACAGGAAAGCGTGAGAGGCA
















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|67570570|gb|BJ943394.1|BJ943394
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100383515|gb|BY950299.1|BY950299
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100356373|gb|BY946332.1|BY946332
EST:     AGAATCGCCTCAAAATCTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100360321|gb|BY966113.1|BY966113
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100352263|gb|BY983120.1|BY983120
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100399937|gb|BY990696.1|BY990696
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|162261958|gb|FC436817.1|FC436817
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|18331554|gb|BJ163565.1|BJ163565
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100354646|gb|BY983494.1|BY983494
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|18326322|gb|BJ158321.1|BJ158321
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100353033|gb|BY945573.1|BY945573
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|18325080|gb|BJ157076.1|BJ157076
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100389903|gb|BY971255.1|BY971255
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|208380333|gb|DC907658.1|DC907658
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|18370446|gb|BJ202048.1|BJ202048
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|208357746|gb|DC902298.1|DC902298
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100372888|gb|BY948750.1|BY948750
EST:     GGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|19780598|gb|BQ039579.1|BQ039579
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|18369243|gb|BJ201328.1|BJ201328
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100441557|gb|BY980979.1|BY980979
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|208399184|gb|DC912427.1|DC912427
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|67573736|gb|BJ946560.1|BJ946560
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|67570680|gb|BJ943504.1|BJ943504
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100429179|gb|BY977979.1|BY977979
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|67571017|gb|BJ943841.1|BJ943841
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|100353317|gb|BY964745.1|BY964745
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
EST: gi|162258694|gb|FC434389.1|FC434389
EST:     AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAA                         GAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC
genomic: AGAATCGCCTCAAAATTTTCTCTGGCACTGCAAATAAGGCTCTTTCCCAAgtatatgcac ... tttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcaacatctatggaaccagttatttatttatttatttatttatttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGCTTCGCGGACGGAGAAATCTACGTACAGCTACAAGAGAGTGTTCGTGGTT
                                     tttatttatttctt  CT-rich tract
                aaccagttatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaggaaacagcttttatttttttattgttagtttttttaaaggagattcaacatctatggaaccagttatttatttatttatttatttatttcttgtagGAAATCGCGTACTACATGGGTCTCGATTTAGGAAAGATAACCATAAAGCGCTTCGCGGACGGAGAAATCTACGTACAGCTACAAGAGAGTGTTCGTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA