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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTGGTTTTAATGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgttatcagcatgttaattttttatttgtaggttcctattgagtatttaatgtcaatggcacctatgttttaggcatactgcttcagttgtattctctcaattatactcttatattttatccgttgatatgttatctgtaatatcttgtatttctaactacttgtgatgatggcag

Basic information

species Physcomitrella patens
transcript PP1S271_49V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S271_49V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT2G24765.1 (Arabidopsis thaliana), 5'ss of exon 3
CTATTGGTTTTAATGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgttatcagcatgttaattttttatttgtaggttcctattgagtatttaatgtcaa-tggcacctatg-ttttaggcatactgcttcagttgtattctctcaattatactcttatattttatccgttgatatgttatctgtaatatcttgtatttctaactacttgtgatgatggcag
||||||| ||||| || |||||||||   ||||||||||| |||||||| |||||||||||||||  || ||   || ||||          || | | |     ||| |   || ||| | || | | |   ||| |||| || ||  |     ||   |||||    || | |||                                                                     
CTATTGGATTTAACGTTGAGACTGTGCAGTACAACAATATCAAGTTTCAGGTCTGGGATTTAGgtatgttttcgaagaatgt---------gttcgaacgc----attaaactttgaatttgaagtagtagaaatgatttttggtattatatggaagggatattcg---aaatctacaa-------------------------------------------------------------------
















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|208386675|gb|DC929121.1|DC929121
EST:     TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAG                         GGGGTCAAACGAGTATCAG
genomic: TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgtta ... atgatggcagGGGGTCAAACGAGTATCAG
EST: gi|208374444|gb|DC940717.1|DC940717
EST:     TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAG                         GGGGTCAAACGAGTATCAG
genomic: TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgtta ... atgatggcagGGGGTCAAACGAGTATCAG
EST: gi|162240378|gb|FC419311.1|FC419311
EST:     TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAG                         GGGGTCAAACGAGTATCAG
genomic: TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgtta ... atgatggcagGGGGTCAAACGAGTATCAG
EST: gi|208392443|gb|DC907920.1|DC907920
EST:     TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAG                         GGGGTCAAACGAGTATCAG
genomic: TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgtta ... atgatggcagGGGGTCAAACGAGTATCAG
EST: gi|67569908|gb|BJ942732.1|BJ942732
EST:     TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAG                         GGGGTCAAACGAGTATCAG
genomic: TGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgtta ... atgatggcagGGGGTCAAACGAGTATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATTGGTTTTAATGTGGAGACTGTGACATACAACAATATAAAGTTTCAAGTCTGGGATTTAGgttcgtgttatcagcatgttaattttttatttgtaggttcctattgagtatttaatgtcaatggcacctatgttttaggcatactgcttcagttgtattctctcaattatactcttatattttatccgttgatatgttatctgtaatatcttgtatttctaactacttgtgatgatggcag

- - - - - - - GTGGAG
- - - - - - -  TGGAGA