Genomicus v110.01 - Gene Search

Here you can choose the oldest ancestor of your phylogenetic range of interest and the view you want to display by clicking on one of the following links.

PhyloView will show the conservation of the neighbourhood of the reference gene in the other species, according to the gene phylogenetic tree.
AlignView will align the gene order of the selected species, according to the species phylogenetic tree.

Root species for RDH16 (ENSTBEG00000015696) (Tree shrew)		AlignView depth	PhyloView depth
Fungi/Metazoa group	~1500 Mya	399 species
Bilateria	~580 Mya	397 species
Chordata	~550 Mya	393 species
Vertebrata	~550 Mya	389 species	714 homologs (oldest homol.)
Gnathostomata	~473 Mya	385 species	711 homologs
Euteleostomi	~420 Mya	383 species	710 homologs
Sarcopterygii	~400 Mya	253 species	709 homologs
Tetrapoda	~359 Mya	251 species	707 homologs
Amniota	~326 Mya	247 species	676 homologs (dupl. node) 428 homologs
Mammalia	~184 Mya	193 species	404 homologs
Theria	~166 Mya	191 species	400 homologs
Eutheria	~102 Mya	181 species	384 homologs
Boreoeutheria	~95 Mya	171 species	375 homologs
Euarchontoglires	~90 Mya	95 species	191 homologs
Euarchontoglires_A	~90 Mya	47 species	113 homologs
Tree shrew	~0 Mya	1 species	1 homolog

Advanced Options

-evalue <Real>
 Expectation value (E) threshold for saving hits
 Default = '10'

-word_size <Integer, >=2>
 Word size for wordfinder algorithm
 Default = '3'

-gapopen <Integer>
 Cost to open a gap
 Default = '11'

-gapextend <Integer>
 Cost to extend a gap
 Default = '1'

-matrix <String>
Scoring matrix name (normally BLOSUM62)

-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
 Default = '11'

-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
 Default = '40'