Genomicus v69.10 - 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 PHF10 (ENSTTRG00000011051) (Dolphin)		AlignView depth	PhyloView depth
Fungi/Metazoa group	~1500 Mya	114 species
Bilateria	~580 Mya	112 species	452 homologs (oldest homol. - dupl. node) 119 homologs
Coelomata	~570 Mya	110 species	117 homologs
Olfactores	~550 Mya	108 species	115 homologs
Pre-1R	~550 Mya	104 species	111 homologs
Vertebrata	~550 Mya	102 species	109 homologs
Euteleostomi	~420 Mya	100 species	108 homologs
Sarcopterygii	~400 Mya	85 species	93 homologs
Tetrapoda	~359 Mya	83 species	91 homologs
Amniota	~326 Mya	81 species	89 homologs
Mammalia	~184 Mya	71 species	79 homologs
Theria	~166 Mya	69 species	77 homologs
Eutheria	~102 Mya	63 species	71 homologs
Boreoeutheria	~95 Mya	54 species	62 homologs
Laurasiatheria	~88 Mya	20 species	26 homologs
Cetartiodactyla	~61 Mya	5 species	7 homologs
Dolphin	~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'

This release of Genomicus is specifically associated with a study describing the evolution of the ancestral vertebrate genome (Pre-1R).

A more recent version of Genomicus without the Pre-1R reconstructed ancestor is available here