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 fgf1a (ENSDARG00000017542) (Zebrafish)		AlignView depth	PhyloView depth
Fungi/Metazoa group	~1500 Mya	114 species
Bilateria	~580 Mya	112 species	523 homologs (oldest homol.)
Coelomata	~570 Mya	110 species	521 homologs
Olfactores	~550 Mya	108 species	519 homologs (dupl. node) 212 homologs
Pre-1R	~550 Mya	104 species	206 homologs
Vertebrata	~550 Mya	102 species	204 homologs
Euteleostomi	~420 Mya	100 species	200 homologs (dupl. node) 113 homologs
Clupeocephala	~320 Mya	14 species	27 homologs (dupl. node) 14 homologs
Zebrafish	~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