Gene Name RM04
Description 39S ribosomal protein L4, mitochondrial
Links Uniprot
Organism Homo sapiens
Length 311
What is the source the Gene Ontology annotation?
The Gene Ontology annotations are retrieved from the EBI's QuickGO webservice. Further informations are available in the external data sources section
What is the quality of these annotations?
For now, all GO term annotations, regardless of their evidence code, are displayed. No quality filter are used to provide the widest possible range of annotations. You can check the labels near each annotation for evidence details: manually reviewed annotations are displayed in blue, while the automatic ones are in grey.
What is the source the domain annotation?
The domain annotations are dynamically queried from the Interpro database, using EBI webservice.
The source of these annotations is represented by a color code (see legend). You can access the corresponding Uniprot entries in Interpro by clicking on the synthetic representation of each domain.
What are the distances?
The distances shown here are Jaccard distances, which are adapted to binary profiles (presence/absence).
How are they computed?
Distances between two protein of a given species are computed on phylogenetic profile of each protein in model species of the considered database.
Threshold
The goal of this section is to provide proteins with similar distributions to the query, to that end, we set a maximum threshold at 0.4
This section gives an overview of the taxonomic distribution of orthologs in representative clades. Clade names correspond to NCBI taxonomy or to the accepted consensus. Classification of each species into clade is available here
Heatmap
Each labelled tile corresponds to a clade and is colored according to the proportion of species in the clade with at least one ortholog using the following scale:
Hover on the heatmap to see the total number of species in which orthologs were found.
Tiles framed in blue indicate the clade for which a 'focused' view is available, you can click the tile to reveal it
Labels
Label colors correspond to one of three domains of Life
Eukaryota
Archaea
Bacteria
Inparalogs
When inparalogs (genes in query species resulting from a duplication event posterior to the speciation with target species) are detected, they can be displayed under the 'See Inparalogs' button. A indicates that this protein is a predicted inparalog to the query protein, relatively to (at least) one species of this clade.
Not found in
The 'Not found in' button offers the list of species in which orthologs where not found, ordered clade by clade
| Relationship type | Query & inparalogs | Orthologs | Orthologs length | Species | Taxid | Taxonomy | Whole Taxonomy |
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