Retinol-binding protein 3, interstitial (RBP3), also known as IRBP is a
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
that in humans is encoded by the ''RBP3''
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
.
RBP3
orthologs have been identified in most
eutherians
Eutheria (; from Greek , 'good, right' and , 'beast'; ) is the clade consisting of all therian mammals that are more closely related to placentals than to marsupials.
Eutherians are distinguished from noneutherians by various phenotypic trai ...
except
tenrecs
A tenrec is any species of mammal within the afrotherian family Tenrecidae endemic to Madagascar. Tenrecs are wildly diverse; as a result of convergent evolution some resemble hedgehogs, shrews, opossums, rats, and mice. They occupy aquatic ...
and
armadillos
Armadillos (meaning "little armored ones" in Spanish) are New World placental mammals in the order Cingulata. The Chlamyphoridae and Dasypodidae are the only surviving families in the order, which is part of the superorder Xenarthra, along w ...
.
Function
The inter-
photoreceptor retinoid
The retinoids are a class of chemical compounds that are vitamers of vitamin A or are chemically related to it. Retinoids have found use in medicine where they regulate epithelial cell growth.
Retinoids have many important functions throughout t ...
-binding protein is a large
glycoprotein
Glycoproteins are proteins which contain oligosaccharide chains covalently attached to amino acid side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycos ...
known to bind retinoids and found primarily in the
interphotoreceptor matrix of the retina between the retinal pigment epithelium and the photoreceptor cells. It is thought to transport retinoids between the retinal pigment epithelium and the photoreceptors, a critical role in the visual process.
Gene
The human IRBP gene is approximately 9.5 kbp in length and consists of four
exons
An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequence ...
separated by three
introns. The introns are 1.6-1.9 kbp long. The gene is transcribed by photoreceptor and retinoblastoma cells into an approximately 4.3-kilobase mRNA that is translated and processed into a glycosylated protein of 135,000 Da.
Structure
The amino acid sequence of human IRBP can be divided into four contiguous
homology
Homology may refer to:
Sciences
Biology
*Homology (biology), any characteristic of biological organisms that is derived from a common ancestor
* Sequence homology, biological homology between DNA, RNA, or protein sequences
*Homologous chrom ...
domains with 33-38% identity, suggesting a series of gene duplication events. In the gene, the boundaries of these domains are not defined by exon-intron junctions, as might have been expected. The first three homology domains and part of the fourth are all encoded by the first large exon, which is 3,180 base pairs long. The remainder of the fourth domain is encoded in the last three exons, which are 191, 143, and approximately 740 base pairs long, respectively.
Application
The ''rbp3'' gene is commonly used in animals as a
nuclear DNA phylogenetic marker.
The exon 1 has first been used in a pioneer study to provide evidence for
monophyly
In cladistics for a group of organisms, monophyly is the condition of being a clade—that is, a group of taxa composed only of a common ancestor (or more precisely an ancestral population) and all of its lineal descendants. Monophyletic grou ...
of
Chiroptera.
Then, it has been used to infer the
phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
of
placental mammal
Mammals () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or ...
orders,
and of the major
clades
A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, t ...
of
Rodent
Rodents (from Latin , 'to gnaw') are mammals of the order Rodentia (), which are characterized by a single pair of continuously growing incisors in each of the upper and lower jaws. About 40% of all mammal species are rodents. They are na ...
ia,
,
and
Primates
Primates are a diverse order of mammals. They are divided into the strepsirrhines, which include the lemurs, galagos, and lorisids, and the haplorhines, which include the tarsiers and the simians (monkeys and apes, the latter including huma ...
.
RBP3 is also useful at lower
taxonomic
Taxonomy is the practice and science of categorization or classification.
A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
levels, ''e.g.'', in muroid rodents
and Malagasy primates,
at the
phylogeography level in ''Geomys'' and ''Apodemus'' rodents,
and even for
carnivora
Carnivora is a Clade, monophyletic order of Placentalia, placental mammals consisting of the most recent common ancestor of all felidae, cat-like and canidae, dog-like animals, and all descendants of that ancestor. Members of this group are f ...
species identification purposes.
Note that the RBP3 intron 1 has also been used to investigate the
platyrrhine primates phylogenetics.
References
Further reading
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External links
GeneReviews/NCBI/NIH/UW entry on Retinitis Pigmentosa Overview* {{cite web , url = http://www.orthomam.univ-montp2.fr/orthomam/data/cds/detailMarkers/ENSG00000107618_RBP3.xml , title = Overview of the coding DNA and protein sequence alignments of the RBP3 marker , work = OrthoMaM – a
biological database
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genom ...
of
orthologous
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spec ...
mammalian markers , quote = The rbp3 evolutionary marker can be found, together with the corresponding gene
phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...