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RBP3
Identifiers
Aliases	RBP3, D10S64, D10S65, D10S66, IRBP, RBPI, RP66, retinol binding protein 3
External IDs	OMIM: 180290; MGI: 97878; HomoloGene: 9261; GeneCards: RBP3; OMA:RBP3 - orthologs
Gene location (Human) Chr. Chromosome 10 (human) Band 10q11.22 Start 47,348,363 bp End 47,357,881 bp
Gene location (Mouse) Chr. Chromosome 14 (mouse) Band 14 B|14 20.8 cM Start 33,675,960 bp End 33,686,173 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in testicle retinal pigment epithelium Epithelium of choroid plexus hippocampal formation hippocampus proper Mesencephalon Frontal Lobe Cortex of frontal lobe prefrontal cortex substantia nigra Top expressed in neural layer of retina epithelium of lens retinal pigment epithelium pineal gland outer nuclear layer right ventricle embryo lumbar subsegment of spinal cord iris embryo More reference expression data BioGPS More reference expression data
Gene ontology Molecular function serine-type peptidase activity retinoid binding retinal binding retinol binding Cellular component extracellular vesicle extracellular region interphotoreceptor matrix extracellular space cone matrix sheath Biological process proteolysis retinoid metabolic process lipid metabolism visual perception transport Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 5949 19661 Ensembl ENSG00000265203 ENSMUSG00000041534 UniProt P10745 P49194 RefSeq (mRNA) NM_002900 NM_015745 RefSeq (protein) NP_002891 NP_056560 Location (UCSC) Chr 10: 47.35 – 47.36 Mb Chr 14: 33.68 – 33.69 Mb PubMed search
Wikidata
View/Edit Human View/Edit Mouse

Retinol-binding protein 3, interstitial (RBP3), also known as interphotoreceptor retinoid-binding protein (IRBP), is a protein that in humans is encoded by the RBP3 gene. RBP3 orthologs have been identified in most eutherians except tenrecs and armadillos. A horizontal gene transfer from bacteria has been proposed to explain the evolution of the eye in chordates.

Function

The inter-photoreceptor retinoid-binding protein is a large glycoprotein known to bind retinoids and found primarily in the interphotoreceptor matrix of the retina between the retinal pigment epithelium (RPE) and the photoreceptor cells. It is thought to transport retinoids between the RPE 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 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 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 of Chiroptera. Then, it has been used to infer the phylogeny of placental mammal orders, and of the major clades of Rodentia, Macroscelidea, and Primates. RBP3 is also useful at lower taxonomic levels, e.g., in muroid rodents and Malagasy primates, at the phylogeography level in Geomys and Apodemus rodents, and even for carnivora species identification purposes.

Note that the RBP3 intron 1 has also been used to investigate the platyrrhine primates phylogenetics.

References

1. ^ GRCh38: Ensembl release 89: ENSG00000265203 – Ensembl, May 2017
2. ^ GRCm38: Ensembl release 89: ENSMUSG00000041534 – Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. ^ "Entrez Gene: RBP3 retinol binding protein 3, interstitial".
6. ^ "OrthoMaM phylogenetic marker: RBP3 gene, exon 1".
7. Kalluraya CA, Weitzel AJ, Tsu BV, Daugherty MD (2023-04-18). "Bacterial origin of a key innovation in the evolution of the vertebrate eye". Proceedings of the National Academy of Sciences. 120 (16): e2214815120. Bibcode:2023PNAS..12014815K. doi:10.1073/pnas.2214815120. ISSN 0027-8424. PMC 10120077. PMID 37036996.
8. Pennisi E (10 Apr 2023). "An ancient gene stolen from bacteria set the stage for human sight". Science. doi:10.1126/science.adi2029. Retrieved 11 Apr 2023.
9. Kusakabe TG, Takimoto N, Jin M, Tsuda M (Oct 2009). "Evolution and the origin of the visual retinoid cycle in vertebrates". Philosophical Transactions B. 364 (1531): 2897–2910. doi:10.1098/rstb.2009.0043. PMC 2781855. PMID 19720652.
10. Stanhope MJ, Czelusniak J, Si JS, Nickerson J, Goodman M (Jun 1992). "A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly". Molecular Phylogenetics and Evolution. 1 (2): 148–60. doi:10.1016/1055-7903(92)90026-D. PMID 1342928.
11. Stanhope MJ, Smith MR, Waddell VG, Porter CA, Shivji MS, Goodman M (Aug 1996). "Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades". Journal of Molecular Evolution. 43 (2): 83–92. Bibcode:1996JMolE..43...83S. doi:10.1007/BF02337352. PMID 8660440. S2CID 25865281.
12. Madsen O, Scally M, Douady CJ, Kao DJ, DeBry RW, Adkins R, Amrine HM, Stanhope MJ, de Jong WW, Springer MS (Feb 2001). "Parallel adaptive radiations in two major clades of placental mammals". Nature. 409 (6820): 610–4. doi:10.1038/35054544. PMID 11214318. S2CID 4398233.
13. Huchon D, Madsen O, Sibbald MJ, Ament K, Stanhope MJ, Catzeflis F, de Jong WW, Douzery EJ (Jul 2002). "Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes". Molecular Biology and Evolution. 19 (7): 1053–65. doi:10.1093/oxfordjournals.molbev.a004164. PMID 12082125.
14. Douady CJ, Catzeflis F, Raman J, Springer MS, Stanhope MJ (Jul 2003). "The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews)". Proceedings of the National Academy of Sciences of the United States of America. 100 (14): 8325–30. Bibcode:2003PNAS..100.8325D. doi:10.1073/pnas.0832467100. PMC 166228. PMID 12821774.
15. Poux C, Douzery EJ (May 2004). "Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP". American Journal of Physical Anthropology. 124 (1): 01–16. doi:10.1002/ajpa.10322. PMID 15085543.
16. Jansa SA, Weksler M (Apr 2004). "Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences". Molecular Phylogenetics and Evolution. 31 (1): 256–76. doi:10.1016/j.ympev.2003.07.002. PMID 15019624.
17. Horvath JE, Weisrock DW, Embry SL, Fiorentino I, Balhoff JP, Kappeler P, Wray GA, Willard HF, Yoder AD (Mar 2008). "Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs". Genome Research. 18 (3): 489–99. doi:10.1101/gr.7265208. PMC 2259113. PMID 18245770.
18. Genoways HH, Hamilton MJ, Bell DM, Chambers RR, Bradley RD (2008). "Hybrid zones, genetic isolation, and systematics of pocket gophers (genus Geomys) in Nebraska". J. Mammal. 89 (4): 826–836. doi:10.1644/07-mamm-a-408.1.
19. Tomozawa M, Suzuki H (Mar 2008). "A trend of central versus peripheral structuring in mitochondrial and nuclear gene sequences of the Japanese wood mouse, Apodemus speciosus". Zoological Science. 25 (3): 273–85. doi:10.2108/zsj.25.273. PMID 18393564. S2CID 38824060.
20. Oliveira R, Castro D, Godinho R, Luikart G, Alves PC (June 2009). "Species identification using a small nuclear gene: application to sympatric wild carnivores from South-western Europe". Conserv. Genet. 11 (3): 1023–1032. doi:10.1007/s10592-009-9947-4. S2CID 21422211.
21. Schneider H, Sampaio I, Harada ML, Barroso CM, Schneider MP, Czelusniak J, Goodman M (Jun 1996). "Molecular phylogeny of the New World monkeys (Platyrrhini, primates) based on two unlinked nuclear genes: IRBP intron 1 and epsilon-globin sequences". American Journal of Physical Anthropology. 100 (2): 153–79. doi:10.1002/(SICI)1096-8644(199606)100:2<153::AID-AJPA1>3.0.CO;2-Z. PMID 8771309.

Further reading

• Fong SL, Fong WB, Morris TA, Kedzie KM, Bridges CD (Mar 1990). "Characterization and comparative structural features of the gene for human interstitial retinol-binding protein". The Journal of Biological Chemistry. 265 (7): 3648–53. doi:10.1016/S0021-9258(19)39642-5. PMID 2303470.
• Albini A, Toffenetti J, Zhu Z, Chader GJ, Noonan DM (Sep 1990). "Hypomethylation of the interphotoreceptor retinoid-binding protein (IRBP) promotor and first exon is linked to expression of the gene". Nucleic Acids Research. 18 (17): 5181–7. doi:10.1093/nar/18.17.5181. PMC 332140. PMID 2402443.
• Liou GI, Ma DP, Yang YW, Geng L, Zhu C, Baehr W (May 1989). "Human interstitial retinoid-binding protein. Gene structure and primary structure". The Journal of Biological Chemistry. 264 (14): 8200–6. doi:10.1016/S0021-9258(18)83169-6. PMID 2542268.
• Si JS, Borst DE, Redmond TM, Nickerson JM (Aug 1989). "Cloning of cDNAs encoding human interphotoreceptor retinoid-binding protein (IRBP) and comparison with bovine IRBP sequences". Gene. 80 (1): 99–108. doi:10.1016/0378-1119(89)90254-0. PMID 2792773. S2CID 34897302.
• Nakamura Y, Lathrop M, Bragg T, Leppert M, O'Connell P, Jones C, Lalouel JM, White R (Nov 1988). "An extended genetic linkage map of markers for human chromosome 10". Genomics. 3 (4): 389–92. doi:10.1016/0888-7543(88)90133-4. PMID 2907505.
• Fong SL, Bridges CD (Oct 1988). "Internal quadruplication in the structure of human interstitial retinol-binding protein deduced from its cloned cDNA". The Journal of Biological Chemistry. 263 (30): 15330–4. doi:10.1016/S0021-9258(19)37592-1. PMID 3170584.
• Liou GI, Fong SL, Gosden J, van Tuinen P, Ledbetter DH, Christie S, Rout D, Bhattacharya S, Cook RG, Li Y (Jul 1987). "Human interstitial retinol-binding protein (IRBP): cloning, partial sequence, and chromosomal localization". Somatic Cell and Molecular Genetics. 13 (4): 315–23. doi:10.1007/BF01534925. PMID 3455009. S2CID 20206120.
• Fong SL, Cook RG, Alvarez RA, Liou GI, Landers RA, Bridges CD (Sep 1986). "N-terminal sequence homologies in interstitial retinol-binding proteins from 10 vertebrate species". FEBS Letters. 205 (2): 309–12. doi:10.1016/0014-5793(86)80918-8. PMID 3743780. S2CID 45787370.
• Redmond TM, Wiggert B, Robey FA, Chader GJ (Nov 1986). "Interspecies conservation of structure of interphotoreceptor retinoid-binding protein. Similarities and differences as adjudged by peptide mapping and N-terminal sequencing". The Biochemical Journal. 240 (1): 19–26. doi:10.1042/bj2400019. PMC 1147370. PMID 3827838.
• Chen Y, Houghton LA, Brenna JT, Noy N (Aug 1996). "Docosahexaenoic acid modulates the interactions of the interphotoreceptor retinoid-binding protein with 11-cis-retinal". The Journal of Biological Chemistry. 271 (34): 20507–15. doi:10.1074/jbc.271.34.20507. PMID 8702792.
• Shaw NS, Noy N (Feb 2001). "Interphotoreceptor retinoid-binding protein contains three retinoid binding sites". Experimental Eye Research. 72 (2): 183–90. doi:10.1006/exer.2000.0945. PMID 11161734.
• Foltz DR, Nye JS (Aug 2001). "Hyperphosphorylation and association with RBP of the intracellular domain of Notch1". Biochemical and Biophysical Research Communications. 286 (3): 484–92. doi:10.1006/bbrc.2001.5421. PMID 11511084.
• Howard OM, Dong HF, Su SB, Caspi RR, Chen X, Plotz P, Oppenheim JJ (Jun 2005). "Autoantigens signal through chemokine receptors: uveitis antigens induce CXCR3- and CXCR5-expressing lymphocytes and immature dendritic cells to migrate". Blood. 105 (11): 4207–14. doi:10.1182/blood-2004-07-2697. PMC 1895027. PMID 15713799.

External links

• GeneReviews/NCBI/NIH/UW entry on Retinitis Pigmentosa Overview
• "Overview of the coding DNA and protein sequence alignments of the RBP3 marker". OrthoMaM – a biological database of orthologous mammalian markers. The rbp3 evolutionary marker can be found, together with the corresponding gene phylogeny

• Genes on human chromosome 10