RBP3

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Retinol binding protein 3, interstitial
Identifiers
Symbols RBP3 ; D10S64; D10S65; D10S66; IRBP; RBPI; RP66
External IDs OMIM180290 MGI97878 HomoloGene9261 ChEMBL: 2831 GeneCards: RBP3 Gene
RNA expression pattern
PBB GE RBP3 210318 at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 5949 19661
Ensembl ENSG00000107618 ENSMUSG00000041534
UniProt P10745 P49194
RefSeq (mRNA) NM_002900 NM_015745
RefSeq (protein) NP_002891 NP_056560
Location (UCSC) Chr 10:
48.38 – 48.39 Mb
Chr 14:
33.95 – 33.96 Mb
PubMed search [1] [2]

Retinol-binding protein 3, interstitial (RBP3), also known as IRBP is a protein that in humans is encoded by the RBP3 gene.[1] RBP3 orthologs [2] have been identified in most eutherians except tenrecs and armadillos.

Function[edit]

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 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[edit]

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[edit]

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.[1]

Application[edit]

The rbp3 gene is commonly used in animals as a nuclear DNA phylogenetic marker.[2] The exon 1 has first been used in a pioneer study to provide evidence for monophyly of Chiroptera.[3] Then, it has been used to infer the phylogeny of placental mammal orders,[4][5] and of the major clades of Rodentia,[6] Macroscelidea,[7] and Primates.[8] RBP3 is also useful at lower taxonomic levels, e.g., in muroid rodents[9] and Malagasy primates,[10] at the phylogeography level in Geomys and Apodemus rodents,[11][12] and even for carnivora species identification purposes.[13]

Note that the RBP3 intron 1 has also been used to investigate the platyrrhine primates phylogenetics.[14]

References[edit]

  1. ^ a b "Entrez Gene: RBP3 retinol binding protein 3, interstitial". 
  2. ^ a b "OrthoMaM phylogenetic marker: RBP3 gene, exon 1". 
  3. ^ Stanhope MJ, Czelusniak J, Si JS, Nickerson J, Goodman M (June 1992). "A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly". Mol. Phylogenet. Evol. 1 (2): 148–60. doi:10.1016/1055-7903(92)90026-D. PMID 1342928. 
  4. ^ Stanhope MJ, Smith MR, Waddell VG, Porter CA, Shivji MS, Goodman M (August 1996). "Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades". J. Mol. Evol. 43 (2): 83–92. doi:10.1007/BF02337352. PMID 8660440. 
  5. ^ Madsen O, Scally M, Douady CJ, Kao DJ, DeBry RW, Adkins R, Amrine HM, Stanhope MJ, de Jong WW, Springer MS (February 2001). "Parallel adaptive radiations in two major clades of placental mammals". Nature 409 (6820): 610–4. doi:10.1038/35054544. PMID 11214318. 
  6. ^ Huchon D, Madsen O, Sibbald MJ, Ament K, Stanhope MJ, Catzeflis F, de Jong WW, Douzery EJ (July 2002). "Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes". Mol. Biol. Evol. 19 (7): 1053–65. doi:10.1093/oxfordjournals.molbev.a004164. PMID 12082125. 
  7. ^ Douady CJ, Catzeflis F, Raman J, Springer MS, Stanhope MJ (July 2003). "The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews)". Proc. Natl. Acad. Sci. U.S.A. 100 (14): 8325–30. doi:10.1073/pnas.0832467100. PMC 166228. PMID 12821774. 
  8. ^ Poux C, Douzery EJ (May 2004). "Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP". Am. J. Phys. Anthropol. 124 (1): 1–16. doi:10.1002/ajpa.10322. PMID 15085543. 
  9. ^ Jansa SA, Weksler M (April 2004). "Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences". Mol. Phylogenet. Evol. 31 (1): 256–76. doi:10.1016/j.ympev.2003.07.002. PMID 15019624. 
  10. ^ Horvath JE, Weisrock DW, Embry SL, Fiorentino I, Balhoff JP, Kappeler P, Wray GA, Willard HF, Yoder AD (March 2008). "Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs". Genome Res. 18 (3): 489–99. doi:10.1101/gr.7265208. PMC 2259113. PMID 18245770. 
  11. ^ Genoways, H.H., Hamilton, M.J., Bell, D.M., Chambers, R.R. & Bradley, R.D. 2008. Hybrid zones, genetic isolation, and systematics of pocket gophers (genus Geomys) in Nebraska. J. Mammal. 89: 826-836.
  12. ^ Tomozawa M, Suzuki H (March 2008). "A trend of central versus peripheral structuring in mitochondrial and nuclear gene sequences of the Japanese wood mouse, Apodemus speciosus". Zool. Sci. 25 (3): 273–85. doi:10.2108/zsj.25.273. PMID 18393564. 
  13. ^ 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. doi:10.1007/s10592-009-9947-4. 
  14. ^ Schneider H, Sampaio I, Harada ML, Barroso CM, Schneider MP, Czelusniak J, Goodman M (June 1996). "Molecular phylogeny of the New World monkeys (Platyrrhini, primates) based on two unlinked nuclear genes: IRBP intron 1 and epsilon-globin sequences". Am. J. Phys. Anthropol. 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[edit]

External links[edit]