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{{PBB|geneid=5949}}
{{PBB|geneid=5949}}
'''Retinol binding protein 3, interstitial''' ('''RBP3'''), also known as '''[[IRBP]]''', is a human [[gene]]<ref name="entrez">{{cite web | title = Entrez Gene: RBP3 retinol binding protein 3, interstitial| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5949| accessdate = }}</ref>, referenced in [[Ensembl]] under accession [http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?g=ENSG00000107618 ENSG00000107618]. RBP3 [[orthologous]] sequences have been identified in most [[eutherians]] except [[tenrecs]] and [[armadillos]].
'''Retinol binding protein 3, interstitial''' ('''RBP3'''), also known as '''[[IRBP]]''', is encoded by a human [[gene]]<ref name="entrez">{{cite web | title = Entrez Gene: RBP3 retinol binding protein 3, interstitial| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5949| accessdate = }}</ref>,
referenced in [[Ensembl]] under accession [http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?g=ENSG00000107618 ENSG00000107618]. RBP3 [[orthologs]] have been identified in most [[eutherians]] except [[tenrecs]] and [[armadillos]].


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{{PBB_Summary
{{PBB_Summary
| section_title =
| section_title =
| summary_text = The interphotoreceptor retinol-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.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. 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.<ref name="entrez">{{cite web | title = Entrez Gene: RBP3 retinol binding protein 3, interstitial| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5949| accessdate = }}</ref>
| summary_text = The interphotoreceptor retinol-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. 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. 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.<ref name="entrez">{{cite web | title = Entrez Gene: RBP3 retinol binding protein 3, interstitial| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5949| accessdate = }}</ref>
}}
}}


The '''rbp3''' gene (and the corresponding '''RBP3''' protein) is commonly used as phylogenetic marker. The [[exon]] 1 has first been used to provide evidence for [[monophyly]] of [[Chiroptera]]<ref>Stanhope, M.J., Czelusniak, J., Si, J.-S., Nickerson, J. and Goodman, M. 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 : 148-160.</ref>. Then, it has been used to infer the [[phylogeny]] of
The '''''rbp3''''' gene, and the corresponding '''RBP3''' protein, are commonly used as phylogenetic markers. The exon 1 has first been used to provide evidence for [[monophyly]] of [[Chiroptera]]<ref>Stanhope, M.J., Czelusniak, J., Si, J.-S., Nickerson, J. and Goodman, M. 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 : 148-160.</ref>. Then, it has been used to infer the [[phylogeny]] of
[[placental]] [[mammal]] orders<ref>Stanhope, M.J., Smith, M.R., Waddell, V.G., Porter, C.A., Shijvi, M.S. and Goodman, M. 1996. Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades. J. Mol. Evol. 43 : 83-92.</ref><ref>Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H., Stanhope, M.J., de Jong, W.W. and Springer, M.S. 2001. Parallel adaptative radiations in two major clades of placental mammals. Nature 409 : 610-614.</ref>, and of the major [[clades]] of [[Rodentia]]<ref>Huchon, D., Madsen, O., Sibbald, M.J.J.B., Ament, K., Stanhope, M., Catzeflis, F., de Jong, W.W. & Douzery, E.J.P. 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: 1053-1065.</ref>,
[[placental]] [[mammal]] orders<ref>Stanhope, M.J., Smith, M.R., Waddell, V.G., Porter, C.A., Shijvi, M.S. and Goodman, M. 1996. Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades. J. Mol. Evol. 43 : 83-92.</ref><ref>Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H., Stanhope, M.J., de Jong, W.W. and Springer, M.S. 2001. Parallel adaptative radiations in two major clades of placental mammals. Nature 409 : 610-614.</ref>, and of the major [[clades]] of [[Rodentia]]<ref>Huchon, D., Madsen, O., Sibbald, M.J.J.B., Ament, K., Stanhope, M., Catzeflis, F., de Jong, W.W. & Douzery, E.J.P. 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: 1053-1065.</ref>,
[[Macroscelidea]]<ref>Douady, C.J., Catzeflis, F., Raman, J., Springer, M.S. & Stanhope, M.J. 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. USA 100: 8325-8330.</ref>,
[[Macroscelidea]]<ref>Douady, C.J., Catzeflis, F., Raman, J., Springer, M.S. & Stanhope, M.J. 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. USA 100: 8325-8330.</ref>,
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</ref>,
</ref>,
and even for species identification purposes ([[Carnivora]]<ref>Oliveira, R., Castro, D., Godinho, R., Luikart, G. & Alves, P.C. 2009. Species identification using a small nuclear gene: application to sympatric wild carnivores from South-western Europe. Conserv. Genet. doi 10.1007/s10592-009-9947-4.</ref>).
and even for species identification purposes ([[Carnivora]]<ref>Oliveira, R., Castro, D., Godinho, R., Luikart, G. & Alves, P.C. 2009. Species identification using a small nuclear gene: application to sympatric wild carnivores from South-western Europe. Conserv. Genet. doi 10.1007/s10592-009-9947-4.</ref>).
Note that the RBP3 [[intron]] 1 has also been used to investigate the [[platyrrhine]] primates phylogenetics <ref>Schneider, H., Sampaio, I., Harada, M.L., Barroso, C.M., Schneider, M.P., Czelusniak, J. & Goodman, M. 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: 153-179.</ref>.
Note that the RBP3 intron 1 has also been used to investigate the [[platyrrhine]] primates phylogenetics <ref>Schneider, H., Sampaio, I., Harada, M.L., Barroso, C.M., Schneider, M.P., Czelusniak, J. & Goodman, M. 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: 153-179.</ref>.


==References==
==References==

Revision as of 08:20, 13 August 2009

Template:PBB Retinol binding protein 3, interstitial (RBP3), also known as IRBP, is encoded by a human gene[1], referenced in Ensembl under accession ENSG00000107618. RBP3 orthologs have been identified in most eutherians except tenrecs and armadillos.

Template:PBB Summary

The rbp3 gene, and the corresponding RBP3 protein, are commonly used as phylogenetic markers. The exon 1 has first been used to provide evidence for monophyly of Chiroptera[2]. Then, it has been used to infer the phylogeny of placental mammal orders[3][4], and of the major clades of Rodentia[5], Macroscelidea[6], and Primates[7]. RBP3 is also useful at lower taxonomic levels, e.g., in rodents [8]and primates[9], at the phylogeography level in rodents[10][11], and even for species identification purposes (Carnivora[12]). Note that the RBP3 intron 1 has also been used to investigate the platyrrhine primates phylogenetics [13].

References

  1. ^ "Entrez Gene: RBP3 retinol binding protein 3, interstitial".
  2. ^ Stanhope, M.J., Czelusniak, J., Si, J.-S., Nickerson, J. and Goodman, M. 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 : 148-160.
  3. ^ Stanhope, M.J., Smith, M.R., Waddell, V.G., Porter, C.A., Shijvi, M.S. and Goodman, M. 1996. Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades. J. Mol. Evol. 43 : 83-92.
  4. ^ Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H., Stanhope, M.J., de Jong, W.W. and Springer, M.S. 2001. Parallel adaptative radiations in two major clades of placental mammals. Nature 409 : 610-614.
  5. ^ Huchon, D., Madsen, O., Sibbald, M.J.J.B., Ament, K., Stanhope, M., Catzeflis, F., de Jong, W.W. & Douzery, E.J.P. 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: 1053-1065.
  6. ^ Douady, C.J., Catzeflis, F., Raman, J., Springer, M.S. & Stanhope, M.J. 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. USA 100: 8325-8330.
  7. ^ Poux, C. & Douzery, E.J.P. 2004. Primate phylogeny, evolutionary rate variations, and divergence times: A contribution from the nuclear gene IRBP. Am. J. Phys. Anthropol. 124: 1-16.
  8. ^ Jansa, S.A. & Weksler, M. 2004. Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences. Mol. Phylogenet. Evol. 31: 256-276.
  9. ^ Horvath, J.E., Weisrock, D.W., Embry, S.L., Fiorentino, I., Balhoff, J.P., Kappeler, P., Wray, G.A., Willard, H.F. & Yoder, A.D. 2008. Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs. Genome Res. 18: 489-499.
  10. ^ 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.
  11. ^ Tomozawa, M. & Suzuki, H. 2008. A trend of central versus peripheral structuring in mitochondrial and nuclear gene sequences of the Japanese wood mouse, Apodemus speciosus. Zool. Sci. 25: 273-285.
  12. ^ Oliveira, R., Castro, D., Godinho, R., Luikart, G. & Alves, P.C. 2009. Species identification using a small nuclear gene: application to sympatric wild carnivores from South-western Europe. Conserv. Genet. doi 10.1007/s10592-009-9947-4.
  13. ^ Schneider, H., Sampaio, I., Harada, M.L., Barroso, C.M., Schneider, M.P., Czelusniak, J. & Goodman, M. 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: 153-179.

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