RGD Reference Report - Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution.

General

Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution.
Authors:	Szpirer, C Szpirer, J Van Vooren, P Tissir, F Simon, JS Koike, G Jacob, HJ Lander, ES Helou, K Linga-Levan K, K Levan, G
Citation:	Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34
RGD ID:	61489
Pubmed:	PMID:9716657 (View Abstract at PubMed)
In order to generate anchor points connecting the rat cytogenetic and genetic maps, the cytogenetic position of 62 rat markers (including 55 genes) already localized genetically was determined by fluorescence in situ hybridization. Whenever possible, markers located near one end of the linkage groups were included. These new localizations allowed us to unambiguously orient the 20 autosomal and the X chromosome linkage groups. The position of the centromere in the linkage map could also be determined in the case of several metacentric chromosomes. In addition, the regional localization of 15 other rat genes was determined. These new data bring useful information with respect to comparative mapping with the mouse and the human and to mammalian evolution. They illustrate, for instance, that groups of genes can remain syntenic during mammalian evolution while being subjected to intrachromosomal rearrangements in some lineages (synteny is conserved while gene order is not). This analysis also disclosed cases of synteny conservation in one the two rodent species and the human, while the synteny is split in the other rodent species: such configurations are likely examples of lineage-specific interchromosomal rearrangements associated with speciation.

Objects referenced in this article

Gene	Acaa1a	acetyl-CoA acyltransferase 1A	Rattus norvegicus
Gene	Acr	acrosin	Rattus norvegicus
Gene	Adra1b	adrenoceptor alpha 1B	Rattus norvegicus
Gene	Afp	alpha-fetoprotein	Rattus norvegicus
Gene	Agt	angiotensinogen	Rattus norvegicus
Gene	Agtr1a	angiotensin II receptor, type 1a	Rattus norvegicus
Gene	Apoa1	apolipoprotein A1	Rattus norvegicus
Gene	Apoc3	apolipoprotein C3	Rattus norvegicus
Gene	Ar	androgen receptor	Rattus norvegicus
Gene	Avp	arginine vasopressin	Rattus norvegicus
Gene	Avpr1a	arginine vasopressin receptor 1A	Rattus norvegicus
Gene	Avpr2	arginine vasopressin receptor 2	Rattus norvegicus
Gene	Camk2d	calcium/calmodulin-dependent protein kinase II delta	Rattus norvegicus
Gene	Chrm3	cholinergic receptor, muscarinic 3	Rattus norvegicus
Gene	Chrm4	cholinergic receptor, muscarinic 4	Rattus norvegicus
Gene	Comt	catechol-O-methyltransferase	Rattus norvegicus
Gene	Crygb	crystallin, gamma B	Rattus norvegicus
Gene	Crygc	crystallin, gamma C	Rattus norvegicus
Gene	Dbi	diazepam binding inhibitor	Rattus norvegicus
Gene	Ddn	dendrin	Rattus norvegicus
Gene	Drd2	dopamine receptor D2	Rattus norvegicus
Gene	Edn3	endothelin 3	Rattus norvegicus
Gene	Ednrb	endothelin receptor type B	Rattus norvegicus
Gene	Fbp1	fructose-bisphosphatase 1	Rattus norvegicus
Gene	Fgfr4	fibroblast growth factor receptor 4	Rattus norvegicus
Gene	Gls	glutaminase	Rattus norvegicus
Gene	Gnal	G protein subunit alpha L	Rattus norvegicus
Gene	H19	H19 imprinted maternally expressed transcript	Rattus norvegicus
Gene	Hsd11b1	hydroxysteroid 11-beta dehydrogenase 1	Rattus norvegicus
Gene	Htr1a	5-hydroxytryptamine receptor 1A	Rattus norvegicus
Gene	Igf1	insulin-like growth factor 1	Rattus norvegicus
Gene	Itga1	integrin subunit alpha 1	Rattus norvegicus
Gene	Klkb1	kallikrein B1	Rattus norvegicus
Gene	Mycs	myc-like oncogene, s-myc protein	Rattus norvegicus
Gene	Nos1	nitric oxide synthase 1	Rattus norvegicus
Gene	Nos3	nitric oxide synthase 3	Rattus norvegicus
Gene	Nr3c1	nuclear receptor subfamily 3, group C, member 1	Rattus norvegicus
Gene	Pck1	phosphoenolpyruvate carboxykinase 1	Rattus norvegicus
Gene	Pcsk2	proprotein convertase subtilisin/kexin type 2	Rattus norvegicus
Gene	Pfkfb1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	Rattus norvegicus
Gene	Pfkfb2	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	Rattus norvegicus
Gene	Pgam2	phosphoglycerate mutase 2	Rattus norvegicus
Gene	Prl	prolactin	Rattus norvegicus
Gene	Prl8a2	prolactin family 8, subfamily A, member 2	Rattus norvegicus
Gene	Pthlh	parathyroid hormone-like hormone	Rattus norvegicus
Gene	Rbp2	retinol binding protein 2	Rattus norvegicus
Gene	Scn2a	sodium voltage-gated channel alpha subunit 2	Rattus norvegicus
Gene	Serpine1	serpin family E member 1	Rattus norvegicus
Gene	Slc2a1	solute carrier family 2 member 1	Rattus norvegicus
Gene	Stat1	signal transducer and activator of transcription 1	Rattus norvegicus
Gene	Stat3	signal transducer and activator of transcription 3	Rattus norvegicus
Gene	Stat5b	signal transducer and activator of transcription 5B	Rattus norvegicus
Gene	Syt2	synaptotagmin 2	Rattus norvegicus
Gene	Tat	tyrosine aminotransferase	Rattus norvegicus
Gene	Tnnt2	troponin T2, cardiac type	Rattus norvegicus
Gene	Ucp1	uncoupling protein 1	Rattus norvegicus

Additional Information

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution.