Rfx5 MGI Mouse Gene Detail - MGI:1858421 - regulatory factor X, 5 (influences HLA class II expression)

Symbol

Rfx5
Name

regulatory factor X, 5 (influences HLA class II expression)

Feature Type

protein coding gene
IDs

MGI:1858421
NCBI Gene: 53970
Alliance

gene page
Transcription Start Sites

1 TSS

Sequence Map

Chr3:94861355-94868685 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 40.74 cM, cytoband F2
Mapping Data

3 experiments

SNPs within 2kb

181 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1858421	protein coding gene	Chr3:94861355-94868872 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0027562	protein coding gene	Chr3:95629690-95637776 (+)
A/J	MGP_AJ_G0027521	protein coding gene	Chr3:92691108-92698592 (+)
AKR/J	MGP_AKRJ_G0027488	protein coding gene	Chr3:94826791-94834275 (+)
BALB/cJ	MGP_BALBcJ_G0027533	protein coding gene	Chr3:92455561-92463044 (+)
C3H/HeJ	MGP_C3HHeJ_G0027266	protein coding gene	Chr3:95100173-95107634 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0027981	protein coding gene	Chr3:99203455-99211005 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025321	protein coding gene	Chr3:89048828-89056013 (+)
CAST/EiJ	MGP_CASTEiJ_G0026716	protein coding gene	Chr3:94391927-94399415 (+)
CBA/J	MGP_CBAJ_G0027243	protein coding gene	Chr3:102780553-102788036 (+)
DBA/2J	MGP_DBA2J_G0027382	protein coding gene	Chr3:91984536-91992020 (+)
FVB/NJ	MGP_FVBNJ_G0027353	protein coding gene	Chr3:90053412-90060871 (+)
LP/J	MGP_LPJ_G0027491	protein coding gene	Chr3:96920896-96929732 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027380	protein coding gene	Chr3:108925013-108932500 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028035	protein coding gene	Chr3:94475740-94483252 (+)
PWK/PhJ	MGP_PWKPhJ_G0026444	protein coding gene	Chr3:91851343-91858593 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026265	protein coding gene	Chr3:92769045-92776941 (+)
WSB/EiJ	MGP_WSBEiJ_G0026798	protein coding gene	Chr3:94862677-94871984 (+)

Human Ortholog

RFX5, regulatory factor X5

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

RFX5, regulatory factor X5
Synonyms

MHC2D3, MHC2D5
Links

HGNC:9986

NCBI Gene ID: 5993

neXtProt AC: NX_P48382

UniProt: P48382
Chr Location

1q21.3; chr1:151340640-151347326 (-) GRCh38

MGI Vertebrate Homology

Rfx5 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: RFX5
Gene Tree

Rfx5

Diseases

1 with human RFX5 associations

				Human Disease	Mouse Models
				severe combined immunodeficiency IDs severe combined immunodeficiency DOID:627 MESH:D016511 NCI:C3472 UMLS_CUI:C0085110

Click on a disease name to see all genes associated with that disease.

References

1 with disease annotations

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Phenotype Summary

11 phenotypes from 2 alleles in 3 genetic backgrounds
16 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

17
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

6
Radiation induced

1
Targeted

7
Genomic Mutations

2 involving Rfx5
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

34 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous null mice have absent or decreased expression of MHC-II complexes on antigen presenting cells, which leads to reduced numbers of CD4⁺ thymocytes and T cells.

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All GO Annotations

18
GO References

4

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

847
Tissues

73
cDNA Data

15
Literature Summary

8

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase rfx5

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All Sequences

112
RefSeq

34
UniProt

9
CCDS

CCDS17598.1

Ensembl

ENSMUSG00000005774 (Evidence)
NCBI Gene

53970

			Length	Strain/Species	Flank
genomic	53970	NCBI Gene Model \| MGI Sequence Detail	7331	C57BL/6J	± kb
transcript	NM_001355706	RefSeq \| MGI Sequence Detail	4482	ZRU/MplStud
polypeptide	Q9JL61	UniProt \| EBI \| MGI Sequence Detail	658	Not Applicable

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UniProt

9 Sequences
Protein Ontology

PR:000013927 DNA-binding protein RFX5

(term hierarchy)
InterPro Domains

IPR003150 DNA-binding RFX-type winged-helix domain

IPR029298 RFX5, C-terminal

IPR039779 RFX-like DNA-binding protein

IPR036390 Winged helix DNA-binding domain superfamily

IPR036388 Winged helix-like DNA-binding domain superfamily

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All nucleic 18

Genomic 1

cDNA 15

Primer pair 2

Microarray probesets 3

Summaries

All 47

Developmental Gene Expression 8

Diseases 1

Gene Ontology 4

Phenotypes 16
Earliest

J:67941 Clausen BE, et al., Residual MHC class II expression on mature dendritic cells and activated B cells in RFX5-deficient mice. Immunity. 1998 Feb;8(2):143-55
Latest

J:302829 Lu J, et al., Mouse models for human hyperuricaemia: a critical review. Nat Rev Rheumatol. 2019 Jul;15(7):413-426

TSS for Rfx5:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr30478	Chr3:94861430-94861531 (+)	126 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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