Rfx1 MGI Mouse Gene Detail - MGI:105982 - regulatory factor X, 1 (influences HLA class II expression)

Symbol

Rfx1
Name

regulatory factor X, 1 (influences HLA class II expression)

Feature Type

protein coding gene
IDs

MGI:105982
NCBI Gene: 19724
Alliance

genome feature page
Transcription Start Sites

9 TSS

Sequence Map

Chr8:84793463-84823621 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 8, 40.28 cM
Mapping Data

5 experiments

SNPs within 2kb

658 from dbSNP Build 142
Strain Annotations

19
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_105982	protein coding gene	Chr8:84789787-84823630 (+)
129S1/SvImJ	ENSMUSG00200024854	protein coding gene	Chr8:79166624-79196894 (+)
A/J	ENSMUSG00195017227	protein coding gene	Chr8:79519762-79550056 (+)
AKR/J	ENSMUSG00220021659	protein coding gene	Chr8:79566051-79596315 (+)
BALB/cJ	ENSMUSG00180017580	protein coding gene	Chr8:79365182-79395440 (+)
C3H/HeJ	ENSMUSG00175010357	protein coding gene	Chr8:79450625-79480919 (+)
C57BL/6NJ	ENSMUSG00215015227	protein coding gene	Chr8:79088471-79118625 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0031291	protein coding gene	Chr8:75406907-75436668 (+)
CAST/EiJ	ENSTCUG00005031619	protein coding gene	Chr8:78975246-79005375 (+)
CBA/J	ENSMUSG00210020207	protein coding gene	Chr8:79442958-79473252 (+)
DBA/2J	ENSMUSG00185033946	protein coding gene	Chr8:85551743-85582029 (+)
FVB/NJ	ENSMUSG00205022035	protein coding gene	Chr8:78499760-78529903 (+)
JF1/MsJ	ENSUMUG00000008486	protein coding gene	Chr8:87854582-87884744 (+)
LP/J	ENSMUSG00230025702	protein coding gene	Chr8:89163594-89193856 (+)
NOD/ShiLtJ	ENSMUSG00190024054	protein coding gene	Chr8:79519789-79550052 (+)
NZO/HlLtJ	ENSMUSG00225040127	protein coding gene	Chr8:92549485-92579643 (+)
PWK/PhJ	ENSLUMG00010025444	protein coding gene	Chr8:79201375-79231490 (+)
SPRET/EiJ	ENSMSPG00010021981	protein coding gene	Chr8:81116697-81146902 (+)
WSB/EiJ	ENSIUOG00005014756	protein coding gene	Chr8:80259534-80289791 (+)

Human Ortholog

RFX1, regulatory factor X1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

RFX1, regulatory factor X1
Synonyms

EFC, RFX
Links

HGNC:9982

NCBI Gene ID: 5989

UniProt: P22670
Chr Location

19p13.12; chr19:13961529-14007084 (-) GRCh38

MGI Vertebrate Homology

Rfx1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: RFX1
Gene Tree

Rfx1

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Phenotype Summary

2 phenotypes from 2 alleles in 2 genetic backgrounds
8 phenotypes from multigenic genotypes
43 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

27
Chemically induced (other)

1
Endonuclease-mediated

3
Gene trapped

17
Radiation induced

1
Targeted

5
Genomic Mutations

2 involving Rfx1
Incidental Mutations

APF , CvDC
Find Mice (IMSR)

44 strains or lines available

Mice homozygous for a gene trap allele die prior to implantation.

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All GO Annotations

15
GO References

7

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

685
Tissues

77
cDNA Data

52
Literature Summary

13

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase rfx1

ZFIN rfx1a, rfx1b

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All Sequences

65
RefSeq

19
UniProt

4
CCDS

CCDS22468.1

Ensembl

ENSMUSG00000031706 (Evidence)
NCBI Gene

19724

			Length	Strain/Species	Flank
genomic	ENSMUSG00000031706	Ensembl Gene Model \| MGI Sequence Detail	30159	C57BL/6J	± kb
transcript	ENSMUST00000005600	Ensembl \| MGI Sequence Detail	4172	Not Applicable
polypeptide	ENSMUSP00000005600	Ensembl \| MGI Sequence Detail	963	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000013923 MHC class II regulatory factor RFX1

(term hierarchy)
InterPro Domains

IPR003150 DNA-binding RFX-type, winged-helix domain

IPR057321 RFX1-4/6/8-like, BCD domain

IPR007668 RFX1 transcription activation region

IPR039779 RFX-like DNA-binding protein

IPR036390 Winged helix DNA-binding domain superfamily

IPR036388 Winged helix-like DNA-binding domain superfamily
GlyGen

P48377 14 sites, 1 O-linked glycan (13 sites)

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All nucleic 61

cDNA 56

Primer pair 3

Other 2

Antibodies 2

Microarray probesets 5

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MGD-MRK-33662, MGI:2142460, MGI:2142518

Summaries

All 93

Developmental Gene Expression 13

Gene Ontology 7

Phenotypes 43
Earliest

J:13049 Gruneberg H, Genetical studies on the skeleton of the mouse. XVIII. Three genes for syndactylism. J Genet. 1956;54(1):113-145
Latest

J:377759 Liu S, et al., Foxn3 is required to suppress aberrant ciliogenesis in nonphotoreceptor retinal neurons. Proc Natl Acad Sci U S A. 2025 Jul 22;122(29):e2500871122

TSS for Rfx1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr78347	Chr8:84793013-84793027 (+)	-443 bp
Tssr78348	Chr8:84793048-84793060 (+)	-409 bp
Tssr78349	Chr8:84793453-84793511 (+)	19 bp
Tssr78350	Chr8:84793531-84793548 (+)	77 bp
Tssr78351	Chr8:84800487-84800503 (+)	7,032 bp
Tssr78352	Chr8:84800505-84800528 (+)	7,054 bp
Tssr78353	Chr8:84800529-84800548 (+)	7,076 bp
Tssr78354	Chr8:84800568-84800575 (+)	7,109 bp
Tssr78355	Chr8:84810703-84810722 (+)	17,250 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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/01/2026 MGI 6.24