Rfx4 MGI Mouse Gene Detail - MGI:1918387 - regulatory factor X, 4 (influences HLA class II expression)

Symbol

Rfx4
Name

regulatory factor X, 4 (influences HLA class II expression)
Synonyms

4933412G19Rik

Feature Type

protein coding gene
IDs

MGI:1918387
NCBI Gene: 71137
Alliance

gene page
Transcription Start Sites

9 TSS

Sequence Map

Chr10:84591926-84742402 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 10, 41.63 cM, cytoband C1
Mapping Data

3 experiments

SNPs within 2kb

6324 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1918387	protein coding gene	Chr10:84591895-84742402 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0017594	protein coding gene	Chr10:85635301-85796914 (+)
A/J	MGP_AJ_G0017574	protein coding gene	Chr10:82725745-82879744 (+)
AKR/J	MGP_AKRJ_G0017533	protein coding gene	Chr10:85028397-85187358 (+)
BALB/cJ	MGP_BALBcJ_G0017537	protein coding gene	Chr10:82976417-83127919 (+)
C3H/HeJ	MGP_C3HHeJ_G0017359	protein coding gene	Chr10:85115699-85272922 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0017994	protein coding gene	Chr10:88541217-88702942 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0015678	protein coding gene	Chr10:78545753-78690226 (+)
CAST/EiJ	MGP_CASTEiJ_G0016926	protein coding gene	Chr10:84965342-85128279 (+)
CBA/J	MGP_CBAJ_G0017329	protein coding gene	Chr10:92249388-92410326 (+)
DBA/2J	MGP_DBA2J_G0017435	protein coding gene	Chr10:81868245-82023549 (+)
FVB/NJ	MGP_FVBNJ_G0017429	protein coding gene	Chr10:81104754-81257517 (+)
LP/J	MGP_LPJ_G0017507	protein coding gene	Chr10:86270448-86429040 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0017457	protein coding gene	Chr10:93834689-94000748 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0018031	protein coding gene	Chr10:84949314-85105741 (+)
PWK/PhJ	MGP_PWKPhJ_G0016707	protein coding gene	Chr10:81731962-81885338 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0016496	protein coding gene	Chr10:83575024-83734277 (+)
WSB/EiJ	MGP_WSBEiJ_G0016985	protein coding gene	Chr10:84936694-85092068 (+)

Human Ortholog

RFX4, regulatory factor X4

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

RFX4, regulatory factor X4
Synonyms

NYD-SP10
Links

HGNC:9985

NCBI Gene ID: 5992

UniProt: Q33E94
Chr Location

12q23.3; chr12:106583004-106762803 (+) GRCh38

MGI Vertebrate Homology

Rfx4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: RFX4
Gene Tree

Rfx4

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Phenotype Summary

10 phenotypes from 1 allele in 2 genetic backgrounds
9 phenotypes from multigenic genotypes
18 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

18
Chemically induced (ENU)

1
Chemically induced (other)

1
Gene trapped

11
Targeted

4
Transgenic

1
Genomic Mutations

1 involving Rfx4
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

48 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Inactivating null allele or homozygous point mutation alleles exhibit missing dorsal midline structure of the cortex including the subcommissural organ and neonatal lethality. Heterozygous null mice have congenital hydrocephalus.

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All GO Annotations

35
GO References

10

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

969
Tissues

108
cDNA Data

32
Literature Summary

18

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA RFX4

Xenbase rfx4

ZFIN rfx4

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All Sequences

59
RefSeq

14
UniProt

2
CCDS

CCDS24082.1, CCDS24083.1

Ensembl

ENSMUSG00000020037 (Evidence)
NCBI Gene

71137

			Length	Strain/Species	Flank
genomic	ENSMUSG00000020037	Ensembl Gene Model \| MGI Sequence Detail	150477	C57BL/6J	± kb
transcript	ENSMUST00000060397	Ensembl \| MGI Sequence Detail	3534	Not Applicable
polypeptide	ENSMUSP00000051107	Ensembl \| MGI Sequence Detail	735	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000013926 transcription factor RFX4

(term hierarchy)
InterPro Domains

IPR003150 DNA-binding RFX-type winged-helix domain

IPR039779 RFX-like DNA-binding protein

IPR036390 Winged helix DNA-binding domain superfamily

IPR036388 Winged helix-like DNA-binding domain superfamily
GlyGen

Q7TNK1 2 sites

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All nucleic 40

cDNA 33

Primer pair 7

Microarray probesets 3

Summaries

All 58

Developmental Gene Expression 18

Gene Ontology 10

Phenotypes 18
Earliest

J:137335 Roderick TH, Chromosomal inversions in studies of mammalian mutagenesis. Genetics. 1979 May;92(1 Pt 1 Suppl):s121-6
Latest

J:363327 Sepp M, et al., Cellular development and evolution of the mammalian cerebellum. Nature. 2024 Jan;625(7996):788-796

TSS for Rfx4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr94909	Chr10:84591897-84591911 (+)	-22 bp
Tssr94910	Chr10:84591919-84591948 (+)	8 bp
Tssr94911	Chr10:84592014-84592028 (+)	95 bp
Tssr94912	Chr10:84592050-84592061 (+)	130 bp
Tssr94913	Chr10:84598076-84598110 (+)	6,167 bp
Tssr94914	Chr10:84673967-84673998 (+)	82,057 bp
Tssr94915	Chr10:84674007-84674017 (+)	82,086 bp
Tssr94916	Chr10:84674024-84674038 (+)	82,105 bp
Tssr94917	Chr10:84674931-84674932 (+)	83,006 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 03/18/2025 MGI 6.24