Alx3 MGI Mouse Gene Detail - MGI:1277097 - aristaless-like homeobox 3

Symbol

Alx3
Name

aristaless-like homeobox 3

Feature Type

protein coding gene
IDs

MGI:1277097
NCBI Gene: 11694
Alliance

genome feature page
Transcription Start Sites

2 TSS

Sequence Map

Chr3:107502347-107513092 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 46.83 cM
Mapping Data

4 experiments

SNPs within 2kb

256 from dbSNP Build 142
Strain Annotations

19
PCR

1
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1277097	protein coding gene	Chr3:107502347-107513191 (+)
129S1/SvImJ	ENSMUSG00200035333	protein coding gene	Chr3:104118105-104128851 (+)
A/J	ENSMUSG00195024940	protein coding gene	Chr3:104544482-104555224 (+)
AKR/J	ENSMUSG00220032020	protein coding gene	Chr3:102908099-102918841 (+)
BALB/cJ	ENSMUSG00180015774	protein coding gene	Chr3:104495336-104505881 (+)
C3H/HeJ	ENSMUSG00175027052	protein coding gene	Chr3:104024642-104035385 (+)
C57BL/6NJ	ENSMUSG00215022124	protein coding gene	Chr3:104752493-104763239 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025505	protein coding gene	Chr3:101794483-101804943 (+)
CAST/EiJ	ENSTCUG00005026135	protein coding gene	Chr3:105029027-105039574 (+)
CBA/J	ENSMUSG00210007419	protein coding gene	Chr3:104646534-104657276 (+)
DBA/2J	ENSMUSG00185020536	protein coding gene	Chr3:105115814-105126556 (+)
FVB/NJ	ENSMUSG00205024197	protein coding gene	Chr3:103679619-103690365 (+)
JF1/MsJ	ENSUMUG00000003482	protein coding gene	Chr3:104083704-104094246 (+)
LP/J	ENSMUSG00230017143	protein coding gene	Chr3:107031126-107041868 (+)
NOD/ShiLtJ	ENSMUSG00190030420	protein coding gene	Chr3:105353940-105364684 (+)
NZO/HlLtJ	ENSMUSG00225017556	protein coding gene	Chr3:109527229-109537760 (+)
PWK/PhJ	ENSLUMG00010022665	protein coding gene	Chr3:103938908-103949448 (+)
SPRET/EiJ	ENSMSPG00010035024	protein coding gene	Chr3:104460238-104470750 (+)
WSB/EiJ	ENSIUOG00005004213	protein coding gene	Chr3:104667962-104678491 (+)

Human Ortholog

ALX3, ALX homeobox 3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

ALX3, ALX homeobox 3
Synonyms

FND, FND1
Links

HGNC:449

NCBI Gene ID: 257

UniProt: O95076
Chr Location

1p13.3; chr1:110059870-110070672 (-) GRCh38

MGI Vertebrate Homology

Alx3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: ALX3
Gene Tree

Alx3

Diseases

1 with human ALX3 associations

				Human Disease	Mouse Models
				frontonasal dysplasia 1 IDs frontonasal dysplasia 1 DOID:0081045 OMIM:136760

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

References

1 with disease annotations

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Phenotype Summary

24 phenotypes from 1 allele in 3 genetic backgrounds
37 phenotypes from multigenic genotypes
14 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

6
Chemically induced (other)

1
Endonuclease-mediated

1
Radiation induced

1
Targeted

3
Genomic Mutations

2 involving Alx3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

15 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Homozygous mutation of this gene results in defects in glucose metabolism. Mice homozygous for a reporter allele exhibit partial preweaning lethality, open neural tube and craniofacial defects in some mice.

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All GO Annotations

20
GO References

8

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

1116
Tissues

299
cDNA Data

14
Literature Summary

49

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

ZFIN alx3

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All Sequences

33
RefSeq

2
UniProt

3
CCDS

CCDS17739.1

Ensembl

ENSMUSG00000014603 (Evidence)
NCBI Gene

11694

			Length	Strain/Species	Flank
genomic	ENSMUSG00000014603	Ensembl Gene Model \| MGI Sequence Detail	10746	C57BL/6J	± kb
transcript	ENSMUST00000014747	Ensembl \| MGI Sequence Detail	1874	Not Applicable
polypeptide	ENSMUSP00000014747	Ensembl \| MGI Sequence Detail	343	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000003979 homeobox protein aristaless-like 3

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR050649 Paired Homeobox Transcription Factors

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All nucleic 31

cDNA 14

Primer pair 7

Other 10

Microarray probesets 4

Summaries

All 88

Developmental Gene Expression 49

Diseases 1

Gene Ontology 8

Phenotypes 14
Earliest

J:48587 ten Berge D, et al., Mouse Alx3: an aristaless-like homeobox gene expressed during embryogenesis in ectomesenchyme and lateral plate mesoderm. Dev Biol. 1998 Jul 1;199(1):11-25
Latest

J:375094 Murillo-Rincon AP, et al., Positional programs in early murine facial development and their role in human facial shape variability. Nat Commun. 2025 Nov 18;16(1):10112

TSS for Alx3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr31211	Chr3:107502454-107502480 (+)	120 bp
Tssr31212	Chr3:107507749-107507757 (+)	5,406 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 09/08/2026 MGI 6.24