Pax9 MGI Mouse Gene Detail - MGI:97493

Symbol

Pax9
Name

paired box 9
Synonyms

Pax-9

Feature Type

protein coding gene
IDs

MGI:97493
NCBI Gene: 18511
Alliance

gene page
Transcription Start Sites

2 TSS

Sequence Map

Chr12:56738552-56759607 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 12, 24.53 cM
Mapping Data

7 experiments

SNPs within 2kb

604 from dbSNP Build 142
Strain Annotations

18
RFLP

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_97493	protein coding gene	Chr12:56738478-56759609 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0019757	protein coding gene	Chr12:55820044-55842106 (+)
A/J	MGP_AJ_G0019716	protein coding gene	Chr12:53783890-53807465 (+)
AKR/J	MGP_AKRJ_G0019691	protein coding gene	Chr12:55485435-55506912 (+)
BALB/cJ	MGP_BALBcJ_G0019696	protein coding gene	Chr12:54133556-54155902 (+)
C3H/HeJ	MGP_C3HHeJ_G0019501	protein coding gene	Chr12:55550746-55573678 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0020148	protein coding gene	Chr12:57476069-57501015 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017768	protein coding gene	Chr12:52250331-52271294 (+)
CAST/EiJ	MGP_CASTEiJ_G0019053	protein coding gene	Chr12:50446175-50473464 (+)
CBA/J	MGP_CBAJ_G0019470	protein coding gene	Chr12:59488770-59509829 (+)
DBA/2J	MGP_DBA2J_G0019586	protein coding gene	Chr12:53687829-53709376 (+)
FVB/NJ	MGP_FVBNJ_G0019574	protein coding gene	Chr12:52989661-53013742 (+)
LP/J	MGP_LPJ_G0019658	protein coding gene	Chr12:55791778-55814082 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019612	protein coding gene	Chr12:61047636-61071084 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020182	protein coding gene	Chr12:54925483-54946436 (+)
PWK/PhJ	MGP_PWKPhJ_G0018820	protein coding gene	Chr12:48059968-48081567 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0018613	protein coding gene	Chr12:49363716-49388932 (+)
WSB/EiJ	MGP_WSBEiJ_G0019104	protein coding gene	Chr12:55451016-55474425 (+)

Human Ortholog

PAX9, paired box 9

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PAX9, paired box 9
Synonyms

STHAG3
Links

HGNC:8623

NCBI Gene ID: 5083

neXtProt AC: NX_P55771

UniProt: P55771
Chr Location

14q13.3; chr14:36657568-36679362 (+) GRCh38

MGI Vertebrate Homology

Pax9 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: PAX9
Gene Tree

Pax9

Diseases

1 with Pax9 mouse models; 1 with human PAX9 associations

Human Disease

Mouse Models

tooth agenesis

IDs

View 2 models

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

Mutations/Alleles

2 with disease annotations

References

1 with disease annotations

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Phenotype Summary

84 phenotypes from 5 alleles in 10 genetic backgrounds
39 phenotypes from multigenic genotypes
35 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

15
Chemically induced (other)

1
Endonuclease-mediated

3
Targeted

11
Genomic Mutations

1 involving Pax9
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

17 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Homozygous inactivation of this gene results in abnormal tooth development and absent teeth and may lead to lack of pharyngeal pouch derivatives, athymia, craniofacial and limb anomalies, a small tympanic ring, various defects of the skeleton and musculature, and neonatal lethality.

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All GO Annotations

26
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

1271
Tissues

272
cDNA Data

16
Literature Summary

200

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA PAX9

Xenbase pax9

ZFIN pax9

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All Sequences

44
RefSeq

8
UniProt

3
CCDS

CCDS25924.1

Ensembl

ENSMUSG00000001497 (Evidence)
NCBI Gene

18511

			Length	Strain/Species	Flank
genomic	ENSMUSG00000001497	Ensembl Gene Model \| MGI Sequence Detail	21056	C57BL/6J	± kb
transcript	ENSMUST00000001538	Ensembl \| MGI Sequence Detail	4166	Not Applicable
polypeptide	ENSMUSP00000001538	Ensembl \| MGI Sequence Detail	342	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000012321 paired box protein Pax-9

(term hierarchy)
InterPro Domains

IPR009057 Homeobox-like domain superfamily

IPR043182 Paired DNA-binding domain

IPR001523 Paired domain

IPR043565 PAX family

IPR036388 Winged helix-like DNA-binding domain superfamily

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All nucleic 67

Genomic 2

cDNA 21

Primer pair 11

Other 33

Microarray probesets 5

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MGD-MRK-13152, MGD-MRK-13161

Summaries

All 256

Developmental Gene Expression 200

Diseases 1

Gene Ontology 10

Phenotypes 35
Earliest

J:4336 Stapleton P, et al., Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9. Nat Genet. 1993 Apr;3(4):292-8
Latest

J:346374 Ushiki A, et al., Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. Cell Rep. 2024 Mar 8;43(3):113907

TSS for Pax9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr113516	Chr12:56738296-56738313 (+)	-247 bp
Tssr113517	Chr12:56742413-56742485 (+)	3,897 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 11/12/2024 MGI 6.24