Usp3 MGI Mouse Gene Detail - MGI:2152450 - ubiquitin specific peptidase 3

Symbol

Usp3
Name

ubiquitin specific peptidase 3
Synonyms

MGC:28886

Feature Type

protein coding gene
IDs

MGI:2152450
NCBI Gene: 235441
Alliance

genome feature page
Transcription Start Sites

18 TSS

Sequence Map

Chr9:66421919-66500424 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 9, 35.96 cM
Mapping Data

1 experiment

SNPs within 2kb

1403 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2152450	protein coding gene	Chr9:66421573-66501996 (-)
129S1/SvImJ	ENSMUSG00200043237	protein coding gene	Chr9:63520118-63598617 (-)
A/J	ENSMUSG00195025050	protein coding gene	Chr9:63240895-63319429 (-)
AKR/J	ENSMUSG00220039995	protein coding gene	Chr9:63378928-63457455 (-)
BALB/cJ	ENSMUSG00180015466	protein coding gene	Chr9:63367471-63446002 (-)
C3H/HeJ	ENSMUSG00175011854	protein coding gene	Chr9:63374169-63452675 (-)
C57BL/6NJ	ENSMUSG00215025367	protein coding gene	Chr9:63362957-63441462 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032380	protein coding gene	Chr9:63713276-63795430 (-)
CAST/EiJ	ENSTCUG00005027167	protein coding gene	Chr9:63278108-63355960 (-)
CBA/J	ENSMUSG00210013975	protein coding gene	Chr9:63460171-63538679 (-)
DBA/2J	ENSMUSG00185032739	protein coding gene	Chr9:63486263-63564743 (-)
FVB/NJ	ENSMUSG00205030509	protein coding gene	Chr9:63807113-63885128 (-)
JF1/MsJ	ENSUMUG00000030760	protein coding gene	Chr9:63563260-63641441 (-)
LP/J	ENSMUSG00230020930	protein coding gene	Chr9:63719037-63797533 (-)
NOD/ShiLtJ	ENSMUSG00190021386	protein coding gene	Chr9:63570415-63648938 (-)
NZO/HlLtJ	ENSMUSG00225045738	protein coding gene	Chr9:63785863-63864374 (-)
PWK/PhJ	ENSLUMG00010025799	protein coding gene	Chr9:63508689-63586560 (-)
SPRET/EiJ	ENSMSPG00010017221	protein coding gene	Chr9:64585482-64666641 (-)
WSB/EiJ	ENSIUOG00005022230	protein coding gene	Chr9:62974817-63053336 (-)

Human Ortholog

USP3, ubiquitin specific peptidase 3

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

USP3, ubiquitin specific peptidase 3
Synonyms

SIH003, UBP
Links

HGNC:12626

NCBI Gene ID: 9960

UniProt: Q9Y6I4
Chr Location

15q22.31; chr15:63504501-63594640 (+) GRCh38

MGI Vertebrate Homology

Usp3 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: USP3
Gene Tree

Usp3

less

Phenotype Summary

1 phenotype from 2 alleles in 2 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

13
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

5
Targeted

5
Genomic Mutations

1 involving Usp3
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

33 strains or lines available

less

All GO Annotations

36
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.

less

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

662
Tissues

48
cDNA Data

13
Literature Summary

3

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase usp3

less

All Sequences

87
RefSeq

25
UniProt

5
CCDS

CCDS23305.1, CCDS81025.1

Ensembl

ENSMUSG00000032376 (Evidence)
NCBI Gene

235441

			Length	Strain/Species	Flank
genomic	ENSMUSG00000032376	Ensembl Gene Model \| MGI Sequence Detail	78506	C57BL/6J	± kb
transcript	ENSMUST00000127569	Ensembl \| MGI Sequence Detail	5607	Not Applicable
polypeptide	ENSMUSP00000122199	Ensembl \| MGI Sequence Detail	520	Not Applicable

less

UniProt

5 Sequences
Protein Ontology

PR:000017168 ubiquitin carboxyl-terminal hydrolase 3

(term hierarchy)
EC

3.4.19.12
InterPro Domains

IPR038765 Papain-like cysteine peptidase superfamily

IPR001394 Peptidase C19, ubiquitin carboxyl-terminal hydrolase

IPR050185 Ubiquitin carboxyl-terminal hydrolase

IPR018200 Ubiquitin specific protease, conserved site

IPR028889 Ubiquitin specific protease USP, catalytic domain

IPR013083 Zinc finger, RING/FYVE/PHD-type

IPR001607 Zinc finger, UBP-type

less

All nucleic 14

cDNA 13

Primer pair 1

Microarray probesets 6

less

MGI:2142934, MGI:2385312

Summaries

All 46

Developmental Gene Expression 3

Gene Ontology 8

Phenotypes 16
Earliest

J:85124 Sousa-Nunes R, et al., Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection. Genome Res. 2003 Dec;13(12):2609-20
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Usp3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr90264	Chr9:66500404-66500413 (-)	15 bp
Tssr90263	Chr9:66500388-66500402 (-)	29 bp
Tssr90262	Chr9:66500361-66500381 (-)	53 bp
Tssr90261	Chr9:66500344-66500353 (-)	75 bp
Tssr90260	Chr9:66500311-66500323 (-)	107 bp
Tssr90259	Chr9:66500275-66500306 (-)	133 bp
Tssr90258	Chr9:66500254-66500267 (-)	163 bp
Tssr90257	Chr9:66500227-66500251 (-)	185 bp
Tssr90256	Chr9:66500099-66500108 (-)	320 bp
Tssr90255	Chr9:66497954-66497957 (-)	2,468 bp
Tssr90254	Chr9:66490464-66490466 (-)	9,959 bp
Tssr90253	Chr9:66487974-66487982 (-)	12,446 bp
Tssr90252	Chr9:66487597-66487603 (-)	12,824 bp
Tssr90251	Chr9:66483310-66483330 (-)	17,104 bp
Tssr90250	Chr9:66427665-66427696 (-)	72,743 bp
Tssr90249	Chr9:66427592-66427624 (-)	72,816 bp
Tssr90248	Chr9:66425926-66425935 (-)	74,493 bp
Tssr90247	Chr9:66425880-66425884 (-)	74,542 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