Usp47 MGI Mouse Gene Detail - MGI:1922246 - ubiquitin specific peptidase 47

Symbol

Usp47
Name

ubiquitin specific peptidase 47
Synonyms

4930502N04Rik, A630020C16Rik

Feature Type

protein coding gene
IDs

MGI:1922246
NCBI Gene: 74996
Alliance

genome feature page
Transcription Start Sites

10 TSS
Regulated by

Rr379 (1 regulatory region)

Sequence Map

Chr7:111622692-111710591 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 7, 58.74 cM, cytoband F2
Mapping Data

3 experiments

SNPs within 2kb

1427 from dbSNP Build 142
Strain Annotations

14

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1922246	protein coding gene	Chr7:111622692-111710868 (+)
129S1/SvImJ	ENSMUSG00200033919	protein coding gene	Chr7:98164167-98252348 (+)
A/J	ENSMUSG00195031513	protein coding gene	Chr7:102667739-102755925 (+)
AKR/J	ENSMUSG00220033273	protein coding gene	Chr7:96070694-96158886 (+)
BALB/cJ	ENSMUSG00180042482	protein coding gene	Chr7:99335838-99424033 (+)
C3H/HeJ	ENSMUSG00175051361	protein coding gene	Chr7:99971692-100059871 (+)
C57BL/6NJ	ENSMUSG00215047839	protein coding gene	Chr7:99278705-99366875 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0030332	protein coding gene	Chr7:114300825-114390322 (+)
CAST/EiJ	no annotation
CBA/J	ENSMUSG00210038764	protein coding gene	Chr7:99798671-99886856 (+)
DBA/2J	ENSMUSG00185019876	protein coding gene	Chr7:104148831-104237014 (+)
FVB/NJ	ENSMUSG00205030017	protein coding gene	Chr7:99761617-99849810 (+)
JF1/MsJ	no annotation
LP/J	ENSMUSG00230043982	protein coding gene	Chr7:110249876-110338054 (+)
NOD/ShiLtJ	ENSMUSG00190043998	protein coding gene	Chr7:99960238-100048429 (+)
NZO/HlLtJ	ENSMUSG00225016665	protein coding gene	Chr7:108499666-108587880 (+)
PWK/PhJ	no annotation
SPRET/EiJ	no annotation
WSB/EiJ	no annotation

Human Ortholog

USP47, ubiquitin specific peptidase 47

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

USP47, ubiquitin specific peptidase 47
Synonyms

TRFP
Links

HGNC:20076

NCBI Gene ID: 55031

UniProt: Q96K76
Chr Location

11p15.3; chr11:11841423-11961887 (+) GRCh38

MGI Vertebrate Homology

Usp47 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: USP47
Gene Tree

Usp47

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Phenotype Summary

5 phenotypes from 2 alleles in 2 genetic backgrounds
29 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

25
Endonuclease-mediated

7
Gene trapped

11
Radiation induced

1
Targeted

6
Genomic Mutations

1 involving Usp47
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

68 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mouse embryonic fibroblasts from mice homozygous for a gene trap allele exhibit increased sensitivity to UV irradiation.

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All GO Annotations

26
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

597
cDNA Data

15

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase usp47

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All Sequences

61
RefSeq

8
UniProt

4
CCDS

CCDS40089.1, CCDS85384.1, CCDS90312.1

Ensembl

ENSMUSG00000059263 (Evidence)
NCBI Gene

74996

			Length	Strain/Species	Flank
genomic	74996	NCBI Gene Model \| MGI Sequence Detail	87900	C57BL/6J	± kb
transcript	NM_001403494	RefSeq \| MGI Sequence Detail	5679	C57BL/6
polypeptide	Q8BY87	UniProt \| EBI \| MGI Sequence Detail	1376	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000017186 ubiquitin carboxyl-terminal hydrolase 47

(term hierarchy)
EC

3.4.19.12
InterPro Domains

IPR038765 Papain-like cysteine peptidase superfamily

IPR001394 Peptidase C19, ubiquitin carboxyl-terminal hydrolase

IPR045578 Ubiquitin carboxyl-terminal hydrolase 47, C-terminal

IPR059974 Ubiquitin carboxyl-terminal hydrolase 47, ubiquitin-like domain

IPR050164 Ubiquitin carboxyl-terminal hydrolases

IPR029071 Ubiquitin-like domain superfamily

IPR018200 Ubiquitin specific protease, conserved site

IPR028889 Ubiquitin specific protease USP, catalytic domain
GlyGen

Q8BY87 3 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (1 site)

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All nucleic 16

cDNA 16

Microarray probesets 4

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MGI:2444648

Summaries

All 61

Gene Ontology 8

Phenotypes 29
Earliest

J:61682 Hagiwara N, et al., Sox6 is a candidate gene for p100H myopathy, heart block, and sudden neonatal death. Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4180-5
Latest

J:353390 Wang QL, et al., USP47 deficiency in mice modulates tumor infiltrating immune cells and enhances antitumor immune responses in prostate cancer. Cancer Immunol Immunother. 2024 Jun 4;73(8):143

Usp47 expression regulated by:

Feature	Feature Type	Location	Reference
Rr379, regulatory region 379	enhancer	Chr7:112423819-112426616	J:333416

TSS for Usp47:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr68546	Chr7:111622458-111622524 (+)	-201 bp
Tssr68547	Chr7:111622640-111622651 (+)	-46 bp
Tssr68548	Chr7:111622654-111622669 (+)	-30 bp
Tssr68549	Chr7:111622676-111622773 (+)	33 bp
Tssr68550	Chr7:111622784-111622797 (+)	99 bp
Tssr68551	Chr7:111673858-111673884 (+)	51,179 bp
Tssr68552	Chr7:111677043-111677056 (+)	54,358 bp
Tssr68553	Chr7:111681668-111681701 (+)	58,993 bp
Tssr68554	Chr7:111682323-111682348 (+)	59,644 bp
Tssr68555	Chr7:111692284-111692334 (+)	69,617 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