Nup54 MGI Mouse Gene Detail - MGI:1920460

Symbol

Nup54
Name

nucleoporin 54
Synonyms

3110079L04Rik, 54kDa

Feature Type

protein coding gene
IDs

MGI:1920460
NCBI Gene: 269113
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr5:92563399-92583078 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 5, 46.75 cM, cytoband E3
Mapping Data

2 experiments

SNPs within 2kb

506 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1920460	protein coding gene	Chr5:92563399-92583117 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0029751	protein coding gene	Chr5:93613339-93633032 (-)
A/J	MGP_AJ_G0029717	protein coding gene	Chr5:89890838-89915076 (-)
AKR/J	MGP_AKRJ_G0029663	protein coding gene	Chr5:92826970-92851600 (-)
BALB/cJ	MGP_BALBcJ_G0029727	protein coding gene	Chr5:90767721-90789041 (-)
C3H/HeJ	MGP_C3HHeJ_G0029450	protein coding gene	Chr5:93228087-93251941 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0030181	protein coding gene	Chr5:97317729-97337911 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0027417	protein coding gene	Chr5:85534156-85554145 (-)
CAST/EiJ	MGP_CASTEiJ_G0028860	protein coding gene	Chr5:92609675-92632349 (-)
CBA/J	MGP_CBAJ_G0029420	protein coding gene	Chr5:100694723-100734125 (-)
DBA/2J	MGP_DBA2J_G0029564	protein coding gene	Chr5:89931880-89954907 (-)
FVB/NJ	MGP_FVBNJ_G0029523	protein coding gene	Chr5:88777502-88798997 (-)
LP/J	MGP_LPJ_G0029652	protein coding gene	Chr5:93974663-93994792 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0029552	protein coding gene	Chr5:105604223-105627479 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0030215	protein coding gene	Chr5:92351973-92372432 (-)
PWK/PhJ	MGP_PWKPhJ_G0028579	protein coding gene	Chr5:88999986-89020958 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0028414	protein coding gene	Chr5:91717265-91738512 (-)
WSB/EiJ	MGP_WSBEiJ_G0028939	protein coding gene	Chr5:92823991-92845325 (-)

Human Ortholog

NUP54, nucleoporin 54

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

NUP54, nucleoporin 54
Synonyms

DYT37
Links

HGNC:17359

NCBI Gene ID: 53371

neXtProt AC: NX_Q7Z3B4

UniProt: Q7Z3B4
Chr Location

4q21.1; chr4:76107562-76148485 (-) GRCh38

MGI Vertebrate Homology

Nup54 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: NUP54
Gene Tree

Nup54

Diseases

1 with human NUP54 associations

				Human Disease	Mouse Models
				dystonia 37, early-onset with striatal lesions IDs dystonia 37, early-onset with striatal lesions DOID:0060956 OMIM:620427

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

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Phenotype Summary

10 phenotypes from 1 allele in 2 genetic backgrounds
1 images
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

17
Chemically induced (other)

1
Endonuclease-mediated

1
Gene trapped

11
Radiation induced

1
Spontaneous

1
Targeted

2
Genomic Mutations

3 involving Nup54
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

31 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele show embryonic growth retardation, a small egg cylinder, disorganized extraembryonic tissue, failure of primitive streak formation and gastrulation, and complete embryonic lethality by E9.5.

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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

707
Tissues

1
cDNA Data

95
Literature Summary

1

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase nup54

ZFIN nup54

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All Sequences

66
RefSeq

13
UniProt

4
CCDS

CCDS19430.1

Ensembl

ENSMUSG00000034826 (Evidence)
NCBI Gene

269113

			Length	Strain/Species	Flank
genomic	ENSMUSG00000034826	Ensembl Gene Model \| MGI Sequence Detail	19680	C57BL/6J	± kb
transcript	ENSMUST00000038514	Ensembl \| MGI Sequence Detail	2352	Not Applicable
polypeptide	ENSMUSP00000046540	Ensembl \| MGI Sequence Detail	510	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000011520 nucleoporin p54

(term hierarchy)
InterPro Domains

IPR025712 Nucleoporin Nup54, alpha-helical domain

IPR024864 Nucleoporin Nup54/Nup57/Nup44

IPR040985 Nup54, C-terminal interacting domain
GlyGen

Q8BTS4 2 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (1 site)

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All nucleic 95

cDNA 95

Microarray probesets 4

Summaries

All 44

Developmental Gene Expression 1

Gene Ontology 8

Phenotypes 14
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

J:139177 Hoffman BG, et al., Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol. 2008;9(6):R99

TSS for Nup54:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr51915	Chr5:92583078-92583094 (-)	-8 bp
Tssr51914	Chr5:92583048-92583075 (-)	16 bp
Tssr51913	Chr5:92582973-92582989 (-)	97 bp
Tssr51912	Chr5:92582934-92582962 (-)	130 bp
Tssr51911	Chr5:92582915-92582924 (-)	158 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