Ndc1 MGI Mouse Gene Detail - MGI:1920037 - NDC1 transmembrane nucleoporin

Symbol

Ndc1
Name

NDC1 transmembrane nucleoporin
Synonyms

2810475A17Rik, sks, Tmem48

Feature Type

protein coding gene
IDs

MGI:1920037
NCBI Gene: 72787
Alliance

gene page
Transcription Start Sites

11 TSS

Sequence Map

Chr4:107225244-107273543 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 50.18 cM, cytoband C7
Mapping Data

6 experiments

SNPs within 2kb

1376 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1920037	protein coding gene	Chr4:107224981-107273543 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0028539	protein coding gene	Chr4:108059701-108108167 (+)
A/J	MGP_AJ_G0028502	protein coding gene	Chr4:104179679-104229110 (+)
AKR/J	MGP_AKRJ_G0028449	protein coding gene	Chr4:106743131-106796805 (+)
BALB/cJ	MGP_BALBcJ_G0028521	protein coding gene	Chr4:104372412-104422148 (+)
C3H/HeJ	MGP_C3HHeJ_G0028235	protein coding gene	Chr4:107486559-107536537 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028961	protein coding gene	Chr4:111936737-111985232 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026252	protein coding gene	Chr4:99463014-99511545 (+)
CAST/EiJ	MGP_CASTEiJ_G0027671	protein coding gene	Chr4:105303762-105355990 (+)
CBA/J	MGP_CBAJ_G0028204	protein coding gene	Chr4:115572139-115632022 (+)
DBA/2J	MGP_DBA2J_G0028352	protein coding gene	Chr4:103803157-103853785 (+)
FVB/NJ	MGP_FVBNJ_G0028320	protein coding gene	Chr4:102671122-102722228 (+)
LP/J	MGP_LPJ_G0028453	protein coding gene	Chr4:108252531-108306572 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028346	protein coding gene	Chr4:120852853-120906096 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028997	protein coding gene	Chr4:106977015-107029821 (+)
PWK/PhJ	MGP_PWKPhJ_G0027397	protein coding gene	Chr4:102049262-102100774 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0027221	protein coding gene	Chr4:104366083-104413731 (+)
WSB/EiJ	MGP_WSBEiJ_G0027752	protein coding gene	Chr4:107153772-107208508 (+)

Human Ortholog

NDC1, NDC1 transmembrane nucleoporin

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

NDC1, NDC1 transmembrane nucleoporin
Synonyms

NET3, TMEM48
Links

HGNC:25525

NCBI Gene ID: 55706

neXtProt AC: NX_Q9BTX1

UniProt: Q9BTX1
Chr Location

1p32.3; chr1:53765478-53838463 (-) GRCh38

MGI Vertebrate Homology

Ndc1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: NDC1
Gene Tree

Ndc1

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Phenotype Summary

16 phenotypes from 1 allele in 1 genetic background
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

27
Chemically induced (other)

2
Endonuclease-mediated

1
Gene trapped

17
Radiation induced

1
Spontaneous

1
Targeted

1
Transgenic

4
Genomic Mutations

4 involving Ndc1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

40 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mutations in this gene produce background sensitive growth rates and skeletal anomalies. Both females and males are sterile.

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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

781
Tissues

23
cDNA Data

9
Literature Summary

2

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA NDC1

Xenbase ndc1

ZFIN ndc1

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All Sequences

49
RefSeq

3
UniProt

3
CCDS

CCDS18438.1

Ensembl

ENSMUSG00000028614 (Evidence)
NCBI Gene

72787

			Length	Strain/Species	Flank
genomic	72787	NCBI Gene Model \| MGI Sequence Detail	48300	C57BL/6J	± kb
transcript	NR_165083	RefSeq \| MGI Sequence Detail	4575	C57BL/6
polypeptide	Q8VCB1	UniProt \| EBI \| MGI Sequence Detail	673	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000016430 nucleoporin NDC1

(term hierarchy)
InterPro Domains

IPR019049 Nucleoporin protein Ndc1-Nup
GlyGen

Q8VCB1 1 site, 1 O-linked glycan (1 site)

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All nucleic 10

cDNA 9

Primer pair 1

Microarray probesets 6

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MGD-MRK-14433, MGI:2140289, MGI:98313

Summaries

All 45

Developmental Gene Expression 2

Gene Ontology 8

Phenotypes 16
Earliest

J:9569 Handel MA, et al., New mutation causing sterility in the mouse. Gamete Res. 1988 Dec;21(4):409-23
Latest

J:319412 Lai TH, et al., SEPT12-NDC1 Complexes Are Required for Mammalian Spermiogenesis. Int J Mol Sci. 2016 Nov 16;17(11):1911

TSS for Ndc1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr38245	Chr4:107224926-107224951 (+)	-305 bp
Tssr38246	Chr4:107224954-107225010 (+)	-262 bp
Tssr38247	Chr4:107225201-107225235 (+)	-26 bp
Tssr38248	Chr4:107225236-107225254 (+)	1 bp
Tssr38249	Chr4:107225258-107225269 (+)	20 bp
Tssr38250	Chr4:107225272-107225281 (+)	33 bp
Tssr38251	Chr4:107225518-107225537 (+)	284 bp
Tssr38252	Chr4:107238298-107238316 (+)	13,063 bp
Tssr38253	Chr4:107238319-107238322 (+)	13,077 bp
Tssr38254	Chr4:107238323-107238327 (+)	13,081 bp
Tssr38255	Chr4:107238339-107238344 (+)	13,098 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)
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