Nid1 MGI Mouse Gene Detail - MGI:97342

Symbol

Nid1
Name

nidogen 1
Synonyms

entactin, entactin 1, entactin-1, nidogen-1

Feature Type

protein coding gene
IDs

MGI:97342
NCBI Gene: 18073
Alliance

gene page
Transcription Start Sites

4 TSS
Candidate for QTL

1 QTL

Sequence Map

Chr13:13612252-13686849 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 13, 5.26 cM
Mapping Data

30 experiments

SNPs within 2kb

2216 from dbSNP Build 142
Strain Annotations

18
RFLP

11

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_97342	protein coding gene	Chr13:13612136-13686854 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0020233	protein coding gene	Chr13:9525873-10457040 (+)
A/J	MGP_AJ_G0020192	protein coding gene	Chr13:10321973-10392506 (+)
AKR/J	MGP_AKRJ_G0020166	protein coding gene	Chr13:10431103-10519277 (+)
BALB/cJ	MGP_BALBcJ_G0020179	protein coding gene	Chr13:10349629-10398182 (+)
C3H/HeJ	MGP_C3HHeJ_G0019979	protein coding gene	Chr13:9657989-10669650 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0020622	protein coding gene	Chr13:10923239-11017520 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018228	protein coding gene	Chr13:9117827-9189831 (+)
CAST/EiJ	MGP_CASTEiJ_G0019516	protein coding gene	Chr13:10230659-10309957 (+)
CBA/J	MGP_CBAJ_G0019946	protein coding gene	Chr13:11276577-11369265 (+)
DBA/2J	MGP_DBA2J_G0020065	protein coding gene	Chr13:9988740-10064572 (+)
FVB/NJ	MGP_FVBNJ_G0020047	protein coding gene	Chr13:9742401-9791307 (+)
LP/J	MGP_LPJ_G0020136	protein coding gene	Chr13:10585347-10643111 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0020082	protein coding gene	Chr13:10477742-11461603 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020649	protein coding gene	Chr13:10179952-10307815 (+)
PWK/PhJ	MGP_PWKPhJ_G0019279	protein coding gene	Chr13:10072395-10155944 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0019086	protein coding gene	Chr13:9386420-9534022 (+)
WSB/EiJ	MGP_WSBEiJ_G0019577	protein coding gene	Chr13:10254628-10340937 (+)

Human Ortholog

NID1, nidogen 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

NID1, nidogen 1
Synonyms

NID
Links

HGNC:7821

NCBI Gene ID: 4811

neXtProt AC: NX_P14543

UniProt: P14543
Chr Location

1q42.3; chr1:235975830-236065109 (-) GRCh38

MGI Vertebrate Homology

Nid1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: NID1
Gene Tree

Nid1

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Phenotype Summary

6 phenotypes from 1 allele in 1 genetic background
1 phenotype from multigenic genotypes
17 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
Endonuclease-mediated

2
Gene trapped

11
Targeted

4
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

63 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit neurologic deficits including seizure-like symptoms and loss of muscle control in the hind legs, and show altered basement membrane morphology in selected locations including brain capillaries and the lens capsule.

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All GO Annotations

34
GO References

30

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

1311
Tissues

269
cDNA Data

197
Literature Summary

113

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA NID1

Xenbase nid1

ZFIN nid1a, nid1b

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All Sequences

42
RefSeq

2
UniProt

1
CCDS

CCDS26244.1

Ensembl

ENSMUSG00000005397 (Evidence)
NCBI Gene

18073

			Length	Strain/Species	Flank
genomic	18073	NCBI Gene Model \| MGI Sequence Detail	74598	C57BL/6J	± kb
transcript	NM_010917	RefSeq \| MGI Sequence Detail	5970	ZRU/MplStud
polypeptide	P10493	UniProt \| EBI \| MGI Sequence Detail	1245	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000011208 nidogen-1

(term hierarchy)
PDB

1GL4, 1H4U, 1NPE
InterPro Domains

IPR026823 Complement Clr-like EGF domain

IPR050778 Cueball/EGF/LRP/Nidogen

IPR024731 EGF domain

IPR018097 EGF-like calcium-binding, conserved site

IPR001881 EGF-like calcium-binding domain

IPR000742 EGF-like domain

IPR000152 EGF-type aspartate/asparagine hydroxylation site

IPR006605 G2 nidogen/fibulin G2F

IPR009017 Green fluorescent protein

IPR009030 Growth factor receptor cysteine-rich domain superfamily

IPR000033 LDLR class B repeat

IPR003886 NIDO domain

IPR049883 NOTCH1 EGF-like calcium-binding domain

IPR011042 Six-bladed beta-propeller, TolB-like

IPR000716 Thyroglobulin type-1

IPR036857 Thyroglobulin type-1 superfamily
GlyGen

P10493 10 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (1 site)

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All nucleic 235

Genomic 28

cDNA 198

Primer pair 7

Other 2

Microarray probesets 4

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MGD-MRK-12878

Summaries

All 196

Developmental Gene Expression 113

Gene Ontology 30

Phenotypes 17
Earliest

J:320095 Paulsson M, et al., Laminin-nidogen complex. Extraction with chelating agents and structural characterization. Eur J Biochem. 1987 Jul 1;166(1):11-9
Latest

J:333810 Elenbaas JS, et al., SVEP1 is an endogenous ligand for the orphan receptor PEAR1. Nat Commun. 2023 Feb 15;14(1):850

TSS for Nid1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr118356	Chr13:13642974-13643000 (+)	30,735 bp
Tssr3994	Chr13:13655588-13655589 (+)	43,337 bp
Tssr118357	Chr13:13664693-13664710 (+)	52,450 bp
Tssr118358	Chr13:13686736-13686743 (+)	74,488 bp

Nid1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Bw15	Chr13, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 13, candidate gene Nid1 (7 cM) shows differential expression between the restricted and unrestricted diets on the A/A background. Diabesity QTL Bw15 (10 cM) maps near Nid1.

*cM position of peak correlated region/marker

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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