Npnt nephronectin [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Npntprovided by MGI
Official Full Name: nephronectinprovided by MGI
Primary source: MGI:MGI:2148811
See related: Ensembl:ENSMUSG00000040998 AllianceGenome:MGI:2148811
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Nctn; POEM; 1110009H02Rik
Summary: Enables integrin binding activity. Involved in several processes, including cell-cell adhesion mediated by integrin; pilomotor reflex; and positive regulation of metabolic process. Acts upstream of or within several processes, including branching involved in ureteric bud morphogenesis; positive regulation of cell-substrate adhesion; and positive regulation of transforming growth factor beta receptor signaling pathway. Located in basement membrane; extracellular region; and smooth muscle contractile fiber. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Used to study bilateral renal aplasia. Orthologous to human NPNT (nephronectin). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in lung adult (RPKM 118.7), kidney adult (RPKM 39.1) and 5 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 G3; 3 61.52 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (132587506..132656052, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (132881745..132950291, complement)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression of Nephronectin in the Descemet's membrane of mouse corneas during development and adult homeostasis.
Title: Expression of Nephronectin in the Descemet's membrane of mouse corneas during development and adult homeostasis.
Nephronectin is required to maintain right lung lobar separation during embryonic development.
Title: Nephronectin is required to maintain right lung lobar separation during embryonic development.
Endotoxin-induced acute lung injury in mice with postnatal deletion of nephronectin.
Title: Endotoxin-induced acute lung injury in mice with postnatal deletion of nephronectin.
Glomerular Endothelial Cell-Derived microRNA-192 Regulates Nephronectin Expression in Idiopathic Membranous Glomerulonephritis.
Title: Glomerular Endothelial Cell-Derived microRNA-192 Regulates Nephronectin Expression in Idiopathic Membranous Glomerulonephritis.
A Biallelic Frameshift Mutation in Nephronectin Causes Bilateral Renal Agenesis in Humans.
Title: A Biallelic Frameshift Mutation in Nephronectin Causes Bilateral Renal Agenesis in Humans.
Npnt gene expression is regulated by extracellular inorganic Phosphate via Pit and Fgfrs.
Title: Nephronectin Expression is Inhibited by Inorganic Phosphate in Osteoblasts.
we show that a novel truncated form of NPNT is found in small extracellular vesicles (sEVs) derived from breast cancer cells.
Title: A Novel Truncated Form of Nephronectin Is Present in Small Extracellular Vesicles Isolated from 66cl4 Cells.
Nephronectin is produced by podocytes and deposited into the GBM. It colocalized with alpha8beta1 integrin to novel, specialized adhesion structures at sites of mesangial cell protrusion at the base of the capillary loops. Nephronectin loss disrupted these structures, mislocalizating alpha8beta1, and caused mesangial sclerosis.
Title: Nephronectin Regulates Mesangial Cell Adhesion and Behavior in Glomeruli.
Results show that Npnt is highly expressed in tooth germ, and localized in the basement membrane between dental epithelium and mesenchyme. The study indicates that Npnt plays a critical scaffold role in dental epithelial stem cell differentiation and proliferation, and regulates Sox2 expression during tooth development.
Title: Nephronectin plays critical roles in Sox2 expression and proliferation in dental epithelial stem cells via EGF-like repeat domains.
Low Nephronectin expression is associated with Metastatic Breast Carcinoma.
Title: Nephronectin is Decreased in Metastatic Breast Carcinoma and Related to Metastatic Organs.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3) 1 citation
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3Mit15 (e-PCR), detects polymorphism
- UniSTS:129561

RH125609 (e-PCR)
- UniSTS:162423

Npnt (e-PCR), detects polymorphism
- UniSTS:536480

Npnt (e-PCR), detects polymorphism
- UniSTS:498344

Npnt (e-PCR), detects polymorphism
- UniSTS:498345

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables integrin binding	IDA Inferred from Direct Assay more info	PubMed
enables integrin binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within branching involved in ureteric bud morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell-cell adhesion mediated by integrin	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cell-matrix adhesion	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cell-matrix adhesion	IPI Inferred from Physical Interaction more info	PubMed
involved_in cellular response to tumor necrosis factor	IDA Inferred from Direct Assay more info	PubMed
involved_in establishment of protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within extracellular matrix organization	IDA Inferred from Direct Assay more info	PubMed
involved_in pilomotor reflex	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of ERK1 and ERK2 cascade	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of alkaline phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of cell-substrate adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of osteoblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smooth muscle contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transforming growth factor beta receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in smooth muscle cell differentiation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of transforming growth factor beta receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ureteric bud development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular matrix	IPI Inferred from Physical Interaction more info	PubMed
located_in extracellular region	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in smooth muscle contractile fiber	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nephronectin

Names: preosteoblast EGF-like repeat protein with MAM domain

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001029836.2 → NP_001025007.1 nephronectin isoform b precursor

See identical proteins and their annotated locations for NP_001025007.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two in-frame exons in the 5' coding region compared to variant 3. The encoded isoform (b) is shorter than isoform c.

Source sequence(s)

AB059656, AC139942, AK160311

Consensus CDS

CCDS17845.1

UniProtKB/Swiss-Prot

Q6NV58, Q80VP6, Q91V88, Q91XL5, Q91ZD3, Q923T5

UniProtKB/TrEMBL

D3Z4D3

Related

ENSMUSP00000040684.10, ENSMUST00000042744.16

Conserved Domains (6) summary

cd06263
Location:422 → 561

MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...

pfam00629
Location:422 → 561

MAM; MAM domain, meprin/A5/mu

pfam07645
Location:169 → 201

EGF_CA; Calcium-binding EGF domain

pfam12662
Location:150 → 172

cEGF; Complement Clr-like EGF-like

pfam12947
Location:218 → 253

EGF_3; EGF domain

cl00057
Location:81 → 125

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_001287101.1 → NP_001274030.1 nephronectin isoform c precursor

See identical proteins and their annotated locations for NP_001274030.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).

Source sequence(s)

AB059656, AC139942, AF397008, AK160311

Consensus CDS

CCDS71323.1

UniProtKB/TrEMBL

D3Z4D3

Related

ENSMUSP00000091505.5, ENSMUST00000093971.5

Conserved Domains (6) summary

cd06263
Location:470 → 609

MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...

cd00054
Location:137 → 169

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam00629
Location:470 → 609

MAM; MAM domain, meprin/A5/mu

pfam07645
Location:217 → 249

EGF_CA; Calcium-binding EGF domain

pfam12662
Location:198 → 220

cEGF; Complement Clr-like EGF-like

pfam12947
Location:266 → 301

EGF_3; EGF domain
NM_001287102.1 → NP_001274031.1 nephronectin isoform d precursor

See identical proteins and their annotated locations for NP_001274031.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region compared to variant 3. The encoded isoform (d) is shorter than isoform c.

Source sequence(s)

AB059656, AC139942, AF397007, AK160311

Consensus CDS

CCDS71322.1

UniProtKB/TrEMBL

D3Z4D3

Related

ENSMUSP00000113419.2, ENSMUST00000117164.8

Conserved Domains (6) summary

cd06263
Location:453 → 592

MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...

cd00054
Location:120 → 152

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

pfam00629
Location:453 → 592

MAM; MAM domain, meprin/A5/mu

pfam07645
Location:200 → 232

EGF_CA; Calcium-binding EGF domain

pfam12662
Location:181 → 203

cEGF; Complement Clr-like EGF-like

pfam12947
Location:249 → 284

EGF_3; EGF domain
NM_001287103.1 → NP_001274032.1 nephronectin isoform e

Status: VALIDATED

Description

Transcript Variant: This variant (5) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region compared to variant 3. The resulting isoform (e) has a shorter N-terminus compared to isoform c.

Source sequence(s)

AC139942, AK158764, AK160311

Consensus CDS

CCDS71321.1

UniProtKB/TrEMBL

D3YTX1, Q3TYB4

Related

ENSMUSP00000112816.2, ENSMUST00000117456.8

Conserved Domains (5) summary

cd06263
Location:318 → 457

MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...

pfam00629
Location:318 → 457

MAM; MAM domain, meprin/A5/mu

pfam07645
Location:65 → 97

EGF_CA; Calcium-binding EGF domain

pfam12662
Location:46 → 68

cEGF; Complement Clr-like EGF-like

pfam12947
Location:114 → 149

EGF_3; EGF domain
NM_033525.3 → NP_277060.2 nephronectin isoform a precursor

See identical proteins and their annotated locations for NP_277060.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) lacks an in-frame exon in the 5' coding region compared to variant 3. The encoded isoform (a) is shorter than isoform c.

Source sequence(s)

AC139942

Consensus CDS

CCDS17846.1

UniProtKB/TrEMBL

D3Z4D3

Related

ENSMUSP00000040071.10, ENSMUST00000042729.16

Conserved Domains (6) summary

cd06263
Location:439 → 578

MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...

pfam00629
Location:439 → 578

MAM; MAM domain, meprin/A5/mu

pfam07645
Location:186 → 218

EGF_CA; Calcium-binding EGF domain

pfam12662
Location:167 → 189

cEGF; Complement Clr-like EGF-like

pfam12947
Location:235 → 270

EGF_3; EGF domain

cl00057
Location:98 → 142

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

132587506..132656052 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006500915.5 → XP_006500978.1 nephronectin isoform X1

UniProtKB/TrEMBL

D3Z4D3

Conserved Domains (5) summary

cd06263
Location:391 → 530

MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...

pfam07645
Location:138 → 170

EGF_CA; Calcium-binding EGF domain

pfam12662
Location:119 → 141

cEGF; Complement Clr-like EGF-like

pfam12947
Location:187 → 222

EGF_3; EGF domain

cl00057
Location:56 → 94

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...