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Npnt nephronectin [ Mus musculus (house mouse) ]

Gene ID: 114249, updated on 9-Dec-2024

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 ERK1 and ERK2 cascade. 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
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Genomic context

See Npnt in Genome Data Viewer
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_000069.7Genomic Context describing neighboring genes Neighboring gene TBC1 domain containing kinase Neighboring gene STARR-seq mESC enhancer starr_09019 Neighboring gene predicted gene, 22322 Neighboring gene STARR-seq mESC enhancer starr_09020 Neighboring gene predicted gene, 29811 Neighboring gene heat shock protein 90 alpha (cytosolic), class B member 1 pseudogene Neighboring gene predicted gene, 23196 Neighboring gene glutathione S-transferase, C-terminal domain containing Neighboring gene TIP41, TOR signalling pathway regulator-like pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E6130 Neighboring gene STARR-positive B cell enhancer ABC_E9573 Neighboring gene STARR-positive B cell enhancer mm9_chr3:132754721-132755022 Neighboring gene STARR-positive B cell enhancer ABC_E11218 Neighboring gene integrator complex subunit 12

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

General gene information

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables calcium ion binding  
enables extracellular matrix structural constituent PubMed 
enables integrin binding PubMed 
enables integrin binding PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within branching involved in ureteric bud morphogenesis PubMed 
involved_in cell-cell adhesion mediated by integrin PubMed 
acts_upstream_of_or_within cell-matrix adhesion PubMed 
acts_upstream_of_or_within cell-matrix adhesion PubMed 
involved_in cellular response to tumor necrosis factor PubMed 
involved_in establishment of protein localization PubMed 
acts_upstream_of_or_within extracellular matrix organization PubMed 
involved_in pilomotor reflex PubMed 
involved_in positive regulation of ERK1 and ERK2 cascade PubMed 
involved_in positive regulation of alkaline phosphatase activity PubMed 
acts_upstream_of_or_within positive regulation of cell-substrate adhesion PubMed 
involved_in positive regulation of osteoblast differentiation PubMed 
involved_in positive regulation of smooth muscle contraction PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
acts_upstream_of_or_within positive regulation of transforming growth factor beta receptor signaling pathway PubMed 
involved_in smooth muscle cell differentiation PubMed 
acts_upstream_of transforming growth factor beta receptor signaling pathway PubMed 
acts_upstream_of_or_within ureteric bud development PubMed 

General protein information

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)

  1. NM_001029836.2NP_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:422561
    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:422561
    MAM; MAM domain, meprin/A5/mu
    pfam07645
    Location:169201
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:150172
    cEGF; Complement Clr-like EGF-like
    pfam12947
    Location:218253
    EGF_3; EGF domain
    cl00057
    Location:81125
    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 ...
  2. NM_001287101.1NP_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:470609
    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:137169
    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:470609
    MAM; MAM domain, meprin/A5/mu
    pfam07645
    Location:217249
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:198220
    cEGF; Complement Clr-like EGF-like
    pfam12947
    Location:266301
    EGF_3; EGF domain
  3. NM_001287102.1NP_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:453592
    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:120152
    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:453592
    MAM; MAM domain, meprin/A5/mu
    pfam07645
    Location:200232
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:181203
    cEGF; Complement Clr-like EGF-like
    pfam12947
    Location:249284
    EGF_3; EGF domain
  4. NM_001287103.1NP_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:318457
    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:318457
    MAM; MAM domain, meprin/A5/mu
    pfam07645
    Location:6597
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:4668
    cEGF; Complement Clr-like EGF-like
    pfam12947
    Location:114149
    EGF_3; EGF domain
  5. NM_033525.3NP_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:439578
    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:439578
    MAM; MAM domain, meprin/A5/mu
    pfam07645
    Location:186218
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:167189
    cEGF; Complement Clr-like EGF-like
    pfam12947
    Location:235270
    EGF_3; EGF domain
    cl00057
    Location:98142
    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

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    132587506..132656052 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006500915.5XP_006500978.1  nephronectin isoform X1

    UniProtKB/TrEMBL
    D3Z4D3
    Conserved Domains (5) summary
    cd06263
    Location:391530
    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:138170
    EGF_CA; Calcium-binding EGF domain
    pfam12662
    Location:119141
    cEGF; Complement Clr-like EGF-like
    pfam12947
    Location:187222
    EGF_3; EGF domain
    cl00057
    Location:5694
    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 ...
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