U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Nphp3 nephronophthisis 3 (adolescent) [ Mus musculus (house mouse) ]

Gene ID: 74025, updated on 8-Dec-2022

Summary

Official Symbol
Nphp3provided by MGI
Official Full Name
nephronophthisis 3 (adolescent)provided by MGI
Primary source
MGI:MGI:1921275
See related
Ensembl:ENSMUSG00000032558 AllianceGenome:MGI:1921275
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
pcy; C230078J01; 3632410F03Rik; D330020E01Rik
Summary
Involved in several processes, including cilium assembly; determination of left/right symmetry; and maintenance of animal organ identity. Acts upstream of or within several processes, including extracellular matrix organization; non-motile cilium assembly; and positive regulation of protein binding activity. Located in ciliary base and ciliary inversin compartment. Is expressed in embryo. Used to study autosomal dominant polycystic kidney disease and nephronophthisis 3. Human ortholog(s) of this gene implicated in Meckel syndrome 7; nephronophthisis; nephronophthisis 3; and renal-hepatic-pancreatic dysplasia. Orthologous to human NPHP3 (nephrocystin 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in limb E14.5 (RPKM 5.9), bladder adult (RPKM 3.2) and 28 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Nphp3 in Genome Data Viewer
Location:
9 F1; 9 56.11 cM
Exon count:
27
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (103879743..103921010)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (104002544..104043811)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene predicted gene 29154 Neighboring gene predicted gene, 32797 Neighboring gene predicted gene, 33054 Neighboring gene NSA2 ribosome biogenesis homolog pseudogene Neighboring gene ubiquitin-like modifier activating enzyme 5

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)
  • Spontaneous (1)  1 citation
  • Targeted (2)  1 citation
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: Acad11

Homology

Clone Names

  • MGC141550

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in atrial septum development ISO
Inferred from Sequence Orthology
more info
 
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in convergent extension IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in convergent extension involved in gastrulation ISO
Inferred from Sequence Orthology
more info
 
involved_in determination of intestine left/right asymmetry ISO
Inferred from Sequence Orthology
more info
 
involved_in determination of left/right symmetry IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in determination of left/right symmetry IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in determination of left/right symmetry ISO
Inferred from Sequence Orthology
more info
 
involved_in determination of liver left/right asymmetry ISO
Inferred from Sequence Orthology
more info
 
involved_in determination of pancreatic left/right asymmetry ISO
Inferred from Sequence Orthology
more info
 
involved_in determination of stomach left/right asymmetry ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within establishment or maintenance of cell polarity IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within extracellular matrix organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in heart looping ISO
Inferred from Sequence Orthology
more info
 
involved_in kidney development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in kidney development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within kidney morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in kidney morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in kidney morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within lipid metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in lung development ISO
Inferred from Sequence Orthology
more info
 
involved_in maintenance of animal organ identity IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in maintenance of animal organ identity ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of canonical Wnt signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within non-motile cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in photoreceptor cell maintenance ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of protein binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ureter development ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in cell projection IEA
Inferred from Electronic Annotation
more info
 
is_active_in ciliary base IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in ciliary base IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in ciliary inversin compartment IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in ciliary inversin compartment IDA
Inferred from Direct Assay
more info
PubMed 
located_in cilium ISO
Inferred from Sequence Orthology
more info
 

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_028721.3NP_082997.3  nephrocystin-3 isoform a

    See identical proteins and their annotated locations for NP_082997.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform a).
    Source sequence(s)
    AK133217, AK173327, BM219539
    Consensus CDS
    CCDS40749.1
    UniProtKB/Swiss-Prot
    Q7TNH6, Q9D6D1
    Related
    ENSMUSP00000035167.9, ENSMUST00000035167.15
    Conserved Domains (7) summary
    sd00006
    Location:11301158
    TPR; TPR repeat [structural motif]
    pfam03938
    Location:120202
    OmpH; Outer membrane protein (OmpH-like)
    pfam04871
    Location:113199
    Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region
    pfam12711
    Location:76145
    Kinesin-relat_1; Kinesin motor
    pfam13374
    Location:11301169
    TPR_10; Tetratricopeptide repeat
    pfam13424
    Location:10851162
    TPR_12; Tetratricopeptide repeat
    cl21455
    Location:502570
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  2. NM_172460.1NP_766048.1  nephrocystin-3 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses a different splice site in the 5' CDS and lacks all of the downstream CDS, compared to variant 1. The resulting protein (isoform b) is much shorter and has a distinct C-terminus when it is compared to isoform a.
    Source sequence(s)
    AK052281, AK133217
    UniProtKB/Swiss-Prot
    Q7TNH6
    Related
    ENSMUST00000191919.2
    Conserved Domains (3) summary
    pfam03938
    Location:120202
    OmpH; Outer membrane protein (OmpH-like)
    pfam04871
    Location:113199
    Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region
    pfam12711
    Location:76145
    Kinesin-relat_1; Kinesin motor

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000075.7 Reference GRCm39 C57BL/6J

    Range
    103879743..103921010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)