Nphp3 nephrocystin 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nphp3provided by RGD
Official Full Name: nephrocystin 3provided by RGD
Primary source: RGD:1563856
See related: EnsemblRapid:ENSRNOG00000048978 AllianceGenome:RGD:1563856
Gene type: protein coding
RefSeq status: INFERRED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1563856
Summary: Predicted to be involved in several processes, including determination of left/right symmetry; photoreceptor cell maintenance; and regulation of Wnt signaling pathway. Predicted to act upstream of or within several processes, including establishment or maintenance of cell polarity; extracellular matrix organization; and non-motile cilium assembly. Predicted to be located in cilium. Predicted to be active in ciliary base and ciliary inversin compartment. Human ortholog(s) of this gene implicated in Meckel syndrome 7; hypertension; nephronophthisis; nephronophthisis 3; and renal-hepatic-pancreatic dysplasia. Orthologous to human NPHP3 (nephrocystin 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 31.7), Lung (RPKM 23.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q32

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (113500708..113541179)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (104621908..104662383)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (112526553..112575745)

Chromosome 8 - NC_086026.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in atrial septum development	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in convergent extension	IBA Inferred from Biological aspect of Ancestor more info
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
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within extracellular matrix organization	ISO Inferred from Sequence Orthology more info
involved_in heart looping	ISO Inferred from Sequence Orthology more info
involved_in kidney development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
involved_in kidney development	ISO Inferred from Sequence Orthology more info
involved_in kidney morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within kidney morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in kidney morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in lung development	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
involved_in regulation of Wnt signaling pathway, planar cell polarity pathway	ISO Inferred from Sequence Orthology more info
involved_in ureter development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in ciliary base	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary base	ISO Inferred from Sequence Orthology more info
is_active_in ciliary inversin compartment	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary inversin compartment	ISO Inferred from Sequence Orthology more info
located_in cilium	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nephrocystin-3

Names: nephronophthisis 3 (adolescent)

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_001191882.1 → NP_001178811.1 nephrocystin-3

Status: INFERRED

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

D4A1W7

Related

ENSRNOP00000014636.7, ENSRNOT00000014636.8

Conserved Domains (6) summary

sd00006
Location:1172 → 1200

TPR; TPR repeat [structural motif]

pfam03938
Location:120 → 202

OmpH; Outer membrane protein (OmpH-like)

pfam13374
Location:1130 → 1169

TPR_10; Tetratricopeptide repeat

pfam13424
Location:1085 → 1162

TPR_12; Tetratricopeptide repeat

cl09111
Location:112 → 207

Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...

cl21455
Location:502 → 556

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases