Pkhd1 PKHD1 ciliary IPT domain containing fibrocystin/polyductin [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Pkhd1provided by RGD
Full Name: PKHD1 ciliary IPT domain containing fibrocystin/polyductinprovided by RGD
Primary source: RGD:1308476
See related: EnsemblRapid:ENSRNOG00000058742 AllianceGenome:RGD:1308476
Gene type: protein coding
RefSeq status: MODEL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: AABR07067023.1
Summary: Predicted to be involved in several processes, including establishment of centrosome localization; regulation of epithelial cell proliferation; and regulation of intracellular signal transduction. Predicted to act upstream of with a positive effect on branching morphogenesis of an epithelial tube and cell-cell junction organization. Predicted to act upstream of or within cilium assembly and kidney development. Predicted to be located in several cellular components, including apical plasma membrane; extracellular exosome; and microtubule cytoskeleton. Used to study autosomal recessive polycystic kidney disease. Biomarker of autosomal recessive polycystic kidney disease. Human ortholog(s) of this gene implicated in autosomal recessive polycystic kidney disease and polycystic kidney disease 4. Orthologous to human PKHD1 (PKHD1 ciliary IPT domain containing fibrocystin/polyductin). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 599.7) and Liver (RPKM 82.8) See more
Orthologs: human mouse all
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Genomic context

Location:: 9q13

Exon count:: 67

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (30040466..30533834, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (22547396..23037443, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (26164969..26736704, complement)

Chromosome 9 - NC_086027.1 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 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?

transplantation with renal cells containing wild type Pkhd1 improves renal structure and function in autosomal recessive polycystic kidney disease
Title: Improved Structure and Function in Autosomal Recessive Polycystic Rat Kidneys with Renal Tubular Cell Therapy.
Both polycystins were detected on the spindle and mid-body of mitotic cells, while fibrocystin was on centrosome throughout cell cycle.
Title: Expression of polycystins and fibrocystin on primary cilia of lung cells.
polycystin-1, polycystin-2, and fibrocystin are shed in membrane particles in the urine, and these particles interact with primary cilia
Title: Characterization of PKD protein-positive exosome-like vesicles.
Cystic cholangiocytes possess short and malformed cilia that do not express fibrocystin, the Pkhd1 protein.
Title: Development and characterization of a cholangiocyte cell line from the PCK rat, an animal model of Autosomal Recessive Polycystic Kidney Disease.
loss of Pkhd1 in rats causes biliary dysgenesis
Title: Biliary dysgenesis in the PCK rat, an orthologous model of autosomal recessive polycystic kidney disease.
Reduced PKHD1 levels in pck rat kidneys and its colocalization with polycystins may underlie the pathogenic basis for cystogenesis in polycystic kidney diseases.
Title: PKHD1 protein encoded by the gene for autosomal recessive polycystic kidney disease associates with basal bodies and primary cilia in renal epithelial cells.

Submit: New GeneRIF Correction

General gene information

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Markers

AU049041 (e-PCR)
- UniSTS:145489

AU028005 (e-PCR)
- UniSTS:112752

D9Got30 (e-PCR)
- UniSTS:113636

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_positive_effect branching morphogenesis of an epithelial tube	ISO Inferred from Sequence Orthology more info
acts_upstream_of_positive_effect cell-cell junction organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in epithelial cell morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in establishment of centrosome localization	ISO Inferred from Sequence Orthology more info
involved_in establishment of mitotic spindle orientation	ISO Inferred from Sequence Orthology more info
involved_in intracellular calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of NF-kappaB transcription factor activity	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of epithelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in regulation of TOR signaling	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell-cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell-matrix adhesion	ISO Inferred from Sequence Orthology more info
involved_in regulation of centrosome duplication	ISO Inferred from Sequence Orthology more info
involved_in regulation of cholangiocyte proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of establishment of planar polarity	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in 9+0 non-motile cilium	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in extracellular exosome	ISO Inferred from Sequence Orthology more info
located_in mitotic spindle	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: PKHD1 ciliary IPT domain containing fibrocystin/polyductin; fibrocystin

Names: PKHD1, fibrocystin/polyductin; polycystic kidney and hepatic disease 1 (autosomal recessive); polycystic kidney and hepatic disease 1 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

30040466..30533834 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008766937.4 → XP_008765159.2 fibrocystin

UniProtKB/TrEMBL

A0A0G2K2W1

Related

ENSRNOP00000072399.2, ENSRNOT00000080948.3

Conserved Domains (4) summary

cd00603
Location:256 → 315

IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...

pfam01833
Location:1378 → 1467

TIG; IPT/TIG domain

pfam10162
Location:1918 → 2036

G8; G8 domain

pfam13229
Location:2988 → 3159

Beta_helix; Right handed beta helix region