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Nphp1 nephrocystin 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 296136, updated on 13-Apr-2024

Summary

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Official Symbol
Nphp1provided by RGD
Official Full Name
nephrocystin 1provided by RGD
Primary source
RGD:1308136
See related
Ensembl:ENSRNOG00000015756 AllianceGenome:RGD:1308136
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to be involved in several processes, including photoreceptor cell outer segment organization; positive regulation of bicellular tight junction assembly; and spermatid differentiation. Predicted to be located in several cellular components, including ciliary base; motile cilium; and photoreceptor distal connecting cilium. Human ortholog(s) of this gene implicated in Bardet-Biedl syndrome; Joubert syndrome 4; Senior-Loken syndrome; nephronophthisis; and nephronophthisis 1. Orthologous to human NPHP1 (nephrocystin 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Testes (RPKM 256.3), Muscle (RPKM 123.4) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Nphp1 in Genome Data Viewer
Location:
3q36
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (135413927..135469505, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (114960650..115016234, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (120316048..120370089, complement)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102555822 Neighboring gene mal, T-cell differentiation protein-like Neighboring gene WW domain containing adaptor with coiled-coil, pseudogene 2 Neighboring gene mitoregulin Neighboring gene BUB1 mitotic checkpoint serine/threonine kinase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Clinical characterization and NPHP1 mutations in nephronophthisis and associated ciliopathies: a single center experience. Soliman NA, et al. Saudi J Kidney Dis Transpl, 2012 Sep. PMID 22982934, Free PMC Article
  2. Pseudodominant inheritance of nephronophthisis caused by a homozygous NPHP1 deletion. Hoefele J, et al. Pediatr Nephrol, 2011 Jun. PMID 21258817, Free PMC Article
  3. Targeted disruption of Nphp1 causes male infertility due to defects in the later steps of sperm morphogenesis in mice. Jiang ST, et al. Hum Mol Genet, 2008 Nov 1. PMID 18684731
  4. Stop codon at arginine 586 is the prevalent nephronopthisis type 1 mutation in Italy. Caridi G, et al. Nephrol Dial Transplant, 2006 Aug. PMID 16762963
  5. Nephrocystin specifically localizes to the transition zone of renal and respiratory cilia and photoreceptor connecting cilia. Fliegauf M, et al. J Am Soc Nephrol, 2006 Sep. PMID 16885411

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in cell projection organization ISO
Inferred from Sequence Orthology
more info
  
involved_in photoreceptor cell outer segment organization ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of bicellular tight junction assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization ISO
Inferred from Sequence Orthology
more info
  
involved_in retina development in camera-type eye ISO
Inferred from Sequence Orthology
more info
  
involved_in spermatid differentiation ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cell-cell junction ISO
Inferred from Sequence Orthology
more info
  
located_in ciliary base ISO
Inferred from Sequence Orthology
more info
  
located_in ciliary transition zone 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 motile cilium ISO
Inferred from Sequence Orthology
more info
  
located_in photoreceptor connecting cilium ISO
Inferred from Sequence Orthology
more info
  
located_in photoreceptor distal connecting cilium ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
nephrocystin-1
Names
nephronophthisis 1 (juvenile)

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_001314002.1 → NP_001300931.1  nephrocystin-1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    B5DEX2, D3ZJ87
    Related
    ENSRNOP00000060013.2, ENSRNOT00000067727.3
    Conserved Domains (1) summary
    cd11770
    Location:161 → 213
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

  2. NM_001314003.1 → NP_001300932.1  nephrocystin-1 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (b) that is 1 aa shorter than isoform a.
    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    B5DEX2
    Conserved Domains (1) summary
    cd11770
    Location:161 → 213
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

  3. NM_001314004.1 → NP_001300933.1  nephrocystin-1 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses two alternate in-frame splice sites in the central coding region, compared to variant 1, resulting in an isoform (c) that is 2 aa shorter than isoform a.
    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    B5DEX2
    Conserved Domains (1) summary
    cd11770
    Location:161 → 213
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

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

  1. NC_086021.1 Reference GRCr8

    Range
    135413927..135469505 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001106506.1: Suppressed sequence

    Description
    NM_001106506.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein Strain
Heading Accession and Version

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