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Nphp1 nephronophthisis 1 (juvenile) homolog (human) [ Mus musculus (house mouse) ]

Gene ID: 53885, updated on 1-Mar-2024

Summary

Official Symbol
Nphp1provided by MGI
Official Full Name
nephronophthisis 1 (juvenile) homolog (human)provided by MGI
Primary source
MGI:MGI:1858233
See related
Ensembl:ENSMUSG00000027378 AllianceGenome:MGI:1858233
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
Summary
Involved in several processes, including photoreceptor cell outer segment organization; retina development in camera-type eye; and spermatid differentiation. Located in ciliary base; cytoplasm; and photoreceptor distal connecting cilium. Is expressed in several structures, including central nervous system; genitourinary system; gut; respiratory system; and white fat. 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 testis adult (RPKM 216.9) and CNS E11.5 (RPKM 14.7) See more
Orthologs
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Genomic context

See Nphp1 in Genome Data Viewer
Location:
2 F1; 2 62.09 cM
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (127582652..127630833, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (127740732..127788913, complement)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene predicted gene 14244 Neighboring gene STARR-seq mESC enhancer starr_05629 Neighboring gene mal, T cell differentiation protein-like Neighboring gene STARR-seq mESC enhancer starr_05630 Neighboring gene mitoregulin Neighboring gene BUB1, mitotic checkpoint serine/threonine kinase Neighboring gene STARR-positive B cell enhancer ABC_E415

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)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
 
located_in bicellular tight junction IEA
Inferred from Electronic Annotation
more info
 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
 
located_in cell-cell junction ISO
Inferred from Sequence Orthology
more info
 
located_in ciliary base IDA
Inferred from Direct Assay
more info
PubMed 
located_in ciliary transition zone IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cilium IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cilium IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
located_in motile cilium ISO
Inferred from Sequence Orthology
more info
 
located_in photoreceptor connecting cilium IDA
Inferred from Direct Assay
more info
PubMed 
located_in photoreceptor distal connecting cilium IDA
Inferred from Direct Assay
more info
PubMed 

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_001291012.1NP_001277941.1  nephrocystin-1 isoform b

    See identical proteins and their annotated locations for NP_001277941.1

    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)
    AA107655, AK159627, BY147655
    Consensus CDS
    CCDS71140.1
    UniProtKB/Swiss-Prot
    Q9D7G8, Q9QY53, Q9QZP0, Q9WUZ2
    UniProtKB/TrEMBL
    Q3TWM5
    Related
    ENSMUSP00000105986.2, ENSMUST00000110357.2
    Conserved Domains (1) summary
    cd11770
    Location:160212
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
  2. NM_001291013.1NP_001277942.1  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)
    AA107655, AL844204, BY147655
    UniProtKB/TrEMBL
    Q0VF70
    Conserved Domains (1) summary
    cd11770
    Location:160212
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
  3. NM_001355429.1NP_001342358.1  nephrocystin-1 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (d) that is 1 aa shorter than isoform a.
    Source sequence(s)
    AL844204
    UniProtKB/Swiss-Prot
    Q9D7G8, Q9QY53, Q9QZP0, Q9WUZ2
    UniProtKB/TrEMBL
    Q0VF70
    Conserved Domains (1) summary
    cd11770
    Location:160212
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
  4. NM_001369236.1NP_001356165.1  nephrocystin-1 isoform e

    Status: VALIDATED

    Source sequence(s)
    AL844204
    Conserved Domains (1) summary
    cd11770
    Location:160212
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
  5. NM_001421487.1NP_001408416.1  nephrocystin-1 isoform f

    Status: VALIDATED

    Source sequence(s)
    AL844204
    UniProtKB/Swiss-Prot
    Q9D7G8, Q9QY53, Q9QZP0, Q9WUZ2
  6. NM_001421488.1NP_001408417.1  nephrocystin-1 isoform g

    Status: VALIDATED

    Source sequence(s)
    AL844204
  7. NM_001421489.1NP_001408418.1  nephrocystin-1 isoform h

    Status: VALIDATED

    Source sequence(s)
    AL844204
  8. NM_001421490.1NP_001408419.1  nephrocystin-1 isoform i

    Status: VALIDATED

    Source sequence(s)
    AL844204
  9. NM_001421491.1NP_001408420.1  nephrocystin-1 isoform j

    Status: VALIDATED

    Source sequence(s)
    AL844204
  10. NM_001421492.1NP_001408421.1  nephrocystin-1 isoform k

    Status: VALIDATED

    Source sequence(s)
    AL844204
  11. NM_001421493.1NP_001408422.1  nephrocystin-1 isoform l

    Status: VALIDATED

    Source sequence(s)
    AL844204
  12. NM_016902.4NP_058598.1  nephrocystin-1 isoform a

    See identical proteins and their annotated locations for NP_058598.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AA107655, AK159627, BY147655, BY353783
    Consensus CDS
    CCDS16709.1
    UniProtKB/Swiss-Prot
    Q9D7G8, Q9QY53, Q9QZP0, Q9WUZ2
    UniProtKB/TrEMBL
    A2APS1
    Related
    ENSMUSP00000028857.8, ENSMUST00000028857.14
    Conserved Domains (1) summary
    cd11770
    Location:160212
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)

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_000068.8 Reference GRCm39 C57BL/6J

    Range
    127582652..127630833 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030251881.1XP_030107741.1  nephrocystin-1 isoform X5

    Conserved Domains (1) summary
    cd11770
    Location:160212
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
  2. XM_036162392.1XP_036018285.1  nephrocystin-1 isoform X2

    Conserved Domains (1) summary
    cd11770
    Location:160212
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)
  3. XM_011239696.2XP_011237998.1  nephrocystin-1 isoform X3

    Conserved Domains (1) summary
    cd11770
    Location:160212
    SH3_Nephrocystin; Src Homology 3 domain of Nephrocystin (or Nephrocystin-1)