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    Nepn nephrocan [ Mus musculus (house mouse) ]

    Gene ID: 66650, updated on 8-Feb-2024

    Summary

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    Official Symbol
    Nepnprovided by MGI
    Official Full Name
    nephrocanprovided by MGI
    Primary source
    MGI:MGI:1913900
    See related
    Ensembl:ENSMUSG00000038624 AllianceGenome:MGI:1913900
    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
    Npn; periolin; 5730521E12Rik
    Summary
    Predicted to enable lipopolysaccharide binding activity. Acts upstream of or within extracellular matrix organization; negative regulation of transcription by RNA polymerase II; and negative regulation of transforming growth factor beta receptor signaling pathway. Located in extracellular space and interstitial matrix. Is expressed in several structures, including embryo endoderm; genitourinary system; gut; humerus; and musculature. Orthologous to human NEPNP (nephrocan, pseudogene). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in kidney adult (RPKM 8.0), subcutaneous fat pad adult (RPKM 0.6) and 1 other tissue See more
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    Genomic context

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    See Nepn in Genome Data Viewer
    Location:
    10 B3; 10 26.6 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (52264961..52280707)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (52388864..52404611)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene Ewing sarcoma breakpoint region 1 pseudogene Neighboring gene golgi associated PDZ and coiled-coil motif containing Neighboring gene ribosomal protein S19, pseudogene 10 Neighboring gene STARR-seq mESC enhancer starr_26676 Neighboring gene STARR-positive B cell enhancer ABC_E2933 Neighboring gene NUS1 dehydrodolichyl diphosphate synthase subunit Neighboring gene STARR-seq mESC enhancer starr_26679 Neighboring gene STARR-seq mESC enhancer starr_26680 Neighboring gene predicted gene, 47612

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Insight into Nephrocan Function in Mouse Endoderm Patterning. Addeo M, et al. Int J Mol Sci, 2019 Dec 18. PMID 31861348, Free PMC Article
    2. Nephrocan, a novel member of the small leucine-rich repeat protein family, is an inhibitor of transforming growth factor-beta signaling. Mochida Y, et al. J Biol Chem, 2006 Nov 24. PMID 16990280
    3. miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm. Yang D, et al. Development, 2014 Feb. PMID 24449834
    4. Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm. Wang Z, et al. Nat Commun, 2022 Sep 19. PMID 36123357, Free PMC Article
    5. A regulatory network controls nephrocan expression and midgut patterning. Hou J, et al. Development, 2014 Oct. PMID 25209250, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A regulatory network, incluing Sox17 and the retinoic acid receptor, controls nephrocan expression and midgut patterning.
      Title: A regulatory network controls nephrocan expression and midgut patterning.
    2. NPN is a novel member of the SLRP family that may play important roles in kidney development and pathophysiology by functioning as an endogenous inhibitor of TGF-beta signaling
      Title: Nephrocan, a novel member of the small leucine-rich repeat protein family, is an inhibitor of transforming growth factor-beta signaling.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (3) 
    • Endonuclease-mediated (1) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables lipopolysaccharide binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within extracellular matrix organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transforming growth factor beta receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cytokine production involved in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in toll-like receptor 4 signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in interstitial matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of lipopolysaccharide receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    nephrocan

    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_025684.3 → NP_079960.1  nephrocan precursor

      See identical proteins and their annotated locations for NP_079960.1

      Status: VALIDATED

      Source sequence(s)
      AC153526
      Consensus CDS
      CCDS23840.1
      UniProtKB/Swiss-Prot
      Q9CQ76
      Related
      ENSMUSP00000070130.5, ENSMUST00000067085.7
      Conserved Domains (3) summary
      cd00116
      Location:210 → 425
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:188 → 211
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:367 → 426
      LRR_8; Leucine rich repeat

    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_000076.7 Reference GRCm39 C57BL/6J

      Range
      52264961..52280707
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006512818.5 → XP_006512881.1  nephrocan isoform X1

      Conserved Domains (2) summary
      PRK15370
      Location:271 → 474
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:237 → 260
      LRR_RI; leucine-rich repeat [structural motif]

    2. XM_006512819.5 → XP_006512882.1  nephrocan isoform X2

      Conserved Domains (2) summary
      PRK15370
      Location:161 → 364
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:127 → 150
      LRR_RI; leucine-rich repeat [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9CQ76.1 GenPept UniProtKB/Swiss-Prot:Q9CQ76

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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