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    Podnl1 podocan-like 1 [ Mus musculus (house mouse) ]

    Gene ID: 244550, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Podnl1provided by MGI
    Official Full Name
    podocan-like 1provided by MGI
    Primary source
    MGI:MGI:2685352
    See related
    Ensembl:ENSMUSG00000012889 AllianceGenome:MGI:2685352
    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
    Gm506; 5832418A03Rik
    Summary
    Located in collagen-containing extracellular matrix. Orthologous to human PODNL1 (podocan like 1). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in ovary adult (RPKM 13.5), spleen adult (RPKM 5.1) and 10 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Podnl1 in Genome Data Viewer
    Location:
    8 C2; 8 40.31 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (84852552..84869620)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (84125928..84142991)

    Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene regulatory factor X, 1 (influences HLA class II expression) Neighboring gene microRNA 709 Neighboring gene STARR-positive B cell enhancer mm9_chr8:86628640-86628941 Neighboring gene predicted gene, 39210 Neighboring gene DDB1 and CUL4 associated factor 15 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86650788-86650941 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86651237-86651346 Neighboring gene coiled-coil and C2 domain containing 1A Neighboring gene break repair meiotic recombinase recruitment factor 1 Neighboring gene nanos C2HC-type zinc finger 3 Neighboring gene microRNA 181d

    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 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. Podocan-like protein: a novel small leucine-rich repeat matrix protein in bone. Mochida Y, et al. Biochem Biophys Res Commun, 2011 Jul 1. PMID 21672516, Free PMC Article
    2. The developing mouse coronal suture at single-cell resolution. Farmer DT, et al. Nat Commun, 2021 Aug 10. PMID 34376651, Free PMC Article
    3. Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors. Kim H, et al. Cell, 2018 Dec 13. PMID 30550785, Free PMC Article
    4. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073
    5. High-efficiency full-length cDNA cloning. Carninci P, et al. Methods Enzymol, 1999. PMID 10349636

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. a novel SLRP member, "Podocan-like (Podnl) protein" identified by a bioinformatics approach was characterized.
      Title: Podocan-like protein: a novel small leucine-rich repeat matrix protein in bone.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Component Evidence Code Pubs
    located_in collagen-containing 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
    		  

    General protein information

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    Preferred Names
    podocan-like protein 1

    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_001013384.3 → NP_001013402.2  podocan-like protein 1 precursor

      See identical proteins and their annotated locations for NP_001013402.2

      Status: VALIDATED

      Source sequence(s)
      AC159266
      Consensus CDS
      CCDS52615.1
      UniProtKB/Swiss-Prot
      A0A0R4J142, A1X874, Q6P3Y9
      Related
      ENSMUSP00000091073.5, ENSMUST00000093380.5
      Conserved Domains (3) summary
      cd00116
      Location:161 → 345
      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:211 → 234
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:210 → 271
      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_000074.7 Reference GRCm39 C57BL/6J

      Range
      84852552..84869620
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011248377.3 → XP_011246679.1  podocan-like protein 1 isoform X1

      Conserved Domains (3) summary
      PRK15370
      Location:166 → 421
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:211 → 234
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:403 → 458
      LRR_8; Leucine rich repeat

    2. XM_011248378.1 → XP_011246680.1  podocan-like protein 1 isoform X2

      Conserved Domains (4) summary
      PRK15370
      Location:13 → 283
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00031
      Location:125 → 136
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:52 → 75
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:264 → 325
      LRR_8; Leucine rich repeat

    3. XM_017312815.3 → XP_017168304.1  podocan-like protein 1 isoform X2

      Conserved Domains (4) summary
      PRK15370
      Location:13 → 283
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00031
      Location:125 → 136
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:52 → 75
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:264 → 325
      LRR_8; Leucine rich repeat
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P3Y9.3 GenPept UniProtKB/Swiss-Prot:Q6P3Y9

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