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    Podn podocan [ Rattus norvegicus (Norway rat) ]

    Gene ID: 102552895, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Podnprovided by RGD
    Official Full Name
    podocanprovided by RGD
    Primary source
    RGD:7545693
    See related
    EnsemblRapid:ENSRNOG00000011413 AllianceGenome:RGD:7545693
    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
    Also known as
    LRRGT00160
    Summary
    Predicted to enable collagen binding activity. Predicted to be involved in negative regulation of cell migration and negative regulation of cell population proliferation. Predicted to be located in cytoplasm and extracellular space. Orthologous to human PODN (podocan). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 50.9), Heart (RPKM 41.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Podn in Genome Data Viewer
    Location:
    5q34
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (128003907..128025518, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (122774536..122796755, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (127617482..127637898, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA2/SNORA34 family Neighboring gene solute carrier family 1 member 7 Neighboring gene U6 spliceosomal RNA Neighboring gene sterol carrier protein 2

    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. Functional characterization of podocan, a member of a new class in the small leucine-rich repeat protein family. Shimizu-Hirota R, et al. FEBS Lett, 2004 Apr 9. PMID 15063725
    2. Proteomics characterization of extracellular space components in the human aorta. Didangelos A, et al. Mol Cell Proteomics, 2010 Sep. PMID 20551380, Free PMC Article
    3. Extracellular matrix remodelling in response to venous hypertension: proteomics of human varicose veins. Barallobre-Barreiro J, et al. Cardiovasc Res, 2016 Jun 1. PMID 27068509, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables acetyl-CoA C-acyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables acetyl-CoA C-myristoyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables acyltransferase activity, transferring groups other than amino-acyl groups IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables collagen binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables propanoyl-CoA C-acyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables propionyl-CoA C2-trimethyltridecanoyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in peroxisome IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    podocan

    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_001421023.1 → NP_001407952.1  podocan precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A8I5ZYJ7

    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_086023.1 Reference GRCr8

      Range
      128003907..128025518 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039111166.2 → XP_038967094.1  podocan isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYJ7
      Conserved Domains (3) summary
      PRK15370
      Location:71 → 309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119 → 583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123 → 148
      LRR_RI; leucine-rich repeat [structural motif]

    2. XM_039111167.2 → XP_038967095.1  podocan isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYJ7
      Conserved Domains (3) summary
      PRK15370
      Location:71 → 309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119 → 583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123 → 148
      LRR_RI; leucine-rich repeat [structural motif]

    3. XM_039111165.2 → XP_038967093.1  podocan isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYJ7
      Conserved Domains (3) summary
      PRK15370
      Location:71 → 309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119 → 583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123 → 148
      LRR_RI; leucine-rich repeat [structural motif]

    4. XM_039111168.2 → XP_038967096.1  podocan isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYJ7
      Conserved Domains (3) summary
      PRK15370
      Location:71 → 309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119 → 583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123 → 148
      LRR_RI; leucine-rich repeat [structural motif]

    5. XM_063287058.1 → XP_063143128.1  podocan isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYJ7
      Related
      ENSRNOP00000084259.1, ENSRNOT00000111786.2

    6. XM_006238575.5 → XP_006238637.2  podocan isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYJ7
      Conserved Domains (3) summary
      PRK15370
      Location:71 → 309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119 → 583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123 → 148
      LRR_RI; leucine-rich repeat [structural motif]

    7. XM_039111163.2 → XP_038967091.1  podocan isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYJ7
      Conserved Domains (3) summary
      PRK15370
      Location:71 → 309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119 → 583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123 → 148
      LRR_RI; leucine-rich repeat [structural motif]

    8. XM_063287057.1 → XP_063143127.1  podocan isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYJ7

    9. XM_039111169.2 → XP_038967097.1  podocan isoform X2

      UniProtKB/TrEMBL
      A6JYT9
      Conserved Domains (3) summary
      PRK15370
      Location:18 → 329
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:8 → 28
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:27 → 89
      LRR_8; Leucine rich repeat
    Nucleotide Protein Strain
    Heading Accession and Version

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