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    PODN podocan [ Homo sapiens (human) ]

    Gene ID: 127435, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PODNprovided by HGNC
    Official Full Name
    podocanprovided by HGNC
    Primary source
    HGNC:HGNC:23174
    See related
    Ensembl:ENSG00000174348 MIM:608661; AllianceGenome:HGNC:23174
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PCAN; SLRR5A
    Summary
    The protein encoded by this gene is a member of the small leucine-rich repeat protein family and contains an amino terminal CX3CXCX7C cysteine-rich cluster followed by a leucine-rich repeat domain. Studies suggest that this protein could function to inhibit smooth muscle cell proliferation and migration following arterial injury. [provided by RefSeq, Jul 2016]
    Expression
    Broad expression in gall bladder (RPKM 52.1), ovary (RPKM 37.5) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PODN in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53062213..53085494)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (52943715..52966996)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53527885..53551166)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene sterol carrier protein 2 Neighboring gene RRAS2 pseudogene 1 Neighboring gene tubulin beta class I pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1040 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:53527863-53528050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53546830-53547381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53547382-53547932 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53560558-53561095 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:53571119-53571620 and GRCh37_chr1:53571621-53572120 Neighboring gene solute carrier family 1 member 7 Neighboring gene Sharpr-MPRA regulatory region 13647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53576791-53577515 Neighboring gene uncharacterized LOC105379783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53580852-53581834 Neighboring gene VISTA enhancer hs2585 Neighboring gene uncharacterized LOC105378724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1041 Neighboring gene carnitine palmitoyltransferase 2 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. MiR 3180-5p promotes proliferation in human bladder smooth muscle cell by targeting PODN under hydrodynamic pressure. Sun Y, et al. Sci Rep, 2016 Sep 9. PMID 27608612, Free PMC Article
    2. Novel small leucine-rich repeat protein podocan is a negative regulator of migration and proliferation of smooth muscle cells, modulates neointima formation, and is expressed in human atheroma. Hutter R, et al. Circulation, 2013 Nov 26. PMID 24043300, Free PMC Article
    3. 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
    4. Podocan, a novel small leucine-rich repeat protein expressed in the sclerotic glomerular lesion of experimental HIV-associated nephropathy. Ross MD, et al. J Biol Chem, 2003 Aug 29. PMID 12796502
    5. Proteomics characterization of extracellular space components in the human aorta. Didangelos A, et al. Mol Cell Proteomics, 2010 Sep. PMID 20551380, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. It was apparent that HP upregulates miR-3180-5p, which inhibits the expression of PODN and promotes HBSMC proliferation via the cdk2 signaling pathway.
      Title: MiR 3180-5p promotes proliferation in human bladder smooth muscle cell by targeting PODN under hydrodynamic pressure.
    2. Podocan appears to be a potent negative regulator of the migration and proliferation of vascular smooth muscle cells.
      Title: Novel small leucine-rich repeat protein podocan is a negative regulator of migration and proliferation of smooth muscle cells, modulates neointima formation, and is expressed in human atheroma.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    5. PODN was characterized in cultured cells.
      Title: Functional characterization of podocan, a member of a new class in the small leucine-rich repeat protein family.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC24995

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables collagen binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables extracellular matrix structural constituent conferring compression resistance RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular space HDA PubMed 
    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 

    General protein information

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    Preferred Names
    podocan
    Names
    podocan proteoglycan

    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.

    Genomic

    1. NG_051094.1 RefSeqGene

      Range
      5162..28443
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001199080.4 → NP_001186009.2  podocan precursor

      Status: REVIEWED

      Source sequence(s)
      AL445183
      Consensus CDS
      CCDS573.2
      UniProtKB/Swiss-Prot
      B4DKN5, B4E373, Q5VVZ2, Q5VVZ3, Q6PIR3, Q6UXL8, Q7Z5L7, Q8N641
      Related
      ENSP00000360555.3, ENST00000371500.8
      Conserved Domains (3) summary
      PRK15370
      Location:55 → 308
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:181 → 588
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:122 → 147
      LRR_RI; leucine-rich repeat [structural motif]

    2. NM_001199081.3 → NP_001186010.2  podocan precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same protein.
      Source sequence(s)
      AL445183
      Consensus CDS
      CCDS573.2
      UniProtKB/Swiss-Prot
      B4DKN5, B4E373, Q5VVZ2, Q5VVZ3, Q6PIR3, Q6UXL8, Q7Z5L7, Q8N641
      Related
      ENSP00000479233.1, ENST00000618387.1
      Conserved Domains (3) summary
      PRK15370
      Location:55 → 308
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:181 → 588
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:122 → 147
      LRR_RI; leucine-rich repeat [structural motif]

    3. NM_153703.5 → NP_714914.3  podocan precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript. Variants 1-3 encode the same protein.
      Source sequence(s)
      AL445183
      Consensus CDS
      CCDS573.2
      UniProtKB/Swiss-Prot
      B4DKN5, B4E373, Q5VVZ2, Q5VVZ3, Q6PIR3, Q6UXL8, Q7Z5L7, Q8N641
      Related
      ENSP00000308315.6, ENST00000312553.10
      Conserved Domains (3) summary
      PRK15370
      Location:55 → 308
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:181 → 588
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:122 → 147
      LRR_RI; leucine-rich repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      53062213..53085494
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005270457.4 → XP_005270514.1  podocan isoform X1

      See identical proteins and their annotated locations for XP_005270514.1

      UniProtKB/Swiss-Prot
      B4DKN5, B4E373, Q5VVZ2, Q5VVZ3, Q6PIR3, Q6UXL8, Q7Z5L7, Q8N641
      Conserved Domains (3) summary
      PRK15370
      Location:55 → 308
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:181 → 588
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:122 → 147
      LRR_RI; leucine-rich repeat [structural motif]

    2. XM_011540677.3 → XP_011538979.1  podocan isoform X2

      UniProtKB/TrEMBL
      B2RA94
      Conserved Domains (3) summary
      cd00116
      Location:23 → 206
      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:29 → 52
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:27 → 89
      LRR_8; Leucine rich repeat

    RNA

    1. XR_001736973.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      52943715..52966996
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334337.1 → XP_054190312.1  podocan isoform X1

      UniProtKB/Swiss-Prot
      B4DKN5, B4E373, Q5VVZ2, Q5VVZ3, Q6PIR3, Q6UXL8, Q7Z5L7, Q8N641

    2. XM_054334338.1 → XP_054190313.1  podocan isoform X2

    RNA

    1. XR_008485928.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001199082.1: Suppressed sequence

      Description
      NM_001199082.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z5L7.2 GenPept UniProtKB/Swiss-Prot:Q7Z5L7

    Gene LinkOut

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

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