U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

PODN podocan [ Homo sapiens (human) ]

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

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
podocan
Names
podocan proteoglycan

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools