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Podn podocan [ Rattus norvegicus (Norway rat) ]

Gene ID: 102552895, updated on 2-Nov-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, Nov 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 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 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 mitochondrion IEA
Inferred from Electronic Annotation
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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