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PODN podocan [ Homo sapiens (human) ]

Gene ID: 127435, updated on 13-Mar-2020

Summary

Official Symbol
PODNprovided by HGNC
Official Full Name
podocanprovided by HGNC
Primary source
HGNC:HGNC:23174
See related
Ensembl:ENSG00000174348 MIM:608661
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

Genomic context

See PODN in Genome Data Viewer
Location:
1p32.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (53062198..53085502)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53527724..53551174)

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 HIG1 hypoxia inducible domain family member 1A pseudogene 11 Neighboring gene solute carrier family 1 member 7 Neighboring gene VISTA enhancer hs2585 Neighboring gene uncharacterized LOC105378724 Neighboring gene carnitine palmitoyltransferase 2 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC24995

Gene Ontology Provided by GOA

Function Evidence Code Pubs
collagen binding IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix structural constituent conferring compression resistance RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
Process Evidence Code Pubs
negative regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
collagen-containing extracellular matrix HDA PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space HDA PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
podocan
Names
podocan proteoglycan

NCBI Reference Sequences (RefSeq)

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..28442
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001199080.4NP_001186009.2  podocan precursor

    Status: REVIEWED

    Source sequence(s)
    AL445183
    Consensus CDS
    CCDS55602.1
  2. NM_001199081.3NP_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
    CCDS55602.1
  3. NM_153703.5NP_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
    CCDS573.1
    Related
    ENSP00000308315.6, ENST00000312553.10

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    53062198..53085502
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005270457.3XP_005270514.1  podocan isoform X2

    See identical proteins and their annotated locations for XP_005270514.1

    UniProtKB/Swiss-Prot
    Q7Z5L7
    Conserved Domains (3) summary
    cd00116
    Location:234417
    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:122147
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:238300
    LRR_8; Leucine rich repeat
  2. XM_017000294.2XP_016855783.1  podocan isoform X1

    Related
    ENSP00000479233.1, ENST00000618387.1
  3. XM_011540677.2XP_011538979.1  podocan isoform X3

    Conserved Domains (3) summary
    cd00116
    Location:23206
    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:2952
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:2789
    LRR_8; Leucine rich repeat

RNA

  1. XR_001736973.2 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.
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