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CD53 CD53 molecule [ Homo sapiens (human) ]

Gene ID: 963, updated on 12-May-2019

Summary

Official Symbol
CD53provided by HGNC
Official Full Name
CD53 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1686
See related
Ensembl:ENSG00000143119 MIM:151525
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
MOX44; TSPAN25
Summary
The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. It contributes to the transduction of CD2-generated signals in T cells and natural killer cells and has been suggested to play a role in growth regulation. Familial deficiency of this gene has been linked to an immunodeficiency associated with recurrent infectious diseases caused by bacteria, fungi and viruses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
Expression
Biased expression in lymph node (RPKM 181.8), appendix (RPKM 156.6) and 12 other tissues See more
Orthologs

Genomic context

See CD53 in Genome Data Viewer
Location:
1p13.3
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (110871167..110899936)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (111413821..111442558)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nuclear receptor binding factor 2 pseudogene 3 Neighboring gene olfactory receptor family 11 subfamily I member 1 pseudogene Neighboring gene ligand dependent nuclear receptor interacting factor 1 Neighboring gene cyclin T2 pseudogene 1 Neighboring gene RNA, 5S ribosomal pseudogene 54

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study does not reveal major genetic determinants for anti-cytomegalovirus antibody response.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Human CD53 is relocalized from plasma membrane to a perinuclear area in the presence of HIV-1 Nef PubMed
nef Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD53 (TSPAN25) PubMed
Vpu vpu Human CD53 is relocalized from plasma membrane to a perinuclear area in the presence of HIV-1 Vpu PubMed
vpu Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD53 (TSPAN25) PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
neutrophil degranulation TAS
Traceable Author Statement
more info
 
positive regulation of myoblast fusion ISS
Inferred from Sequence or Structural Similarity
more info
 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cell surface IEA
Inferred from Electronic Annotation
more info
 
cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular exosome HDA PubMed 
immunological synapse IDA
Inferred from Direct Assay
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
specific granule membrane TAS
Traceable Author Statement
more info
 
tertiary granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
leukocyte surface antigen CD53
Names
CD53 antigen
CD53 glycoprotein
CD53 tetraspan antigen
antigen MOX44 identified by monoclonal antibody MRC-OX44
cell surface antigen
cell surface glycoprotein CD53
tetraspanin-25
transmembrane glycoprotein
tspan-25

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.

mRNA and Protein(s)

  1. NM_000560.4NP_000551.1  leukocyte surface antigen CD53 isoform 1

    See identical proteins and their annotated locations for NP_000551.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL391064, BC040693, BG536920
    Consensus CDS
    CCDS829.1
    UniProtKB/Swiss-Prot
    P19397
    Related
    ENSP00000271324.5, ENST00000271324.6
    Conserved Domains (1) summary
    cd03164
    Location:104186
    CD53_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), CD53_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model ...
  2. NM_001040033.1NP_001035122.1  leukocyte surface antigen CD53 isoform 1

    See identical proteins and their annotated locations for NP_001035122.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL391064, BC035456, CA453414
    Consensus CDS
    CCDS829.1
    UniProtKB/Swiss-Prot
    P19397
    Related
    ENSP00000497382.1, ENST00000648608.1
    Conserved Domains (1) summary
    cd03164
    Location:104186
    CD53_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), CD53_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model ...
  3. NM_001320638.1NP_001307567.1  leukocyte surface antigen CD53 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks exons in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AK298723, AL354713, AL391064
    UniProtKB/TrEMBL
    B4DQB5
    Conserved Domains (2) summary
    pfam00335
    Location:9110
    Tetraspannin; Tetraspanin family
    cl02781
    Location:106127
    tetraspanin_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    110871167..110899936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451057.1XP_024306825.1  leukocyte surface antigen CD53 isoform X1

    Conserved Domains (1) summary
    cd03164
    Location:103185
    CD53_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), CD53_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model ...
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