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    CD53 CD53 molecule [ Homo sapiens (human) ]

    Gene ID: 963, updated on 10-Oct-2023

    Summary

    Official Symbol
    CD53provided by HGNC
    Official Full Name
    CD53 moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:1686
    See related
    Ensembl:ENSG00000143119 MIM:151525; AllianceGenome:HGNC:1686
    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
    NEW
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    Try the new Transcript table

    Genomic context

    See CD53 in Genome Data Viewer
    Location:
    1p13.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (110871210..110899922)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (110885966..110914720)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (111413832..111442544)

    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 ATAC-STARR-seq lymphoblastoid active region 1476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1478 Neighboring gene Sharpr-MPRA regulatory region 4566 Neighboring gene ligand dependent nuclear receptor interacting factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:111506132-111506668 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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of myoblast fusion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell-cell junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in immunological synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in specific granule membrane TAS
    Traceable Author Statement
    more info
     
    located_in 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)

    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.

    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
      B2R905, P19397, Q5U0D6
      Related
      ENSP00000271324.5, ENST00000271324.6
      Conserved Domains (2) 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 ...
      pfam00335
      Location:9206
      Tetraspannin; Tetraspanin family
    2. NM_001040033.2NP_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
      B2R905, P19397, Q5U0D6
      Related
      ENSP00000497382.1, ENST00000648608.1
      Conserved Domains (2) 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 ...
      pfam00335
      Location:9206
      Tetraspannin; Tetraspanin family
    3. NM_001320638.2NP_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: GCF_000001405.40-RS_2023_10

    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
      110871210..110899922
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435014.1XP_047290970.1  leukocyte surface antigen CD53 isoform X2

    2. XM_047435013.1XP_047290969.1  leukocyte surface antigen CD53 isoform X1

    3. XM_047435015.1XP_047290971.1  leukocyte surface antigen CD53 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      110885966..110914720
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339723.1XP_054195698.1  leukocyte surface antigen CD53 isoform X2

    2. XM_054339722.1XP_054195697.1  leukocyte surface antigen CD53 isoform X1

    3. XM_054339724.1XP_054195699.1  leukocyte surface antigen CD53 isoform X3