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MS4A6A membrane spanning 4-domains A6A [ Homo sapiens (human) ]

Gene ID: 64231, updated on 21-Dec-2019

Summary

Official Symbol
MS4A6Aprovided by HGNC
Official Full Name
membrane spanning 4-domains A6Aprovided by HGNC
Primary source
HGNC:HGNC:13375
See related
Ensembl:ENSG00000110077 MIM:606548
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
CDA01; MS4A6; 4SPAN3; CD20L3; MST090; MSTP090; 4SPAN3.2
Summary
This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. The gene encoding this protein is localized to 11q12.1, among a cluster of family members. Alternative splicing of this gene results in several transcript variants that encode different protein isoforms. [provided by RefSeq, Oct 2011]
Expression
Broad expression in lymph node (RPKM 27.7), spleen (RPKM 26.2) and 22 other tissues See more
Orthologs

Genomic context

See MS4A6A in Genome Data Viewer
Location:
11q12.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (60171607..60184666, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (59939080..59952139, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene membrane spanning 4-domains A2 Neighboring gene long intergenic non-protein coding RNA 2705 Neighboring gene CRISPRi-validated cis-regulatory element chr11.2530 Neighboring gene membrane spanning 4-domains A4E Neighboring gene microRNA 6503

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

NHGRI GWAS Catalog

Description
Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease.
NHGRI GWA Catalog
Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease.
NHGRI GWA Catalog
Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of membrane-spanning 4-domains, subfamily A, member 6A (MS4A6A) in peptide-treated PBMCs PubMed

Go to the HIV-1, Human Interaction Database

General gene information

Markers

Homology

Clone Names

  • MGC22650, MGC131944

Gene Ontology Provided by GOA

Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
membrane-spanning 4-domains subfamily A member 6A
Names
CD20 antigen-like 3
CD20-like precusor
HAIRB-iso
MS4A6A-polymorph
four-span transmembrane protein 3
four-span transmembrane protein 3.1
four-span transmembrane protein 3.2
membrane-spanning 4-domains, subfamily A, member 6A, isoform 2

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_033978.1 RefSeqGene

    Range
    5001..18060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001247999.1NP_001234928.1  membrane-spanning 4-domains subfamily A member 6A isoform 4

    See identical proteins and their annotated locations for NP_001234928.1

    Status: REVIEWED

    Source sequence(s)
    AF142409, AF212240, AK300725, AV720078, DC295707
    Consensus CDS
    CCDS58134.1
    UniProtKB/Swiss-Prot
    Q9H2W1
    UniProtKB/TrEMBL
    B4DUN6
    Related
    ENSP00000392770.3, ENST00000426738.6
    Conserved Domains (1) summary
    pfam04103
    Location:75236
    CD20; CD20-like family
  2. NM_001330275.1NP_001317204.1  membrane-spanning 4-domains subfamily A member 6A isoform 5

    Status: REVIEWED

    Source sequence(s)
    AA731356, BQ003409, CB853877, DC297033, EL735363
    Consensus CDS
    CCDS81568.1
    UniProtKB/TrEMBL
    E9PSA9
    Related
    ENSP00000435844.1, ENST00000529054.5
    Conserved Domains (1) summary
    pfam04103
    Location:75236
    CD20; CD20-like family
  3. NM_022349.3NP_071744.2  membrane-spanning 4-domains subfamily A member 6A isoform 2

    See identical proteins and their annotated locations for NP_071744.2

    Status: REVIEWED

    Source sequence(s)
    AF142409, AF354930, AV720078, CD684503, DA917243
    Consensus CDS
    CCDS44615.1
    UniProtKB/Swiss-Prot
    Q9H2W1
    UniProtKB/TrEMBL
    A0A024R516
    Related
    ENSP00000431901.1, ENST00000528851.5
    Conserved Domains (1) summary
    pfam04103
    Location:47208
    CD20; CD20-like family
  4. NM_152851.2NP_690590.1  membrane-spanning 4-domains subfamily A member 6A isoform 3

    See identical proteins and their annotated locations for NP_690590.1

    Status: REVIEWED

    Source sequence(s)
    AB013104, BC022854, CD684503, DA979138
    Consensus CDS
    CCDS44616.1
    UniProtKB/Swiss-Prot
    Q9H2W1
    Related
    ENSP00000392921.2, ENST00000420732.6
    Conserved Domains (1) summary
    pfam04103
    Location:47159
    CD20; CD20-like family
  5. NM_152852.3NP_690591.1  membrane-spanning 4-domains subfamily A member 6A isoform 1

    See identical proteins and their annotated locations for NP_690591.1

    Status: REVIEWED

    Source sequence(s)
    AF212240, AK291870, BC022854
    Consensus CDS
    CCDS7981.1
    UniProtKB/Swiss-Prot
    Q9H2W1
    UniProtKB/TrEMBL
    A0A024R554
    Related
    ENSP00000436979.1, ENST00000530839.5
    Conserved Domains (1) summary
    pfam04103
    Location:47208
    CD20; CD20-like family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    60171607..60184666 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024448654.1XP_024304422.1  membrane-spanning 4-domains subfamily A member 6A isoform X5

    Conserved Domains (1) summary
    pfam04103
    Location:50163
    CD20; CD20-like family
  2. XM_024448655.1XP_024304423.1  membrane-spanning 4-domains subfamily A member 6A isoform X6

    Conserved Domains (1) summary
    pfam04103
    Location:50163
    CD20; CD20-like family
  3. XM_006718660.2XP_006718723.1  membrane-spanning 4-domains subfamily A member 6A isoform X3

    Conserved Domains (1) summary
    pfam04103
    Location:78191
    CD20; CD20-like family
  4. XM_024448652.1XP_024304420.1  membrane-spanning 4-domains subfamily A member 6A isoform X1

    Conserved Domains (1) summary
    pfam04103
    Location:75236
    CD20; CD20-like family
  5. XM_024448653.1XP_024304421.1  membrane-spanning 4-domains subfamily A member 6A isoform X2

    Conserved Domains (1) summary
    pfam04103
    Location:47208
    CD20; CD20-like family
  6. XM_005274177.3XP_005274234.1  membrane-spanning 4-domains subfamily A member 6A isoform X1

    See identical proteins and their annotated locations for XP_005274234.1

    UniProtKB/TrEMBL
    E9PSA9
    Conserved Domains (1) summary
    pfam04103
    Location:75236
    CD20; CD20-like family
  7. XM_006718661.2XP_006718724.1  membrane-spanning 4-domains subfamily A member 6A isoform X4

    Conserved Domains (1) summary
    pfam04103
    Location:78191
    CD20; CD20-like family
  8. XM_017018125.1XP_016873614.1  membrane-spanning 4-domains subfamily A member 6A isoform X8

  9. XM_011545209.1XP_011543511.1  membrane-spanning 4-domains subfamily A member 6A isoform X7

    Conserved Domains (1) summary
    pfam04103
    Location:75148
    CD20; CD20-like family
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