Human Gene MS4A6A (uc010rlb.2) Description and Page Index
  Description: Homo sapiens membrane-spanning 4-domains, subfamily A, member 6A (MS4A6A), transcript variant 2, mRNA.
RefSeq Summary (NM_022349): 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]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AF142409.1, SRR1803617.205516.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968540, SAMEA2142670 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:59,939,971-59,950,804 Size: 10,834 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr11:59,940,474-59,949,200 Size: 8,727 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr11:59,939,971-59,950,804)mRNA (may differ from genome)Protein (180 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Membrane-spanning 4-domains subfamily A member 6A;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MS4A6A
CDC HuGE Published Literature: MS4A6A
Positive Disease Associations: Alzheimer Disease , Magnesium
Related Studies:
  1. Alzheimer Disease
    Paul Hollingworth et al. Nature genetics 2011, Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease., Nature genetics. [PubMed 21460840]
  2. Magnesium
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 60.17 RPKM in Spleen
Total median expression: 307.39 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -91.70368-0.249 Picture PostScript Text
3' UTR -140.00503-0.278 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007237 - CD20-like

Pfam Domains:
PF04103 - CD20-like family

ModBase Predicted Comparative 3D Structure on E7EMT7
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog

-  Descriptions from all associated GenBank mRNAs
  BC022854 - Homo sapiens membrane-spanning 4-domains, subfamily A, member 6A, mRNA (cDNA clone MGC:22650 IMAGE:3934920), complete cds.
AF286866 - Homo sapiens MS4A6A-polymorph mRNA, complete cds.
AF350502 - Homo sapiens four-span transmembrane protein 3.1 (4SPAN3) mRNA, complete cds.
BC108728 - Homo sapiens membrane-spanning 4-domains, subfamily A, member 6A, mRNA (cDNA clone MGC:131944 IMAGE:6196213), complete cds.
AF212240 - Homo sapiens CDA01 mRNA, complete cds.
AF237908 - Homo sapiens MS4A6A protein mRNA, complete cds.
AF253977 - Homo sapiens HAIRB-iso mRNA, complete cds.
AF261136 - Homo sapiens HAIERB-like protein mRNA, complete cds.
AB013104 - Homo sapiens mRNA for MS4A6, complete cds.
AK291870 - Homo sapiens cDNA FLJ75744 complete cds, highly similar to Homo sapiens membrane-spanning 4-domains, subfamily A, member 6A (MS4A6A), transcript variant 1, mRNA.
AK301387 - Homo sapiens cDNA FLJ60178 complete cds, moderately similar to Membrane-spanning 4-domains subfamily Amember 6A.
CU692740 - Synthetic construct Homo sapiens gateway clone IMAGE:100021839 5' read MS4A6A mRNA.
KJ899454 - Synthetic construct Homo sapiens clone ccsbBroadEn_08848 MS4A6A gene, encodes complete protein.
DQ893511 - Synthetic construct clone IMAGE:100006141; FLH194747.01X; RZPDo839E0880D membrane-spanning 4-domains, subfamily A, member 6A (MS4A6A) gene, encodes complete protein.
DQ896484 - Synthetic construct Homo sapiens clone IMAGE:100010944; FLH194743.01L; RZPDo839E0870D membrane-spanning 4-domains, subfamily A, member 6A (MS4A6A) gene, encodes complete protein.
AF142409 - Homo sapiens CD20-like precusor mRNA, complete cds.
AF350503 - Homo sapiens four-span transmembrane protein 3.2 (4SPAN3) mRNA, complete cds.
AK300725 - Homo sapiens cDNA FLJ54795 complete cds, highly similar to Membrane-spanning 4-domains subfamily Amember 6A.
JD295797 - Sequence 276821 from Patent EP1572962.
JD449745 - Sequence 430769 from Patent EP1572962.
JD269182 - Sequence 250206 from Patent EP1572962.
AF354930 - Homo sapiens MS4A6A mRNA, complete cds, alternatively spliced.
JD431676 - Sequence 412700 from Patent EP1572962.
JD287552 - Sequence 268576 from Patent EP1572962.
AK026454 - Homo sapiens cDNA: FLJ22801 fis, clone KAIA2674.
AF172819 - Homo sapiens MSTP090 (MST090) mRNA, complete cds.
JD249395 - Sequence 230419 from Patent EP1572962.
JD185002 - Sequence 166026 from Patent EP1572962.
JD502005 - Sequence 483029 from Patent EP1572962.
JD420713 - Sequence 401737 from Patent EP1572962.
JD312834 - Sequence 293858 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AK301387, E7EMT7, E7EMT7_HUMAN
UCSC ID: uc010rlb.2
RefSeq Accession: NM_022349
Protein: E7EMT7

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: AK301387.1
exon count: 5CDS single in 3' UTR: no RNA size: 1536
ORF size: 543CDS single in intron: no Alignment % ID: 99.61
txCdsPredict score: 1041.00frame shift in genome: no % Coverage: 72.20
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 530# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.