CD1B Gene (Protein Coding)

CD1b Molecule

GC01M158297
GIFtS:
39
This gene encodes a member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family g... See more...

Aliases for CD1B Gene

Aliases for CD1B Gene

  • CD1b Molecule 2 3 5
  • T-Cell Surface Glycoprotein CD1b 3 4
  • CD1B Antigen, B Polypeptide 2 3
  • CD1b Antigen 2 4
  • Differentiation Antigen CD1-Alpha-3 3
  • Cortical Thymocyte Antigen CD1B 3
  • CD1A 3
  • CD1B 5
  • CD1 3
  • R1 3

External Ids for CD1B Gene

Previous HGNC Symbols for CD1B Gene

  • CD1

Previous GeneCards Identifiers for CD1B Gene

  • GC01M156089
  • GC01M154030
  • GC01M155075
  • GC01M155514
  • GC01M155110
  • GC01M156564
  • GC01M129655

Summaries for CD1B Gene

Entrez Gene Summary for CD1B Gene

  • This gene encodes a member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail, and requires vesicular acidification to bind lipid antigens. [provided by RefSeq, Jul 2008]

GeneCards Summary for CD1B Gene

CD1B (CD1b Molecule) is a Protein Coding gene. Diseases associated with CD1B include Mycobacterium Malmoense and Non-Langerhans-Cell Histiocytosis. Among its related pathways are Hematopoietic cell lineage and Innate Immune System. Gene Ontology (GO) annotations related to this gene include beta-2-microglobulin binding and endogenous lipid antigen binding. An important paralog of this gene is CD1C.

UniProtKB/Swiss-Prot Summary for CD1B Gene

  • Antigen-presenting protein that binds self and non-self lipid and glycolipid antigens and presents them to T-cell receptors on natural killer T-cells.

Additional gene information for CD1B Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CD1B Gene

Genomics for CD1B Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CD1B Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J158332 Promoter/Enhancer 0.5 Ensembl dbSUPER 600.7 -1.0 -970 1 CD1B piR-33422-023 CD1E
GH01J158331 Promoter/Enhancer 0.5 EPDnew dbSUPER 600.7 0.0 -20 0.1 CD1B piR-33422-023 CD1E
GH01J158283 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.1 +43.1 43081 9.2 CREB1 POLR2A BACH1 STAT3 ZNF143 RELA TCF12 IKZF2 TRIM22 PKNOX1 CD1C CD1B CD1E piR-33605-032 CD1A
GH01J158247 Promoter/Enhancer 1.3 EPDnew FANTOM5 ENCODE dbSUPER 3.8 +83.1 83104 1.4 IKZF2 SCRT2 EED RELB RUNX3 CBFB IKZF1 SPI1 POLR2A MYC CD1A CD1C CD1E CD1D CD1B OR10T2 lnc-CD1B-4 HMGN1P5
GH01J158284 Promoter/Enhancer 0.5 Ensembl dbSUPER 10.1 +48.2 48230 0.2 CD1B piR-33605-032 CD1C CD1A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CD1B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CD1B

Top Transcription factor binding sites by QIAGEN in the CD1B gene promoter:
  • CREB
  • deltaCREB
  • LCR-F1
  • MRF-2
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for CD1B Gene

Genomic Locations for CD1B Gene
chr1:158,285,406-158,331,531
(GRCh38/hg38)
Size:
46,126 bases
Orientation:
Minus strand
chr1:158,297,740-158,301,321
(GRCh37/hg19)
Size:
3,582 bases
Orientation:
Minus strand

Genomic View for CD1B Gene

Genes around CD1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CD1B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CD1B Gene

Proteins for CD1B Gene

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  • Protein details for CD1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P29016-CD1B_HUMAN
    Recommended name:
    T-cell surface glycoprotein CD1b
    Protein Accession:
    P29016
    Secondary Accessions:
    • Q5TDK9
    • Q5TDL0
    • Q9UMM2

    Protein attributes for CD1B Gene

    Size:
    333 amino acids
    Molecular mass:
    36939 Da
    Quaternary structure:
    • Heterodimer with B2M (beta-2-microglobulin). Interacts with saposin C.
    Miscellaneous:
    • During protein synthesis and maturation, CD1 family members bind endogenous lipids that are replaced by lipid or glycolipid antigens when the proteins are internalized and pass through endosomes or lysosomes, before trafficking back to the cell surface. Interaction with saposin C is required for the loading of bacterial lipid antigens onto CD1B in the lysosome.

    Three dimensional structures from OCA and Proteopedia for CD1B Gene

    Alternative splice isoforms for CD1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CD1B Gene

Protein Expression for CD1B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CD1B Gene

  • Glycosylation at Asn38, Asn75, Asn146, and Asn258
  • Ubiquitination at Lys145, Lys196, and Lys204
  • Modification sites at PhosphoSitePlus

Other Protein References for CD1B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CD1B Gene

Domains & Families for CD1B Gene

Gene Families for CD1B Gene

HGNC:
Human Protein Atlas (HPA):
  • CD markers
  • Predicted membrane proteins

Protein Domains for CD1B Gene

InterPro:
Blocks:
  • Immunoglobulin C-type
ProtoNet:

Suggested Antigen Peptide Sequences for CD1B Gene

GenScript: Design optimal peptide antigens:
  • T-cell surface glycoprotein CD1b (CD1B_HUMAN)
  • Thymocyte antigen CD1b (Q9UN97_HUMAN)
genes like me logo Genes that share domains with CD1B: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CD1B Gene

Function for CD1B Gene

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  2. CRISPR
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  6. Cell Line

Molecular function for CD1B Gene

UniProtKB/Swiss-Prot Function:
Antigen-presenting protein that binds self and non-self lipid and glycolipid antigens and presents them to T-cell receptors on natural killer T-cells.
GENATLAS Biochemistry:
cell differentiation antigen CD1B,45kDa,membrane glycoprotein,B2M associated,identified by monoclonal antibodies WM-25,4A76,NUT2 (see CD1@)

Phenotypes From GWAS Catalog for CD1B Gene

Gene Ontology (GO) - Molecular Function for CD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12118248
GO:0030883 endogenous lipid antigen binding IBA 21873635
GO:0030884 exogenous lipid antigen binding IBA 21873635
GO:0071723 lipopeptide binding IBA 21873635
genes like me logo Genes that share ontologies with CD1B: view
genes like me logo Genes that share phenotypes with CD1B: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CD1B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CD1B Gene

Localization for CD1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD1B Gene

Cell membrane. Single-pass type I membrane protein. Endosome membrane. Single-pass type I membrane protein. Lysosome membrane. Single-pass type I membrane protein. Note=Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes. {ECO:0000269 PubMed:10899914, ECO:0000269 PubMed:10981968, ECO:0000269 PubMed:14716313}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CD1B gene
Compartment Confidence
plasma membrane 5
extracellular 4
endosome 4
lysosome 4
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
golgi apparatus 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for CD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome IEA --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with CD1B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CD1B Gene

Pathways & Interactions for CD1B Gene

genes like me logo Genes that share pathways with CD1B: view

Gene Ontology (GO) - Biological Process for CD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001916 positive regulation of T cell mediated cytotoxicity IBA 21873635
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0006955 immune response IBA 21873635
GO:0048006 antigen processing and presentation, endogenous lipid antigen via MHC class Ib IBA 21873635
genes like me logo Genes that share ontologies with CD1B: view

No data available for SIGNOR curated interactions for CD1B Gene

Drugs & Compounds for CD1B Gene

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  1. Drug

(5) Drugs for CD1B Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phytosphingosine Experimental Pharma 0
Sphingosine Experimental Pharma 0
sphinganine Pharma 0
Sphingosine-1-phosphate Pharma Agonist, Full agonist endogenous second messenger and ligand for S1PR1, Endogenous agonist at S1P1-5 0

(517) Additional Compounds for CD1B Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Dehydrosphinganine
  • 3-dehydro-D-Sphinganine
  • 3-Ketodihydrosphingosine
  • 3-Ketosphinganine
  • (2S)-2-amino-1-Hydroxyoctadecan-3-one
  • 1-Hydroxy-2-amino-3-oxo-octadecane
 16105-69-4
3-O-Sulfogalactosylceramide (d18:1/12:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-SulfO-beta-D-galactosylceramide
  • 3-O-SulfO-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
 852100-88-0
3-O-Sulfogalactosylceramide (d18:1/14:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-SulfO-beta-D-galactosylceramide
  • 3-O-SulfO-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
3-O-Sulfogalactosylceramide (d18:1/16:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-SulfO-beta-D-galactosylceramide
  • 3-O-SulfO-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
 862509-48-6
3-O-Sulfogalactosylceramide (d18:1/18:0)
  • 3'-O-Sulphogalactosylceramide
  • 3-O-SulfO-beta-D-galactosylceramide
  • 3-O-SulfO-beta-delta-galactosylceramide
  • 3-O-Sulfogalactosylceramide
  • Cerebroside 3-sulfate
 244215-65-4
genes like me logo Genes that share compounds with CD1B: view

Transcripts for CD1B Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CD1B Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CD1B

Alternative Splicing Database (ASD) splice patterns (SP) for CD1B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7
SP1: -
SP2:
SP3:

Relevant External Links for CD1B Gene

GeneLoc Exon Structure for
CD1B

Expression for CD1B Gene

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  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CD1B Gene

mRNA expression in normal human tissues for CD1B Gene
mRNA expression by BioGPS for CD1B GenemRNA expression by GTEx for CD1B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CD1B Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x6.5), Spleen (x4.9), and Whole Blood (x4.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CD1B Gene



Protein tissue co-expression partners for CD1B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CD1B

SOURCE GeneReport for Unigene cluster for CD1B Gene:

Hs.1310

mRNA Expression by UniProt/SwissProt for CD1B Gene:

P29016-CD1B_HUMAN
Tissue specificity: Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues.

Evidence on tissue expression from TISSUES for CD1B Gene

  • Lung(4.5)
  • Blood(3.7)
  • Lymph node(3.5)
  • Spleen(3.3)
  • Skin(3.2)
  • Bone marrow(2.7)
  • Intestine(2.6)
  • Kidney(2.6)
  • Nervous system(2.5)
  • Liver(2.5)
  • Bone(2.2)
  • Heart(2.1)
  • Thyroid gland(2)
genes like me logo Genes that share expression patterns with CD1B: view

Primer Products

No data available for Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CD1B Gene

Orthologs for CD1B Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD1B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CD1B 30 31
  • 99.3 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CD1B5 30 31
  • 81.01 (n)
 OneToMany
-- 31
  • 76 (a)
 OneToMany
CD1B3 31
  • 76 (a)
 OneToMany
-- 31
  • 74 (a)
 OneToMany
-- 31
  • 70 (a)
 OneToMany
-- 31
  • 68 (a)
 OneToMany
-- 31
  • 61 (a)
 OneToMany
Dog
(Canis familiaris)
 Mammalia CD1B 30 31
  • 75.57 (n)
 OneToOne
Chicken
(Gallus gallus)
 Aves CD1A1 31
  • 25 (a)
 ManyToMany
CD1.2 31
  • 23 (a)
 ManyToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 25 (a)
 OneToMany
Species where no ortholog for CD1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for CD1B Gene

ENSEMBL:
Gene Tree for CD1B (if available)
TreeFam:
Gene Tree for CD1B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CD1B: view image

Paralogs for CD1B Gene

Paralogs for CD1B Gene

(5) SIMAP similar genes for CD1B Gene using alignment to 2 proteins:

  • CD1B_HUMAN
  • H7C0I2_HUMAN
genes like me logo Genes that share paralogs with CD1B: view

Variants for CD1B Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CD1B Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
709334 Likely Benign: not provided 158,292,833(-) G/C MISSENSE_VARIANT
716049 Benign: not provided 158,293,276(-) C/A SYNONYMOUS_VARIANT
732731 Likely Benign: not provided 158,292,829(-) G/T MISSENSE_VARIANT
770494 Benign: not provided 158,330,814(-) C/T MISSENSE_VARIANT
773640 Benign: not provided 158,293,221(-) T/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CD1B Gene

Structural Variations from Database of Genomic Variants (DGV) for CD1B Gene

Variant ID Type Subtype PubMed ID
nsv831692 CNV gain 17160897
nsv946439 CNV duplication 23825009
nsv999542 CNV loss 25217958

Variation tolerance for CD1B Gene

Residual Variation Intolerance Score: 80.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.03; 37.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CD1B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CD1B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD1B Gene

Disorders for CD1B Gene

MalaCards: The human disease database

(48) MalaCards diseases for CD1B Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
mycobacterium malmoense
  • m. malmoense
non-langerhans-cell histiocytosis
  • histiocytosis, non-langerhans-cell
langerhans cell sarcoma
  • malignant langerhans cell sarcoma
histiocytic and dendritic cell cancer
  • histiocytic and dendritic cell
reticulohistiocytic granuloma
  • reticulohistiocytoma
- elite association - COSMIC cancer census association via MalaCards
Search CD1B in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CD1B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CD1B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CD1B Gene

Publications for CD1B Gene

  1. Endogenous phosphatidylcholine and a long spacer ligand stabilize the lipid-binding groove of CD1b. (PMID: 16874306) Garcia-Alles LF … Mourey L (The EMBO journal 2006) 3 4 23
  2. Saposin C is required for lipid presentation by human CD1b. (PMID: 14716313) Winau F … Schaible UE (Nature immunology 2004) 3 4 23
  3. Human CD1b and CD1c isoforms survey different intracellular compartments for the presentation of microbial lipid antigens. (PMID: 10899914) Briken V … Porcelli SA (The Journal of experimental medicine 2000) 3 4 23
  4. Structure and expression of the human thymocyte antigens CD1a, CD1b, and CD1c. (PMID: 2447586) Martin LH … Milstein C (Proceedings of the National Academy of Sciences of the United States of America 1987) 2 3 4
  5. CD1-restricted adaptive immune responses to Mycobacteria in human group 1 CD1 transgenic mice. (PMID: 19808251) Felio K … Wang CR (The Journal of experimental medicine 2009) 3 23

ExternalLinks

View latest publications for CD1B gene in Mastermind

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