Human Gene CD1A (ENST00000289429.6_4) from GENCODE V47lift37
  Description: CD1a molecule, transcript variant 1 (from RefSeq NM_001763.3)
Gencode Transcript: ENST00000289429.6_4
Gencode Gene: ENSG00000158477.7_7
Transcript (Including UTRs)
   Position: hg19 chr1:158,224,214-158,228,059 Size: 3,846 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr1:158,224,460-158,227,480 Size: 3,021 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:158,224,214-158,228,059)mRNA (may differ from genome)Protein (327 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD1A_HUMAN
DESCRIPTION: RecName: Full=T-cell surface glycoprotein CD1a; AltName: Full=T-cell surface antigen T6/Leu-6; Short=hTa1 thymocyte antigen; AltName: CD_antigen=CD1a; Flags: Precursor;
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.
SUBUNIT: Heterodimer with B2M (beta-2-microglobulin). Interacts with CD74.
INTERACTION: P61769:B2M; NbExp=2; IntAct=EBI-1036766, EBI-714718;
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein. Endosome membrane. Note=Subject to intracellular trafficking between the cell membrane and endosomes. Localizes to cell surface lipid rafts.
TISSUE SPECIFICITY: Expressed on cortical thymocytes, epidermal Langerhans cells, dendritic cells, on certain T-cell leukemias, and in various other tissues.
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, before trafficking back to the cell surface.
SIMILARITY: Contains 1 Ig-like (immunoglobulin-like) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CD1A
Diseases sorted by gene-association score: histiocytosis (19), eosinophilic granuloma (18), letterer-siwe disease (15), cyclosporiasis (15), langerhans cell sarcoma (13), mycobacterium malmoense (13), alk+ histiocytosis (13), myofibroma (12), middle ear carcinoma (10), diverticulitis of colon (8), discrete subaortic stenosis (8), multifocal motor neuropathy (6), dendritic cell tumor (5), immune system organ benign neoplasm (5), thymus lipoma (5), pharyngitis (5), epidermodysplasia verruciformis (5), acquired thrombocytopenia (5), punctate epithelial keratoconjunctivitis (5), abetalipoproteinemia (5), cholesterol ester storage disease (5), spinal cord ependymoma (4), aortic valve disease 1 (1), aortic valve disease 2 (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.79 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 11.43 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -59.00246-0.240 Picture PostScript Text
3' UTR -133.00579-0.230 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
IPR007110 - Ig-like
IPR003597 - Ig_C1-set
IPR011161 - MHC_I-like_Ag-recog
IPR011162 - MHC_I/II-like_Ag-recog
IPR001039 - MHC_I_a_a1/a2

Pfam Domains:
PF00129 - Class I Histocompatibility antigen, domains alpha 1 and 2
PF07654 - Immunoglobulin C1-set domain
PF16497 - MHC-I family domain

SCOP Domains:
48726 - Immunoglobulin
54452 - MHC antigen-recognition domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1ONQ - X-ray MuPIT 1XZ0 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P06126
FrontTopSide
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
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0030881 beta-2-microglobulin binding
GO:0030883 endogenous lipid antigen binding
GO:0030884 exogenous lipid antigen binding
GO:0071723 lipopeptide binding

Biological Process:
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0006955 immune response
GO:0048007 antigen processing and presentation, exogenous lipid antigen via MHC class Ib
GO:0050776 regulation of immune response

Cellular Component:
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0045121 membrane raft


-  Descriptions from all associated GenBank mRNAs
  CU693322 - Synthetic construct Homo sapiens gateway clone IMAGE:100016728 5' read CD1D mRNA.
BC031645 - Homo sapiens CD1a molecule, mRNA (cDNA clone MGC:35168 IMAGE:5170038), complete cds.
M28825 - Human thymocyte antigen CD1a mRNA, complete cds.
AK312945 - Homo sapiens cDNA, FLJ93398, highly similar to Homo sapiens CD1a antigen (CD1A), mRNA.
JD373854 - Sequence 354878 from Patent EP1572962.
JD566791 - Sequence 547815 from Patent EP1572962.
JD528198 - Sequence 509222 from Patent EP1572962.
JD219345 - Sequence 200369 from Patent EP1572962.
JD298508 - Sequence 279532 from Patent EP1572962.
DQ891346 - Synthetic construct clone IMAGE:100003976; FLH171271.01X; RZPDo839G06100D CD1a molecule (CD1A) gene, encodes complete protein.
DQ894526 - Synthetic construct Homo sapiens clone IMAGE:100008986; FLH171267.01L; RZPDo839G0699D CD1a molecule (CD1A) gene, encodes complete protein.
KJ901320 - Synthetic construct Homo sapiens clone ccsbBroadEn_10714 CD1A gene, encodes complete protein.
M27735 - Human epidermal dendritic cell marker (CD1a) mRNA, 3' end (mature peptide).
X04450 - Homo sapiens partial mRNA for CD1a antigen (CD1a gene).
X79308 - H.sapiens CD1A mRNA, 84bp.
X79309 - H.sapiens CD1A mRNA, 66bp.
JD063683 - Sequence 44707 from Patent EP1572962.
JD300983 - Sequence 282007 from Patent EP1572962.
JD218015 - Sequence 199039 from Patent EP1572962.
JD544521 - Sequence 525545 from Patent EP1572962.
JD347102 - Sequence 328126 from Patent EP1572962.
JD459222 - Sequence 440246 from Patent EP1572962.
JD327657 - Sequence 308681 from Patent EP1572962.
JD271717 - Sequence 252741 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P06126 (Reactome details) participates in the following event(s):

R-HSA-8850356 TCR binds microbial lipid-based antigen via CD1
R-HSA-8850326 TCR binds self-lipid-based antigen via CD1
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: CD1A_HUMAN, D3DVD7, ENST00000289429.1, ENST00000289429.2, ENST00000289429.3, ENST00000289429.4, ENST00000289429.5, NM_001763, P06126, Q13962, Q5TDJ8, Q9UMM4, Q9Y5M5, uc317ksb.1, uc317ksb.2
UCSC ID: ENST00000289429.6_4
RefSeq Accession: NM_001763.3
Protein: P06126 (aka CD1A_HUMAN)

-  Gene Model Information
  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.