Human Gene CD8B (ENST00000331469.6) from GENCODE V44
  Description: Homo sapiens CD8b molecule (CD8B), transcript variant 2, mRNA. (from RefSeq NM_172213)
RefSeq Summary (NM_172213): The CD8 antigen is a cell surface glycoprotein found on most cytotoxic T lymphocytes that mediates efficient cell-cell interactions within the immune system. The CD8 antigen, acting as a coreceptor, and the T-cell receptor on the T lymphocyte recognize antigens displayed by an antigen presenting cell (APC) in the context of class I MHC molecules. The functional coreceptor is either a homodimer composed of two alpha chains, or a heterodimer composed of one alpha and one beta chain. Both alpha and beta chains share significant homology to immunoglobulin variable light chains. This gene encodes the CD8 beta chain isoforms. Multiple alternatively spliced transcript variants encoding distinct membrane associated or secreted isoforms have been described. A pseudogene, also located on chromosome 2, has been identified. [provided by RefSeq, May 2010].
Gencode Transcript: ENST00000331469.6
Gencode Gene: ENSG00000172116.23
Transcript (Including UTRs)
   Position: hg38 chr2:86,815,557-86,861,915 Size: 46,359 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr2:86,815,607-86,861,865 Size: 46,259 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:86,815,557-86,861,915)mRNA (may differ from genome)Protein (243 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD8B_HUMAN
DESCRIPTION: RecName: Full=T-cell surface glycoprotein CD8 beta chain; AltName: CD_antigen=CD8b; Flags: Precursor;
FUNCTION: Identifies cytotoxic/suppressor T-cells that interact with MHC class I bearing targets. CD8 is thought to play a role in the process of T-cell mediated killing.
SUBUNIT: In general heterodimer of an alpha and a beta chain linked by two disulfide bonds.
SUBCELLULAR LOCATION: Isoform 1: Cell membrane; Single-pass type I membrane protein (Probable).
SUBCELLULAR LOCATION: Isoform 2: Cell membrane; Single-pass type I membrane protein (Probable).
SUBCELLULAR LOCATION: Isoform 3: Secreted (Probable).
SUBCELLULAR LOCATION: Isoform 4: Cell membrane; Single-pass type I membrane protein (Probable).
SUBCELLULAR LOCATION: Isoform 5: Cell membrane; Single-pass type I membrane protein (Probable).
SUBCELLULAR LOCATION: Isoform 6: Secreted (Probable).
SUBCELLULAR LOCATION: Isoform 7: Secreted (Probable).
SUBCELLULAR LOCATION: Isoform 8: Secreted (Probable).
TISSUE SPECIFICITY: Isoform 1, isoform 3, isoform 5, isoform 6, isoform 7 and isoform 8 are expressed in both thymus and peripheral CD8+ T-cells. Expression of isoform 1 is higher in thymus CD8+ T-cells than in peripheral CD8+ T-cells. Expression of isoform 6 is higher in peripheral CD8+ T-cells than in thymus CD8+ T-cells.
PTM: Phosphorylated as a consequence of T-cell activation (Potential).
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.
SEQUENCE CAUTION: Sequence=AAD13877.1; Type=Erroneous gene model prediction;
WEB RESOURCE: Name=Wikipedia; Note=CD8 entry; URL="http://en.wikipedia.org/wiki/CD8";

-  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: CD8B
Diseases sorted by gene-association score: mucinous stomach adenocarcinoma (2)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.81 RPKM in Small Intestine - Terminal Ileum
Total median expression: 48.83 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 -21.6050-0.432 Picture PostScript Text
3' UTR -8.6050-0.172 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
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR013106 - Ig_V-set

Pfam Domains:
PF07686 - Immunoglobulin V-set domain

ModBase Predicted Comparative 3D Structure on P10966
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0015026 coreceptor activity
GO:0042288 MHC class I protein binding

Biological Process:
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0006955 immune response
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway
GO:0042110 T cell activation
GO:0050690 regulation of defense response to virus by virus
GO:0050776 regulation of immune response

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031901 early endosome membrane
GO:0042101 T cell receptor complex


-  Descriptions from all associated GenBank mRNAs
  X13445 - Human mRNA for CD8 beta-chain glycoprotein (CD8-beta.2).
BX647150 - Homo sapiens mRNA; cDNA DKFZp686B15223 (from clone DKFZp686B15223).
X13446 - Human mRNA for CD8 beta-chain glycoprotein (CD8-beta.3).
BC100911 - Homo sapiens CD8b molecule, mRNA (cDNA clone MGC:119114 IMAGE:40003720), complete cds.
BC100912 - Homo sapiens CD8b molecule, mRNA (cDNA clone MGC:119115 IMAGE:40003723), complete cds.
BC100913 - Homo sapiens CD8b molecule, mRNA (cDNA clone MGC:119116 IMAGE:40003724), complete cds.
BC100914 - Homo sapiens CD8b molecule, mRNA (cDNA clone MGC:119117 IMAGE:40003725), complete cds.
KJ896562 - Synthetic construct Homo sapiens clone ccsbBroadEn_05956 CD8B gene, encodes complete protein.
JD073603 - Sequence 54627 from Patent EP1572962.
X13452 - Human mRNA for Lyt-3 protein.
M36712 - Human T lymphocyte surface glycoprotein (CD8-beta) mRNA, complete cds.
Y00805 - Human mRNA for CD8 T lymphocyte surface glycoprotein beta chain (mouse and rat Ly-3, Lyt-3 homologue).
LP880232 - Sequence 36 from Patent WO2017181111.
LP882061 - Sequence 3 from Patent WO2017181079.
X13444 - Human mRNA for CD8 beta-chain glycoprotein (CD8 beta.1).
AK303595 - Homo sapiens cDNA FLJ57765 complete cds, highly similar to T-cell surface glycoprotein CD8 beta chain precursor.
AK303360 - Homo sapiens cDNA FLJ61012 complete cds, highly similar to T-cell surface glycoprotein CD8 beta chain precursor.
JD128906 - Sequence 109930 from Patent EP1572962.
MB143791 - JP 2019515670-A/2: METHODS FOR MONITORING AND TREATING CANCER.
MB423115 - JP 2019521641-A/2: METHODS FOR MONITORING AND TREATING CANCER.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)
hsa04612 - Antigen processing and presentation
hsa04640 - Hematopoietic cell lineage
hsa04660 - T cell receptor signaling pathway
hsa05340 - Primary immunodeficiency

Reactome (by CSHL, EBI, and GO)

Protein P10966 (Reactome details) participates in the following event(s):

R-HSA-182186 Formation of CD8:Nef:AP-2 Complex:v-ATPase Complex
R-HSA-182198 Internalization of the CD8:Nef:AP-2 Complex:v-ATPase Complex
R-HSA-198955 TCR complex interacts with peptide antigen-presenting MHC Class I
R-HSA-182218 Nef Mediated CD8 Down-regulation
R-HSA-164938 Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-164952 The role of Nef in HIV-1 replication and disease pathogenesis
R-HSA-1280218 Adaptive Immune System
R-HSA-162909 Host Interactions of HIV factors
R-HSA-168256 Immune System
R-HSA-162906 HIV Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: CD8B1, CD8B_HUMAN, ENST00000331469.1, ENST00000331469.2, ENST00000331469.3, ENST00000331469.4, ENST00000331469.5, NM_172213, P10966, P14860, P14861, Q15980, Q496E0, Q496E1, Q496E2, Q9UDB4, Q9UDB5, Q9UDB6, Q9UDB7, Q9UDB8, Q9UDB9, Q9UDC0, Q9UQ55, uc002srw.1, uc002srw.2, uc002srw.3, uc002srw.4
UCSC ID: ENST00000331469.6
RefSeq Accession: NM_172213
Protein: P10966 (aka CD8B_HUMAN)
CCDS: CCDS1995.1

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