Human Gene CD19 (ENST00000538922.8_9) from GENCODE V47lift37
  Description: CD19 molecule, transcript variant 4 (from RefSeq NR_169755.1)
Gencode Transcript: ENST00000538922.8_9
Gencode Gene: ENSG00000177455.15_13
Transcript (Including UTRs)
   Position: hg19 chr16:28,943,292-28,950,663 Size: 7,372 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr16:28,943,322-28,950,284 Size: 6,963 Coding Exon Count: 14 

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 (chr16:28,943,292-28,950,663)mRNA (may differ from genome)Protein (556 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD19_HUMAN
DESCRIPTION: RecName: Full=B-lymphocyte antigen CD19; AltName: Full=B-lymphocyte surface antigen B4; AltName: Full=Differentiation antigen CD19; AltName: Full=T-cell surface antigen Leu-12; AltName: CD_antigen=CD19; Flags: Precursor;
FUNCTION: Assembles with the antigen receptor of B-lymphocytes in order to decrease the threshold for antigen receptor-dependent stimulation.
SUBUNIT: Forms a complex with CD21, CD81 and CD225 in the membrane of mature B-cells. Interacts with VAV. Interacts with GRB2 and SOS when phosphorylated on Tyr-348 and/or Tyr-378. Interacts with PLCG2 when phosphorylated on Tyr-409. Interacts with LYN.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
PTM: Phosphorylated on serine and threonine upon DNA damage, probably by ATM or ATR. Phosphorylated on tyrosine following B- cell activation. Phosphorylated on tyrosine residues by LYN.
DISEASE: Defects in CD19 are the cause of immunodeficiency common variable type 3 (CVID3) [MIM:613493]; also called antibody deficiency due to CD19 defect. CVID3 is a primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low.
SIMILARITY: Contains 2 Ig-like C2-type (immunoglobulin-like) domains.
SEQUENCE CAUTION: Sequence=AAA35533.1; Type=Frameshift; Positions=396;
WEB RESOURCE: Name=CD19base; Note=CD19 mutation db; URL="http://bioinf.uta.fi/CD19base/";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CD19";

-  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: CD19
Diseases sorted by gene-association score: immunodeficiency, common variable, 3* (919), cd19-related common variable immune deficiency* (500), common variable immunodeficiency* (163), transient hypogammaglobulinemia of infancy (22), transient hypogammaglobulinemia (16), invasive malignant thymoma (15), b cell prolymphocytic leukemia (9), multiple myeloma (9), central nervous system leukemia (8), gastrointestinal defects and immunodeficiency syndrome (8), congenital hypogammaglobulinemia (7), rhinoscleroma (7), solitary osseous plasmacytoma (7), lung lymphoma (6), posterior scleritis (6), agammaglobulinemia (6), rheumatic myocarditis (6), adenoid hypertrophy (6), plasma protein metabolism disease (6), appendicitis (6), mantle cell lymphoma (6), encephalitozoonosis (6), bladder lymphoma (6), lobomycosis (5), lymphoma, non-hodgkin (5), b cell deficiency (5), colon lymphoma (5), mature b-cell neoplasm (5), pericoronitis (5), lateral medullary syndrome (4), marginal zone b-cell lymphoma (4), plasma cell neoplasm (4), anterior scleritis (4), gamma heavy chain disease (4), diffuse infiltrative lymphocytosis syndrome (4), small intestine lymphoma (4), chronic lymphocytic leukemia (3), leukemia, acute lymphoblastic 3 (3), immune system disease (1), combined t cell and b cell immunodeficiency (1), leukemia, acute myeloid (1)
* = Manually curated disease association

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

+  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: 85.15 RPKM in Spleen
Total median expression: 173.30 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 -6.0030-0.200 Picture PostScript Text
3' UTR -52.50217-0.242 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

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on P15391
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005057 signal transducer activity, downstream of receptor
GO:0005515 protein binding
GO:0046934 phosphatidylinositol-4,5-bisphosphate 3-kinase activity

Biological Process:
GO:0006968 cellular defense response
GO:0007166 cell surface receptor signaling pathway
GO:0030449 regulation of complement activation
GO:0046854 phosphatidylinositol phosphorylation
GO:0050776 regulation of immune response
GO:0050853 B cell receptor signaling pathway
GO:0051281 positive regulation of release of sequestered calcium ion into cytosol
GO:0051897 positive regulation of protein kinase B signaling

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0032991 macromolecular complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC006338 - Homo sapiens CD19 molecule, mRNA (cDNA clone MGC:12802 IMAGE:4054919), complete cds.
AK301363 - Homo sapiens cDNA FLJ60916 complete cds, highly similar to B-lymphocyte antigen CD19 precursor.
AK313577 - Homo sapiens cDNA, FLJ94141.
BC052294 - Homo sapiens CD19 molecule, mRNA (cDNA clone IMAGE:6301752), with apparent retained intron.
M21097 - Human differentiation antigen (CD19) mRNA, complete cds.
X13312 - H.sapiens RNA for CD19.
AK307295 - Homo sapiens cDNA, FLJ97243.
M28170 - Human cell surface protein CD19 (CD19) gene, complete cds.
JD439007 - Sequence 420031 from Patent EP1572962.
DQ893016 - Synthetic construct clone IMAGE:100005646; FLH191702.01X; RZPDo839G0177D CD19 molecule (CD19) gene, encodes complete protein.
DQ896261 - Synthetic construct Homo sapiens clone IMAGE:100010721; FLH191698.01L; RZPDo839G0167D CD19 molecule (CD19) gene, encodes complete protein.
KJ890856 - Synthetic construct Homo sapiens clone ccsbBroadEn_00250 CD19 gene, encodes complete protein.
AK130657 - Homo sapiens cDNA FLJ27147 fis, clone SPL09574, highly similar to B-lymphocyte antigen CD19 precursor.
AK301167 - Homo sapiens cDNA FLJ61427 complete cds, highly similar to B-lymphocyte antigen CD19 precursor.
AK304456 - Homo sapiens cDNA FLJ54955 complete cds, highly similar to B-lymphocyte antigen CD19 precursor.
JD252903 - Sequence 233927 from Patent EP1572962.
JD419747 - Sequence 400771 from Patent EP1572962.
MP541156 - Sequence 117 from Patent WO2020047164.

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

Protein P15391 (Reactome details) participates in the following event(s):

R-HSA-199518 C3d-complexed antigen binds to complement receptor
R-HSA-8853252 CR2:C3d,C3dg,iC3b binds CD19:CD81
R-HSA-2076220 CD19 Signalosome phosphorylates PI(4,5)P2 forming PI(3,4,5)P3
R-HSA-2400009 PI3K inhibitors block PI3K catalytic activity
R-HSA-2316434 PI3K phosphorylates PIP2 to PIP3
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-983695 Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
R-HSA-977606 Regulation of Complement cascade
R-HSA-1280218 Adaptive Immune System
R-HSA-983705 Signaling by the B Cell Receptor (BCR)
R-HSA-166658 Complement cascade
R-HSA-168256 Immune System
R-HSA-168249 Innate Immune System
R-HSA-2219530 Constitutive Signaling by Aberrant PI3K in Cancer
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-6811558 PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
R-HSA-2219528 PI3K/AKT Signaling in Cancer
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-199418 Negative regulation of the PI3K/AKT network
R-HSA-5663202 Diseases of signal transduction
R-HSA-162582 Signal Transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A0N0P9, CD19_HUMAN, ENST00000538922.1, ENST00000538922.2, ENST00000538922.3, ENST00000538922.4, ENST00000538922.5, ENST00000538922.6, ENST00000538922.7, F5H635, NR_169755, P15391, Q96S68, Q9BRD6, uc324qwr.1, uc324qwr.2
UCSC ID: ENST00000538922.8_9
RefSeq Accession: NM_001770.6
Protein: P15391 (aka CD19_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.