Human Gene VPREB3 (uc002zxt.3)
  Description: Homo sapiens pre-B lymphocyte 3 (VPREB3), mRNA.
RefSeq Summary (NM_013378): The protein encoded by this gene is the human ortholog of the mouse VpreB3 (8HS20) protein, is thought to be involved in B-cell maturation, and may play a role in assembly of the pre-B cell receptor (pre-BCR). While the role of this protein in B-cell development has not yet been elucidated, studies with the chicken ortholog of this protein have found that when overexpressed, this protein localizes to the endoplasmic reticulum. The mouse ortholog of this protein has been shown to associate with membrane mu heavy chains early in the course of pre-B cell receptor biosynthesis. Expression of this gene has been observed in some lymphomas. [provided by RefSeq, Apr 2015].
Transcript (Including UTRs)
   Position: hg19 chr22:24,094,930-24,096,630 Size: 1,701 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr22:24,095,063-24,096,550 Size: 1,488 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:24,094,930-24,096,630)mRNA (may differ from genome)Protein (123 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VPRE3_HUMAN
DESCRIPTION: RecName: Full=Pre-B lymphocyte protein 3; AltName: Full=N27C7-2; AltName: Full=Protein VPreB3; Flags: Precursor;
FUNCTION: Associates with the Ig-mu chain to form a molecular complex that is expressed on the surface of pre-B-cells.
TISSUE SPECIFICITY: Expressed in B-cell precursors. Expressed in fetal liver, bone marrow, spleen and lymph node.
SIMILARITY: Belongs to the immunoglobulin superfamily.
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


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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 37.56 RPKM in Spleen
Total median expression: 82.18 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 -17.3080-0.216 Picture PostScript Text
3' UTR -31.97133-0.240 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
IPR013106 - Ig_V-set
IPR003596 - Ig_V-set_subgr

Pfam Domains:
PF07686 - Immunoglobulin V-set domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on Q9UKI3
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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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0002377 immunoglobulin production
GO:0006955 immune response
GO:0050900 leukocyte migration

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005783 endoplasmic reticulum


-  Descriptions from all associated GenBank mRNAs
  BC020666 - Homo sapiens pre-B lymphocyte 3, mRNA (cDNA clone MGC:22350 IMAGE:4772032), complete cds.
AY359000 - Homo sapiens clone DNA49821 VPREB3 (UNQ355) mRNA, complete cds.
AF163825 - Homo sapiens pre-B lymphocyte protein 3 (VPREB3) mRNA, complete cds.
JD042198 - Sequence 23222 from Patent EP1572962.
CR456610 - Homo sapiens VPREB3 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.VPREB3.V2).
JD397678 - Sequence 378702 from Patent EP1572962.
JD450033 - Sequence 431057 from Patent EP1572962.
JD176269 - Sequence 157293 from Patent EP1572962.
JD220735 - Sequence 201759 from Patent EP1572962.
JD166501 - Sequence 147525 from Patent EP1572962.
DQ893106 - Synthetic construct clone IMAGE:100005736; FLH193794.01X; RZPDo839C0279D pre-B lymphocyte gene 3 (VPREB3) gene, encodes complete protein.
CU013206 - Homo sapiens VPREB3, mRNA (cDNA clone IMAGE:100000559), complete cds, with stop codon, in Gateway system.
AK312098 - Homo sapiens cDNA, FLJ92380, Homo sapiens pre-B lymphocyte gene 3 (VPREB3), mRNA.
KJ893701 - Synthetic construct Homo sapiens clone ccsbBroadEn_03095 VPREB3 gene, encodes complete protein.
CU013494 - Homo sapiens VPREB3, mRNA (cDNA clone IMAGE:100000463), complete cds, without stop codon, in Gateway system.
DQ896379 - Synthetic construct Homo sapiens clone IMAGE:100010839; FLH193790.01L; RZPDo839C0269D pre-B lymphocyte gene 3 (VPREB3) gene, encodes complete protein.
JD460260 - Sequence 441284 from Patent EP1572962.
JD145365 - Sequence 126389 from Patent EP1572962.
JD403045 - Sequence 384069 from Patent EP1572962.

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

Protein Q9UKI3 (Reactome details) participates in the following event(s):

R-HSA-8858498 SL (surrogate light chain) binds IgH to form pre-BCR
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: B2R587, NM_013378, NP_037510, Q9UKI3, UNQ355/PRO619, VPRE3_HUMAN
UCSC ID: uc002zxt.3
RefSeq Accession: NM_013378
Protein: Q9UKI3 (aka VPRE3_HUMAN or VPR3_HUMAN)
CCDS: CCDS13813.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_013378.2
exon count: 2CDS single in 3' UTR: no RNA size: 602
ORF size: 372CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 572.00frame shift in genome: no % Coverage: 97.18
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: 0# 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.