Human Gene TNFRSF13B (ENST00000261652.7) from GENCODE V44
  Description: Homo sapiens TNF receptor superfamily member 13B (TNFRSF13B), mRNA. (from RefSeq NM_012452)
RefSeq Summary (NM_012452): The protein encoded by this gene is a lymphocyte-specific member of the tumor necrosis factor (TNF) receptor superfamily. It interacts with calcium-modulator and cyclophilin ligand (CAML). The protein induces activation of the transcription factors NFAT, AP1, and NF-kappa-B and plays a crucial role in humoral immunity by interacting with a TNF ligand. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000261652.7
Gencode Gene: ENSG00000240505.9
Transcript (Including UTRs)
   Position: hg38 chr17:16,939,081-16,972,118 Size: 33,038 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr17:16,939,547-16,972,075 Size: 32,529 Coding Exon Count: 5 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:16,939,081-16,972,118)mRNA (may differ from genome)Protein (293 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  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: TNFRSF13B
Diseases sorted by gene-association score: immunodeficiency, common variable, 2* (1255), immunoglobulin a deficiency 2* (1253), tnfrsf13b-related common variable immune deficiency* (525), common variable immunodeficiency* (274), immunoglobulin alpha deficiency (14), primary agammaglobulinemia (14), smith-magenis syndrome (13), cryptococcal meningitis (8), primary immunodeficiency disease (7), macroglobulinemia (6), b cell deficiency (6), chronic lymphocytic leukemia (2), lymphoma, non-hodgkin (1)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 66.42 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 86.13 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 -2.5043-0.058 Picture PostScript Text
3' UTR -101.10466-0.217 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
IPR015384 - TACI_Cys-rich-dom
IPR022317 - TNFR_13B

Pfam Domains:
PF09305 - TACI, cysteine-rich domain

ModBase Predicted Comparative 3D Structure on Q4ACX1
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
  Cellular Component:
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK303298 - Homo sapiens cDNA FLJ52819 complete cds, highly similar to Tumor necrosis factor receptor superfamilymember 13B.
AX772740 - Sequence 1 from Patent WO03045421.
AF023614 - Homo sapiens transmembrane activator and CAML interactor (TACI) mRNA, complete cds.
AX766384 - Sequence 1 from Patent WO03041730.
AK097261 - Homo sapiens cDNA FLJ39942 fis, clone SPLEN2023024, highly similar to Macaca mulatta transmembrane activator (NF-AT) mRNA.
JD254208 - Sequence 235232 from Patent EP1572962.
AK223453 - Homo sapiens mRNA for tumor necrosis factor receptor 13B variant, clone: FCC114F06.
JD437986 - Sequence 419010 from Patent EP1572962.
JD064277 - Sequence 45301 from Patent EP1572962.
JD441090 - Sequence 422114 from Patent EP1572962.
JD186242 - Sequence 167266 from Patent EP1572962.
JD178949 - Sequence 159973 from Patent EP1572962.
JD064245 - Sequence 45269 from Patent EP1572962.
JD442170 - Sequence 423194 from Patent EP1572962.
JD204928 - Sequence 185952 from Patent EP1572962.
JD064275 - Sequence 45299 from Patent EP1572962.
JD178952 - Sequence 159976 from Patent EP1572962.
JD064249 - Sequence 45273 from Patent EP1572962.
JD064250 - Sequence 45274 from Patent EP1572962.
JD445451 - Sequence 426475 from Patent EP1572962.
JD103757 - Sequence 84781 from Patent EP1572962.
JD437368 - Sequence 418392 from Patent EP1572962.
JD103604 - Sequence 84628 from Patent EP1572962.
JD186222 - Sequence 167246 from Patent EP1572962.
JD064020 - Sequence 45044 from Patent EP1572962.
JD330766 - Sequence 311790 from Patent EP1572962.
JD043493 - Sequence 24517 from Patent EP1572962.
JD202846 - Sequence 183870 from Patent EP1572962.
JD214242 - Sequence 195266 from Patent EP1572962.
JD064248 - Sequence 45272 from Patent EP1572962.
JD436276 - Sequence 417300 from Patent EP1572962.
JD483635 - Sequence 464659 from Patent EP1572962.
JD317006 - Sequence 298030 from Patent EP1572962.
JD442070 - Sequence 423094 from Patent EP1572962.
JD331248 - Sequence 312272 from Patent EP1572962.
JD442009 - Sequence 423033 from Patent EP1572962.
JD064268 - Sequence 45292 from Patent EP1572962.
JD178951 - Sequence 159975 from Patent EP1572962.
JD063852 - Sequence 44876 from Patent EP1572962.
BC109392 - Homo sapiens tumor necrosis factor receptor superfamily, member 13B, mRNA (cDNA clone MGC:133214 IMAGE:40030781), complete cds.
JD331227 - Sequence 312251 from Patent EP1572962.
JD077119 - Sequence 58143 from Patent EP1572962.
JD178496 - Sequence 159520 from Patent EP1572962.
JD471484 - Sequence 452508 from Patent EP1572962.
JD342729 - Sequence 323753 from Patent EP1572962.
JD445340 - Sequence 426364 from Patent EP1572962.
JD108476 - Sequence 89500 from Patent EP1572962.
JD492695 - Sequence 473719 from Patent EP1572962.
AY302137 - Homo sapiens transmembrane activator and CAML interactor (TNFRSF13B) mRNA, complete cds; alternatively spliced.
AK313302 - Homo sapiens cDNA, FLJ93815, highly similar to Homo sapiens tumor necrosis factor receptor superfamily, member 13B (TNFRSF13B), mRNA.
KJ902345 - Synthetic construct Homo sapiens clone ccsbBroadEn_11739 TNFRSF13B gene, encodes complete protein.
KR711554 - Synthetic construct Homo sapiens clone CCSBHm_00025940 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR711555 - Synthetic construct Homo sapiens clone CCSBHm_00025943 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR711556 - Synthetic construct Homo sapiens clone CCSBHm_00025946 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR711557 - Synthetic construct Homo sapiens clone CCSBHm_00025951 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR712223 - Synthetic construct Homo sapiens clone CCSBHm_00900178 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR712231 - Synthetic construct Homo sapiens clone CCSBHm_00900189 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR712232 - Synthetic construct Homo sapiens clone CCSBHm_00900190 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
AK301032 - Homo sapiens cDNA FLJ52770 complete cds, highly similar to Tumor necrosis factor receptor superfamily member 13B.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04672 - Intestinal immune network for IgA production
hsa05340 - Primary immunodeficiency

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000261652.1, ENST00000261652.2, ENST00000261652.3, ENST00000261652.4, ENST00000261652.5, ENST00000261652.6, hCG_28297, NM_012452, Q4ACX1, Q4ACX1_HUMAN, TACI, uc002gqs.1, uc002gqs.2, uc002gqs.3
UCSC ID: ENST00000261652.7
RefSeq Accession: NM_012452
Protein: Q4ACX1 CCDS: CCDS11181.1

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