Protein:TNFRSF13B |
Protein Summary |
 Gene summary |
| Gene name: TNFRSF13B | ASpdb.0 ID: 23495 | Gene | Gene symbol | TNFRSF13B | Gene ID | 23495 |
| Gene name | TNF receptor superfamily member 13B |
| Synonyms | CD267|CVID|CVID2|IGAD2|RYZN|TACI|TNFRSF14B |
| Cytomap | 17p11.2 |
| Type of gene | protein-coding |
| Description | tumor necrosis factor receptor superfamily member 13Btransmembrane activator and CAML interactortumor necrosis factor receptor 13B |
| Modification date | 20240305 |
| UniProtAcc | O14836 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| O14836-1 | O14836-1_1xu1_T.pdb | 1XU1 | X-ray | 1.9 | T | 71 | 109 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| O14836 | TNFRSF13B | O14836-1 | O14836-2 | 293 | 247 | 21 | 67 | Substitution | FPQGLWTGVAMRSCPEEQYWDPLLGTCMSCKTICNHQSQRTCAAFCR | W | 21 | 21 |
| O14836 | TNFRSF13B | O14836-1 | O14836-3 | 293 | 176 | 150 | 176 | Substitution | LPGLKLSADQVALVYSTLGLCLCAVLC | PRGCPAPGTRKSFWDKENFQGEGFHLG | 150 | 176 |
| O14836 | TNFRSF13B | O14836-1 | O14836-3 | 293 | 176 | 177 | 293 | Deletion | none | none | 176 | 176 |
| Multiple sequence alignment of our canonical and alternatively spliced TNFRSF13B |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of TNFRSF13B |
| UniProt-id | ENSG | ENST | ENSP |
| O14836-1 | ENSG00000240505.9 | ENST00000261652.7 | ENSP00000261652.2 |
| O14836-2 | ENSG00000240505.9 | ENST00000583789.1 | ENSP00000462952.1 |
| UniProt-id | NM ID | NP ID |
| O14836-1 | NM_012452.2 | NP_036584.1 |
| Amino acid sequences of our canonical and alternatively spliced TNFRSF13B |
| accession_id | Protein sequence |
| O14836-1 | MSGLGRSRRGGRSRVDQEERFPQGLWTGVAMRSCPEEQYWDPLLGTCMSCKTICNHQSQRTCAAFCRSLSCRKEQGKFYDHLLRDCISCA SICGQHPKQCAYFCENKLRSPVNLPPELRRQRSGEVENNSDNSGRYQGLEHRGSEASPALPGLKLSADQVALVYSTLGLCLCAVLCCFLV AVACFLKKRGDPCSCQPRSRPRQSPAKSSQDHAMEAGSPVSTSPEPVETCSFCFPECRAPTQESAVTPGTPDPTCAGRWGCHTRTTVLQP |
| O14836-2 | MSGLGRSRRGGRSRVDQEERWSLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLRSPVNLPPELRRQRSGEVENNSDNSGRY QGLEHRGSEASPALPGLKLSADQVALVYSTLGLCLCAVLCCFLVAVACFLKKRGDPCSCQPRSRPRQSPAKSSQDHAMEAGSPVSTSPEP |
| O14836-3 | MSGLGRSRRGGRSRVDQEERFPQGLWTGVAMRSCPEEQYWDPLLGTCMSCKTICNHQSQRTCAAFCRSLSCRKEQGKFYDHLLRDCISCA |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| TNFRSF13B (go to UniProt):O14836 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| O14836 | Topological domain | 1 | 165 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=21;End=67 |
| O14836 | Topological domain | 1 | 165 | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=150;End=176 |
| O14836 | Transmembrane | 166 | 186 | Note=Helical%3B Signal-anchor for type III membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Substitution;Start=150;End=176 |
| O14836 | Transmembrane | 166 | 186 | Note=Helical%3B Signal-anchor for type III membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=177;End=293 |
| O14836 | Topological domain | 187 | 293 | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=177;End=293 |
| O14836 | Repeat | 33 | 67 | Note=TNFR-Cys 1 | Type=Substitution;Start=21;End=67 |
| O14836 | Region | 192 | 226 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=177;End=293 |
| O14836 | Compositional bias | 197 | 226 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=177;End=293 |
Gene Isoform Structures and Expression Levels for TNFRSF13B |
| Gene structures of our canonical and alternative spliced genes of TNFRSF13B * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of O14836-1 |
| 3D view using mol* of O14836-2 |
| 3D view using mol* of O14836-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of O14836-1 |
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| pLDDT distribution across the protein length of O14836-2 |
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| pLDDT distribution across the protein length of O14836-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of O14836-1 |
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| Ramachandran plot of O14836-2 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| O14836-1 | 0.825 | 41 | 0.843 | 113.876 | 0.539 | 0.676 | 0.919 | 1.517 | 0.505 | 3.006 | 4.33 | 90,93,103,107,108,110,111,113,114,115,118
|
| O14836-2 | 0.699 | 46 | 0.618 | 147.147 | 0.701 | 0.6 | 0.815 | 0.13 | 1.166 | 0.111 | 0.823 | 22,25,26,28,29,30,31,32,33,34,35,53,54,56,57
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| O14836-3 | 0.743 | 56 | 0.73 | 174.93 | 0.755 | 0.566 | 0.711 | 0.186 | 0.962 | 0.193 | 1.175 | 34,35,36,37,38,61,62,64,65,68,72,74,75,76,77,78,79 ,80,81,84,89,99,103 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of O14836-1_O14836-1_1xu1_T.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of O14836-1_1xu1_T_O14836-2.pdb |
| 3D view using mol* of O14836-1_1xu1_T_O14836-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of O14836-1_O14836-2.pdb |
| 3D view using mol* of O14836-1_O14836-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/O14836-1_vs_O14836-2.png |
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| ./stats/secondary_structure/figure/O14836-1_vs_O14836-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/O14836-1_vs_O14836-2.png |
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| ./stats/relative_asa/O14836-1_vs_O14836-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to TNFRSF13B |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to TNFRSF13B |
| Previous studies relating to the alternative splicing of TNFRSF13B and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| TNFRSF13B | 25631768 | Differential induction of plasma cells by isoforms of human TACI. | Subjects with common variable immune deficiency may have mutations in transmembrane activator calcium modulator and cyclophilin ligand interactor (TACI). Unlike the murine gene, human TACI undergoes alternative messenger (m)RNA splicing to produce isoforms with 1 or 2 ligand-binding domains. Because both isoforms are found in human B cells, we compared their functions in transduced murine B and human pre-B cells. Although murine cells and pre-B cells transduced with the long TACI isoform retained surface CD19 and immunoglobulin G, cells transduced with the short TACI isoform completely lost these B-cell characteristics. Expression of the short TACI isoform produced intense nuclear factor κB activation, nuclear p65 translocation, and colocalization with myeloid differentiation factor 88 and calcium-modulating cyclophilin ligand. The short TACI-transduced cells became larger and CD138 positive, demonstrated upregulated BLIMP1 and XBP1 mRNA, and acquired the morphology of plasma cells. In contrast, cells bearing the long isoform had significantly less BLIMP1 and XBP1 mRNA and, for human pre-B cells, remained CD138 negative. Although human B cells express both isoforms, the short isoform predominates in CD27(+) B cells, toll-like receptor 9-activated peripheral B cells, and splenic marginal zone B cells. Although the transcriptional controls for alternative splicing of isoforms remain unknown, differential signals via isoforms may control plasma-cell generation in humans. | D017074 | Common Variable Immunodeficiency |
Clinically important variants in TNFRSF13B |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
| O14836 | O14836-1 | TNFRSF13B | Indel | p.Ser194Ter | Pathogenic |
| O14836 | O14836-1 | TNFRSF13B | Indel | p.Ser194Ter | Pathogenic |
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