Protein:UPF3B |
Protein Summary |
 Gene summary |
| Gene name: UPF3B | ASpdb.0 ID: 65109 | Gene | Gene symbol | UPF3B | Gene ID | 65109 |
| Gene name | UPF3B regulator of nonsense mediated mRNA decay |
| Synonyms | HUPF3B|MRX62|MRX82|MRXS14|RENT3B|UPF3BP1|UPF3BP2|UPF3BP3|UPF3X|Upf3p-X |
| Cytomap | Xq24 |
| Type of gene | protein-coding |
| Description | regulator of nonsense transcripts 3BUPF3 regulator of nonsense transcripts homolog BUPF3B pseudogene 1UPF3B pseudogene 2UPF3B pseudogene 3nonfunctional UPF3B regulator of nonsense mediated mRNA decaynonsense mRNA reducing factor 3Bup-frameshift sup |
| Modification date | 20240407 |
| UniProtAcc | Q9BZI7 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | UPF3B | GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 16601204 |
| Gene | UPF3B | GO:0003729 | mRNA binding | 11163187|11546873 |
| Gene | UPF3B | GO:0005654 | nucleoplasm | - |
| Gene | UPF3B | GO:0005730 | nucleolus | - |
| Gene | UPF3B | GO:0005829 | cytosol | - |
| Gene | UPF3B | GO:0034451 | centriolar satellite | - |
| Gene | UPF3B | GO:0035145 | exon-exon junction complex | 11546873|12718880|16601204 |
| Gene | UPF3B | GO:0045727 | positive regulation of translation | 16601204 |
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 |
| Q9BZI7-1 | Q9BZI7-1_1uw4_A.pdb | 1UW4 | X-ray | 1.95 | A | 50 | 140 |
| 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 |
| Q9BZI7 | UPF3B | Q9BZI7-1 | Q9BZI7-2 | 483 | 470 | 270 | 282 | Deletion | none | none | 269 | 269 |
| Multiple sequence alignment of our canonical and alternatively spliced UPF3B |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of UPF3B |
| UniProt-id | ENSG | ENST | ENSP |
| Q9BZI7-1 | ENSG00000125351.14 | ENST00000276201.7 | ENSP00000276201.3 |
| Q9BZI7-2 | ENSG00000125351.14 | ENST00000345865.6 | ENSP00000245418.2 |
| UniProt-id | NM ID | NP ID |
| Q9BZI7-1 | NM_080632.2 | NP_542199.1 |
| Q9BZI7-2 | NM_023010.3 | NP_075386.1 |
| Amino acid sequences of our canonical and alternatively spliced UPF3B |
| accession_id | Protein sequence |
| Q9BZI7-1 | MKEEKEHRPKEKRVTLLTPAGATGSGGGTSGDSSKGEDKQDRNKEKKEALSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLY PHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPEYRKFLESYATDNEKMTSTPET LLEEIEAKNRELIAKKTTPLLSFLKNKQRMREEKREERRRREIERKRQREEERRKWKEEEKRKRKDIEKLKKIDRIPERDKLKDEPKIKV HRFLLQAVNQKNLLKKPEKGDEKELDKREKAKKLDKENLSDERASGQSCTLPKRSDSELKDEKPKRPEDESGRDYREREREYERDQERIL RERERLKRQEEERRRQKERYEKEKTFKRKEEEMKKEKDTLRDKGKKAESTESIGSSEKTEKKEEVVKRDRIRNKDRPAMQLYQPGARSRN |
| Q9BZI7-2 | MKEEKEHRPKEKRVTLLTPAGATGSGGGTSGDSSKGEDKQDRNKEKKEALSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLY PHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPEYRKFLESYATDNEKMTSTPET LLEEIEAKNRELIAKKTTPLLSFLKNKQRMREEKREERRRREIERKRQREEERRKWKEEEKRKRKDIEKLKKIDRIPERDKLKDEPKIKL LKKPEKGDEKELDKREKAKKLDKENLSDERASGQSCTLPKRSDSELKDEKPKRPEDESGRDYREREREYERDQERILRERERLKRQEEER RRQKERYEKEKTFKRKEEEMKKEKDTLRDKGKKAESTESIGSSEKTEKKEEVVKRDRIRNKDRPAMQLYQPGARSRNRLCPPDDSTKSGD |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| UPF3B (go to UniProt):Q9BZI7 |
| 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 |
| Q9BZI7 | Region | 206 | 483 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=270;End=282 |
| Q9BZI7 | Compositional bias | 206 | 271 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=270;End=282 |
Gene Isoform Structures and Expression Levels for UPF3B |
| Gene structures of our canonical and alternative spliced genes of UPF3B * 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 Q9BZI7-1 |
| 3D view using mol* of Q9BZI7-2 |
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 Q9BZI7-1 |
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| pLDDT distribution across the protein length of Q9BZI7-2 |
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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 Q9BZI7-1 |
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| Ramachandran plot of Q9BZI7-2 |
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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 |
| Q9BZI7-1 | 0.686 | 34 | 0.664 | 56.595 | 0.575 | 0.605 | 0.907 | 1.317 | 0.759 | 1.736 | 2.833 | 71,73,74,75,106,109,110,113,114
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| Q9BZI7-2 | 0.629 | 22 | 0.605 | 46.991 | 0.645 | 0.598 | 0.874 | 1.61 | 0.597 | 2.698 | 1.858 | 71,73,74,75,101,106,109,110,113,114
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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 Q9BZI7-1_Q9BZI7-1_1uw4_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9BZI7-1_1uw4_A_Q9BZI7-2.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9BZI7-1_Q9BZI7-2.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q9BZI7-1_vs_Q9BZI7-2.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q9BZI7-1_vs_Q9BZI7-2.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 UPF3B |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to UPF3B |
| Previous studies relating to the alternative splicing of UPF3B and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
Clinically important variants in UPF3B |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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