Protein:POU5F1 |
Protein Summary |
 Gene summary |
| Gene name: POU5F1 | ASpdb.0 ID: 5460 | Gene | Gene symbol | POU5F1 | Gene ID | 5460 |
| Gene name | POU class 5 homeobox 1 |
| Synonyms | OCT3|OCT4|OTF-3|OTF3|OTF4|Oct-3|Oct-4|Oct3/4 |
| Cytomap | 6p21.33 |
| Type of gene | protein-coding |
| Description | POU domain, class 5, transcription factor 1POU domain transcription factor OCT4POU-type homeodomain-containing DNA-binding proteinoctamer-binding protein 3octamer-binding protein 4octamer-binding transcription factor 3 |
| Modification date | 20240407 |
| UniProtAcc | Q01860 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | POU5F1 | GO:0000122 | negative regulation of transcription by RNA polymerase II | 19409607 |
| Gene | POU5F1 | GO:0000976 | transcription cis-regulatory region binding | 19409607 |
| Gene | POU5F1 | GO:0001227 | DNA-binding transcription repressor activity, RNA polymerase II-specific | 19409607 |
| Gene | POU5F1 | GO:0001714 | endodermal cell fate specification | 20713518 |
| Gene | POU5F1 | GO:0003677 | DNA binding | 16153702 |
| Gene | POU5F1 | GO:0003700 | DNA-binding transcription factor activity | 16153702 |
| Gene | POU5F1 | GO:0005634 | nucleus | 18000303|18191611|19274063|21828274 |
| Gene | POU5F1 | GO:0005654 | nucleoplasm | 20458727 |
| Gene | POU5F1 | GO:0005737 | cytoplasm | 18281244|20458727|21828274 |
| Gene | POU5F1 | GO:0005739 | mitochondrion | - |
| Gene | POU5F1 | GO:0005829 | cytosol | 18000303 |
| Gene | POU5F1 | GO:0006355 | regulation of DNA-templated transcription | 16153702 |
| Gene | POU5F1 | GO:0035019 | somatic stem cell population maintenance | 19409607 |
| Gene | POU5F1 | GO:0035198 | miRNA binding | 18710938|19409607 |
| Gene | POU5F1 | GO:0043565 | sequence-specific DNA binding | 20713518 |
| Gene | POU5F1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20713518 |
| Gene | POU5F1 | GO:1902894 | negative regulation of miRNA transcription | 19409607 |
| Gene | POU5F1 | GO:1990837 | sequence-specific double-stranded DNA binding | 28473536 |
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 |
| Q01860-1 | Q01860-1_6t90_K.pdb | 6T90 | EM | 3.05 | K | 138 | 210 |
| 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 |
| Q01860 | POU5F1 | Q01860-1 | Q01860-2 | 360 | 265 | 1 | 135 | Substitution | MAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGGLETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEE | MHFYRLFLGATRRFLNPEWKGEIDNWCVYVLTSLLPFKIQ | 1 | 40 |
| Multiple sequence alignment of our canonical and alternatively spliced POU5F1 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of POU5F1 |
| UniProt-id | ENSG | ENST | ENSP |
| Q01860-1 | ENSG00000204531.21 | ENST00000259915.13 | ENSP00000259915.7 |
| Q01860-1 | ENSG00000206454.12 | ENST00000383524.4 | ENSP00000373016.4 |
| Q01860-1 | ENSG00000233911.9 | ENST00000429603.2 | ENSP00000392877.2 |
| Q01860-1 | ENSG00000235068.9 | ENST00000433063.6 | ENSP00000405041.2 |
| Q01860-1 | ENSG00000229094.9 | ENST00000434616.2 | ENSP00000388842.2 |
| Q01860-1 | ENSG00000237582.10 | ENST00000437747.6 | ENSP00000391681.2 |
| Q01860-1 | ENSG00000230336.9 | ENST00000454714.6 | ENSP00000400047.2 |
| Q01860-2 | ENSG00000206454.12 | ENST00000376243.8 | ENSP00000365419.4 |
| Q01860-2 | ENSG00000229094.9 | ENST00000412166.6 | ENSP00000387646.2 |
| Q01860-2 | ENSG00000235068.9 | ENST00000419095.2 | ENSP00000413622.2 |
| Q01860-2 | ENSG00000237582.10 | ENST00000429314.2 | ENSP00000387619.2 |
| Q01860-2 | ENSG00000230336.9 | ENST00000433348.2 | ENSP00000412665.2 |
| Q01860-2 | ENSG00000233911.9 | ENST00000451077.6 | ENSP00000391507.2 |
| UniProt-id | NM ID | NP ID |
| Q01860-1 | NM_002701.5 | NP_002692.2 |
| Q01860-2 | NM_001285987.1 | NP_001272916.1 |
| Amino acid sequences of our canonical and alternatively spliced POU5F1 |
| accession_id | Protein sequence |
| Q01860-1 | MAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGGL ETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFS QTTICRFEALQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLE KDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPVSVTTLGSPMHSN |
| Q01860-2 | MHFYRLFLGATRRFLNPEWKGEIDNWCVYVLTSLLPFKIQSQDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTIC RFEALQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVR |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| POU5F1 (go to UniProt):Q01860 |
| 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 |
| Q01860 | Region | 1 | 52 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=1;End=135 |
| Q01860 | Region | 88 | 114 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=1;End=135 |
| Q01860 | Motif | 4 | 12 | Note=9aaTAD;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:34342803;Dbxref=PMID:34342803 | Type=Substitution;Start=1;End=135 |
Gene Isoform Structures and Expression Levels for POU5F1 |
| Gene structures of our canonical and alternative spliced genes of POU5F1 * 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 Q01860-1 |
| 3D view using mol* of Q01860-2 |
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 Q01860-1 |
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| pLDDT distribution across the protein length of Q01860-2 |
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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 Q01860-1 |
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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 |
| Q01860-1 | 0.846 | 64 | 0.879 | 175.273 | 0.665 | 0.586 | 0.753 | 0.779 | 0.689 | 1.13 | 0.462 | 234,235,236,237,239,242,246,272,273,276,277,280,28 1,284 |
| Q01860-2 | 0.874 | 38 | 0.932 | 111.475 | 0.563 | 0.678 | 0.877 | 2.736 | 0.166 | 16.507 | 3.395 | 3,6,7,10,11,14,27,30,31,34
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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 Q01860-1_Q01860-1_6t90_K.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q01860-1_6t90_K_Q01860-2.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q01860-1_Q01860-2.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q01860-1_vs_Q01860-2.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q01860-1_vs_Q01860-2.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 POU5F1 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to POU5F1 |
| Previous studies relating to the alternative splicing of POU5F1 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| POU5F1 | 20433421 | Oct-4B isoform is differentially expressed in breast cancer cells: hypermethylation of regulatory elements of Oct-4A suggests an alternative promoter and transcriptional start site for Oct-4B transcription. | The human Oct-4 gene has three isoforms, Oct-4A, Oct-4B and Oct-4B1, which are thought to be derived from alternative splicing. It remains controversial whether the Oct-4 gene is expressed in cancer cells. Expression of Oct-4A is regulated by two elements, the PE (proximal enhancer) and DE (distal enhancer), but the expression and regulation of Oct-4B are not well known. Here, we firstly report that Oct-4B is expressed at low levels in MCF-7 cells, while the Oct-4A gene is inactivated. By analysing the function of different promoter constructs and the DNA methylation status of three regulatory regions, we demonstrate that the Oct-4A gene in MCF-7 cells is repressed by epigenetic control rather than transcriptional control. In addition, we speculate that the transcription of Oct-4B in MCF-7 cells is differentially regulated by additional regulatory elements. This work will enhance the understanding of Oct-4 gene in differential regulation. | D001943 | Breast Neoplasms |
| POU5F1 | 23636800 | Prognostication of OCT4 isoform expression in prostate cancer. | Cancer stem cells (CSCs) refer to a subset of tumor cells that self-renew and affect tumor heterogeneity. This model has attracted considerable interest in recent years due to its implications in the prognosis and clinical management of cancer because CSCs mediate the occurrence, growth, and recurrence of tumors. OCT4 is central to embryonic stem cell self-renewal and differentiation into specific lineages and encodes two chief isoforms that are generated by alternative splicing--OCT4A and OCT4B. Their function in prostate cancer (PCa) is unknown. The prognostic function of OCT4 isoforms in PCa samples was examined by immunohistochemistry (IHC) and sensitivity and specificity of the antibodies used were evaluated by molecular biology techniques. Biochemical and pathological data and specimens from 193 patients with PCa were evaluated retrospectively. IHC, western blot, immunofluorescence, and automated image analysis were also performed. IHC was performed on a tissue microarray, and western blot and immunofluorescence were performed using the PCa cell line DU-145. IHC expression of OCT4 isoforms correlated with biochemical and pathological parameters, particularly biochemical recurrence-free survival (BCRFS). Patients with higher levels of OCT4B had lower Gleason scores and decreased likelihood of experiencing biochemical recurrence (BR). OCT4A(+) OCT4B(-) patients had the shortest BCRFS, and positivity for OCT4B expression was an independent prognostic factor for BCRFS in the multivariate analysis. We conclude that the expression of OCT4B is a strong marker of good prognosis, and its presence is associated with a decreased likelihood of BR. Thus, OCT4B might represent a powerful clinical prognostic biomarker for PCa patients. | D000230 | Adenocarcinoma |
| POU5F1 | 23636800 | Prognostication of OCT4 isoform expression in prostate cancer. | Cancer stem cells (CSCs) refer to a subset of tumor cells that self-renew and affect tumor heterogeneity. This model has attracted considerable interest in recent years due to its implications in the prognosis and clinical management of cancer because CSCs mediate the occurrence, growth, and recurrence of tumors. OCT4 is central to embryonic stem cell self-renewal and differentiation into specific lineages and encodes two chief isoforms that are generated by alternative splicing--OCT4A and OCT4B. Their function in prostate cancer (PCa) is unknown. The prognostic function of OCT4 isoforms in PCa samples was examined by immunohistochemistry (IHC) and sensitivity and specificity of the antibodies used were evaluated by molecular biology techniques. Biochemical and pathological data and specimens from 193 patients with PCa were evaluated retrospectively. IHC, western blot, immunofluorescence, and automated image analysis were also performed. IHC was performed on a tissue microarray, and western blot and immunofluorescence were performed using the PCa cell line DU-145. IHC expression of OCT4 isoforms correlated with biochemical and pathological parameters, particularly biochemical recurrence-free survival (BCRFS). Patients with higher levels of OCT4B had lower Gleason scores and decreased likelihood of experiencing biochemical recurrence (BR). OCT4A(+) OCT4B(-) patients had the shortest BCRFS, and positivity for OCT4B expression was an independent prognostic factor for BCRFS in the multivariate analysis. We conclude that the expression of OCT4B is a strong marker of good prognosis, and its presence is associated with a decreased likelihood of BR. Thus, OCT4B might represent a powerful clinical prognostic biomarker for PCa patients. | D011471 | Prostatic Neoplasms |
Clinically important variants in POU5F1 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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