{"uniprot":"Q2KHR2","gene":"RFX7","name":"DNA-binding protein RFX7","organism":"Homo sapiens (Human)","status":"dark","length":1460,"sequence":"MAEEQQQPPPQQPDAHQQLPPSAPNSGVALPALVPGLPGTEASALQHKIKNSICKTVQSKVDCILQEVEKFTDLEKLYLYLQLPSGLSNGEKSDQNAMSSSRAQQMHAFSWIRNTLEEHPETSLPKQEVYDEYKSYCDNLGYHPLSAADFGKIMKNVFPNMKARRLGTRGKSKYCYSGLRKKAFVHMPTLPNLDFHKTGDGLEGAEPSGQLQNIDEEVISSACRLVCEWAQKVLSQPFDTVLELARFLVKSHYIGTKSMAALTVMAAAPAGMKGITQPSAFIPTAESNSFQPQVKTLPSPIDAKQQLQRKIQKKQQEQKLQSPLPGESAAKKSESATSNGVTNLPNGNPSILSPQPIGIVVAAVPSPIPVQRTRQLVTSPSPMSSSDGKVLPLNVQVVTQHMQSVKQAPKTPQNVPASPGGDRSARHRYPQILPKPANTSALTIRSPTTVLFTSSPIKTAVVPASHMSSLNVVKMTTISLTPSNSNTPLKHSASVSSATGTTEESRSVPQIKNGSVVSLQSPGSRSSSAGGTSAVEVKVEPETSSDEHPVQCQENSDEAKAPQTPSALLGQKSNTDGALQKPSNEGVIEIKATKVCDQRTKCKSRCNEMLPGTSTGNNQSTITLSVASQNLTFTSSSSPPNGDSINKDPKLCTKSPRKRLSSTLQETQVPPVKKPIVEQLSAATIEGQKQGSVKKDQKVPHSGKTEGSTAGAQIPSKVSVNVSSHIGANQPLNSSALVISDSALEQQTTPSSSPDIKVKLEGSVFLLDSDSKSVGSFNPNGWQQITKDSEFISASCEQQQDISVMTIPEHSDINDLEKSVWELEGMPQDTYSQQLHSQIQESSLNQIQAHSSDQLPLQSELKEFEPSVSQTNESYFPFDDELTQDSIVEELVLMEQQMSMNNSHSYGNCLGMTLQSQSVTPGAPMSSHTSSTHFYHPIHSNGTPIHTPTPTPTPTPTPTPTPTPTSEMIAGSQSLSRESPCSRLAQTTPVDSALGSSRHTPIGTPHSNCSSSVPPSPVECRNPFAFTPISSSMAYHDASIVSSSPVKPMQRPMATHPDKTKLEWMNNGYSGVGNSSVSGHGILPSYQELVEDRFRKPHAFAVPGQSYQSQSRHHDTHFGRLTPVSPVQHQGATVNNTNKQEGFAVPAPLDNKGTNSSASSNFRCRSVSPAVHRQRNLSGSTLYPVSNIPRSNVTPFGSPVTPEVHVFTNVHTDACANNIAQRSQSVPLTVMMQTAFPNALQKQANSKKITNVLLSKLDSDNDDAVRGLGMNNLPSNYTARMNLTQILEPSTVFPSANPQNMIDSSTSVYEFQTPSYLTKSNSTGQINFSPGDNQAQSEIGEQQLDFNSTVKDLLSGDSLQTNQQLVGQGASDLTNTASDFSSDIRLSSELSGSINDLNTLDPNLLFDPGRQQGQDDEATLEELKNDPLFQQICSESMNSMTSSGFEWIESKDHPTVEMLG","function_summary":"A nuclear transcriptional regulator that uses a central winged-helix DNA-binding module to recognize specific promoter elements and assemble coactivator complexes that enhance RNA polymerase II–dependent transcription. By coupling high-affinity DNA recognition with multivalent protein-binding surfaces, it promotes gene activation programs that shape developmental pathways and likely fine-tunes transcriptional circuits in embryonic stem cells within the nucleoplasm.","plain_language":"RFX7 has barely been studied. The model's best guess: A nuclear transcriptional regulator that uses a central winged-helix DNA-binding module to recognize specific promoter elements and assemble coactivator complexes that enhance RNA polymerase II–dependent transcription. By coupling high-affinity DNA recognition with multivalent protein-binding surfaces, it promotes gene activation programs that shape developmental pathways and likely fine-tunes transcriptional circuits in embryonic stem cells within the nucleoplasm.","uniprot_summary":"Probable transcription factor that may have a role in the development of malformations of the heart, brain, eyes, ears and kidneys (By similarity). May have a role in embryonic stem cell self-renewal.","go_terms":{"molecular_function":[{"id":"GO:1990837","label":"sequence-specific double-stranded DNA binding"},{"id":"GO:0005515","label":"protein binding"}],"biological_process":[{"id":"GO:0045944","label":"positive regulation of transcription by RNA polymerase II"}],"cellular_component":[{"id":"GO:0005654","label":"nucleoplasm"}]},"interpro":[{"id":"IPR036388","name":"Winged helix-like DNA-binding domain superfamily","type":"homologous_superfamily","start":108,"end":183},{"id":"IPR036390","name":"Winged helix DNA-binding domain superfamily","type":"homologous_superfamily","start":109,"end":182},{"id":"IPR003150","name":"DNA-binding RFX-type, winged-helix domain","type":"domain","start":106,"end":183},{"id":"IPR039779","name":"RFX-like DNA-binding protein","type":"family","start":5,"end":1061}],"reasoning":"I begin with the InterPro architecture. The protein carries a central winged-helix DNA-binding module annotated by IPR003150 (DNA-binding RFX-type, winged-helix domain, residues 106–183). This fold is reinforced by two overlapping superfamily signatures—IPR036388 (Winged helix-like DNA-binding domain superfamily, residues 108–183) and IPR036390 (Winged helix DNA-binding domain superfamily, residues 109–182)—which together define a compact helix-turn-helix core with β-strands that form “wings” for sequence-specific DNA recognition and minor-groove contacts. The N-to-C layout therefore places a single RFX-type winged-helix domain centrally, embedded within a much larger family-defining scaffold IPR039779 (RFX-like DNA-binding protein family, residues 5–1061) that spans nearly the entire polypeptide and typically encodes regulatory and oligomerization surfaces. This architecture causes high-affinity, sequence-specific binding to double-stranded DNA and provides extensive protein–protein interaction interfaces.\n\nFrom this domain logic, the molecular function resolves into two complementary activities. First, the winged-helix core directly confers GO:1990837 sequence-specific double-stranded DNA binding, consistent with recognition of defined promoter elements. Second, the extended family scaffold and flanking regions supply multivalent surfaces for assembling transcriptional complexes, supporting GO:0005515 protein binding. Together, these features define a DNA-anchored transcriptional regulator that recruits cofactors.\n\nAnchoring to DNA and recruiting cofactors naturally drives transcriptional control. The RFX-type architecture is classically used to activate RNA polymerase II–dependent genes by stabilizing preinitiation and coactivator assemblies. This causally links the DNA-binding and protein-binding capacities to GO:0045944 positive regulation of transcription by RNA polymerase II. In developmental contexts, such activation can tune gene networks that specify cell fate and organ patterning.\n\nCellular localization follows from function and architecture. A soluble, sequence-specific DNA-binding regulator operates in the nuclear interior where chromatin and the transcriptional machinery reside. Thus, the most precise compartmentalization is the GO:0005654 nucleoplasm, consistent with a nuclear soluble regulator rather than a chromatin-embedded enzyme or membrane-bound factor.\n\nMechanistically, I hypothesize that the protein binds promoter-proximal elements via its RFX-type winged-helix domain and nucleates assemblies with general transcription factors and coactivators to enhance RNA polymerase II initiation and elongation. Likely partners include TFIID and Mediator for core promoter engagement, CBP/p300 and SWI/SNF for chromatin acetylation and nucleosome remodeling, and other RFX-like factors for homo-/hetero-oligomerization. In embryonic stem cell contexts, this assembly would bias transcriptional programs that balance self-renewal and differentiation cues within the nucleoplasm.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-Q2KHR2.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/Q2KHR2"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/Q2KHR2/entry","atlas":"/p/Q2KHR2"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}