RFX4 (regulatory factor X4)

Gene

• Entrez ID: 5992
• Gene name: Regulatory factor X4
• Gene symbol: RFX4
• Synonyms (NCBI Gene): NYD-SP10
• Chromosome: 12
• Chromosome location: 12q23.3
• Summary: This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X3, a

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1302415	hsa-miR-129-3p	CLIP-seq
MIRT1302416	hsa-miR-3907	CLIP-seq
MIRT1302417	hsa-miR-4687-5p	CLIP-seq
MIRT1302418	hsa-miR-548q	CLIP-seq
MIRT1302419	hsa-miR-665	CLIP-seq
MIRT1302420	hsa-miR-199a-3p	CLIP-seq
MIRT1302421	hsa-miR-199b-3p	CLIP-seq
MIRT1302422	hsa-miR-3129-5p	CLIP-seq
MIRT1302423	hsa-miR-421	CLIP-seq
MIRT1302424	hsa-miR-4539	CLIP-seq
MIRT1302425	hsa-miR-4709-5p	CLIP-seq
MIRT1302426	hsa-miR-4762-3p	CLIP-seq
MIRT1302427	hsa-miR-505	CLIP-seq
MIRT1302428	hsa-miR-561	CLIP-seq
MIRT1302429	hsa-miR-936	CLIP-seq
MIRT1302430	hsa-miR-101	CLIP-seq
MIRT1302431	hsa-miR-124	CLIP-seq
MIRT1302432	hsa-miR-144	CLIP-seq
MIRT1302433	hsa-miR-19a	CLIP-seq
MIRT1302434	hsa-miR-19b	CLIP-seq
MIRT1302435	hsa-miR-3117-5p	CLIP-seq
MIRT1302436	hsa-miR-4289	CLIP-seq
MIRT1302437	hsa-miR-4452	CLIP-seq
MIRT1302438	hsa-miR-4704-5p	CLIP-seq
MIRT1302439	hsa-miR-502-5p	CLIP-seq
MIRT1302440	hsa-miR-506	CLIP-seq
MIRT1302441	hsa-miR-548an	CLIP-seq
MIRT1302442	hsa-miR-628-5p	CLIP-seq
MIRT2089799	hsa-miR-4744	CLIP-seq
MIRT2314674	hsa-miR-132	CLIP-seq
MIRT2314675	hsa-miR-139-5p	CLIP-seq
MIRT2314676	hsa-miR-212	CLIP-seq
MIRT2314677	hsa-miR-3160-3p	CLIP-seq
MIRT1302431	hsa-miR-124	CLIP-seq
MIRT1302440	hsa-miR-506	CLIP-seq
MIRT1302441	hsa-miR-548an	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	16893423
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	16893423
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005515	Function	Protein binding	IPI	22458338
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0021537	Process	Telencephalon development	IEA
GO:0045879	Process	Negative regulation of smoothened signaling pathway	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	16893423
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0060271	Process	Cilium assembly	IEA
GO:0070613	Process	Regulation of protein processing	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 603958
• HGNC: 9985
• e!Ensembl: ENSG00000111783

Protein

• UniProt ID: Q33E94
• Protein name: Transcription factor RFX4 (Regulatory factor X 4) (Testis development protein NYD-SP10)
• Protein function: Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development. May be required for
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02257	RFX_DNA_binding	58 → 136	RFX DNA-binding domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Isoform 1: Expressed in brain and gliomas (at protein level). Isoform 2: Testis-specific (at protein level). Isoform 3: Testis-specific (at protein level). Isoform 3: Expressed at a higher level in adult testes and ejaculated spermatoz
• Sequence:

  MHCGLLEEPDMDSTESWIERCLNESENKRYSSHTSLGNVSNDENEEKENNRASKPHSTPA
  TLQWLEENYEIAEGVCIPRSALYMHYLDFCEKNDTQPVNAASFGKIIRQQFPQLTTRRLG
  TRGQSKYHYYGIAVKESSQYYDVMYSKKGAAWVSETGKKEVSKQTVAYSPRSKLGTLLPE
  FPNVKDLNLPASLPEEKVSTFIMMYRTHCQRILDTVIRANFDEVQSFLLHFWQGMPPHML
  PVLGSSTVVNIVGVCDSILYKAISGVLMPTVLQALPDSLTQVIRKFAKQLDEWLKVALHD
  LPENLRNIKFELSRRFSQILRRQTSLNHLCQASRTVIHSADITFQMLEDWRNVDLNSITK
  QTLYTMEDSRDEHRKLITQLYQEFDHLLEEQSPIESYIEWLDTMVDRCVVKVAAKRQGSL
  KKVAQQFLLMWSCFGTRVIRDMTLHSAPSFGSFHLIHLMFDDYVLYLLESLHCQERANEL
  MRAMKGEGSTAEVREEIILTEAAAPTPSPVPSFSPAKSATSVEVPPPSSPVSNPSPEYTG
  LSTTGAMQSYTWSLTYTVTTAAGSPAENSQQLPCMRNTHVPSSSVTHRIPVYPHREEHGY
  TGSYNYGSYGNQHPHPMQSQYPALPHDTAISGPLHYAPYHRSSAQYPFNSPTSRMEPCLM
  SSTPRLHPTPVTPRWPEVPSANTCYTSPSVHSARYGNSSDMYTPLTTRRNSEYEHMQHFP
  GFAYINGEASTGWAK

• Sequence length: 735

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FLUTTER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PARKINSON DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RFX4-related disorder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	33658631	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	33658631	Associate	★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	Pubtator	18378158	Associate	★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar Disorder	BEFREE	15940297, 17510980		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	LHGDN	15940297		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	PSYGENET_DG	15940297, 17510980		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar disorder	Pubtator	24393808	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain Diseases	Brain disease	Pubtator	18378158	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	11682486	Associate	★☆☆☆☆ Found in Text Mining only
Common ventricle	Complete Atrioventricular Canal Defect	BEFREE	29298325		★☆☆☆☆ Found in Text Mining only
Congenital Hydrocephalus	Congenital Hydrocephalus	BEFREE	29298325		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	16271074	Associate	★☆☆☆☆ Found in Text Mining only
Holoprosencephaly	Holoprosencephaly	BEFREE	29298325		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	33658631	Associate	★☆☆☆☆ Found in Text Mining only
Narcolepsy	Narcolepsy	Pubtator	33837283	Associate	★☆☆☆☆ Found in Text Mining only
Narcolepsy 1	Narcolepsy	Pubtator	33837283	Associate	★☆☆☆☆ Found in Text Mining only
Single Ventricle Defect	Single Ventricle Defect	BEFREE	29298325		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	36045400	Stimulate	★☆☆☆☆ Found in Text Mining only