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NFX1 nuclear transcription factor, X-box binding 1 [ Homo sapiens (human) ]

Gene ID: 4799, updated on 3-Apr-2024

Summary

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Official Symbol
NFX1provided by HGNC
Official Full Name
nuclear transcription factor, X-box binding 1provided by HGNC
Primary source
HGNC:HGNC:7803
See related
Ensembl:ENSG00000086102 MIM:603255; AllianceGenome:HGNC:7803
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NFX2; Tex42; TEG-42
Summary
MHC class II gene expression is controlled primarily at the transcriptional level by transcription factors that bind to the X and Y boxes, two highly conserved elements in the proximal promoter of MHC class II genes. The protein encoded by this gene is a transcriptional repressor capable of binding to the conserved X box motif of HLA-DRA and other MHC class II genes in vitro. The protein may play a role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by IFN-gamma. Three alternative splice variants, each of which encodes a different isoform, have been identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 8.4), lymph node (RPKM 6.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
9p13.3
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (33290516..33371157)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (33309149..33389758)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (33290514..33371155)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28291 Neighboring gene charged multivesicular body protein 5 Neighboring gene nucleus accumbens associated 1, BEN and BTB (POZ) domain containing pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33288443-33289404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28292 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:33290559-33291758 Neighboring gene MPRA-validated peak7217 silencer Neighboring gene uncharacterized LOC105376018 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:33372618-33373118 Neighboring gene uncharacterized LOC124902142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33380602-33381202 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33381203-33381801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33383370-33383870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33383871-33384371 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:33385863-33387062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33390288-33391075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33391076-33391862 Neighboring gene aquaporin 7 Neighboring gene Sharpr-MPRA regulatory region 4081 Neighboring gene uncharacterized LOC105376020

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. High expression of NFX1-123 in HPV positive head and neck squamous cell carcinomas. Chintala S, et al. Head Neck, 2022 Jan. PMID 34693597, Free PMC Article
  2. Congenital immunodeficiencies associated with absence of HLA class II antigens on lymphocytes result from distinct mutations in trans-acting factors. Hume CR, et al. Hum Immunol, 1989 Dec. PMID 2511169
  3. NFX1-123 is highly expressed in cervical cancer and increases growth and telomerase activity in HPV 16E6 expressing cells. Vliet-Gregg PA, et al. Cancer Lett, 2019 May 1. PMID 30776478, Free PMC Article
  4. Human papillomavirus type 16 E6 and NFX1-123 mislocalize immune signaling proteins and downregulate immune gene expression in keratinocytes. Levan J, et al. PLoS One, 2017. PMID 29117186, Free PMC Article
  5. NFX1 plays a role in human papillomavirus type 16 E6 activation of NFkappaB activity. Xu M, et al. J Virol, 2010 Nov. PMID 20739528, Free PMC Article

See all (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. High expression of NFX1-123 in HPV positive head and neck squamous cell carcinomas.
    Title: High expression of NFX1-123 in HPV positive head and neck squamous cell carcinomas.
  2. we found that NFX1-123 was a bona fide substrate of the deubiquitinase USP9X and that it could be degraded by the ubiquitin-proteasome system. The present study provided new insight into understanding the biological function of USP9X by targeting its substrate NFX1-123.
    Title: Identification of a USP9X Substrate NFX1-123 by SILAC-Based Quantitative Proteomics.
  3. initial mRNP binding to the NPC did not require NXF1 in the NPC, whereas release into the cytoplasm did. NXF1 localization in the NPC did not require RNA or RNA binding. Superresolution microscopy showed that NXF1 consistently occupied positions on the cytoplasmic side of the NPC.
    Title: Imaging within single NPCs reveals NXF1's role in mRNA export on the cytoplasmic side of the pore.
  4. Results indicate that NFX1-123 is markedly increased in cervical cancer, its greater expression in 16E6 expressing cells is associated with improved growth and telomerase activity, and that this association is maintained in HPV 16 positive cervical cancer cell lines.
    Title: NFX1-123 is highly expressed in cervical cancer and increases growth and telomerase activity in HPV 16E6 expressing cells.
  5. NFX1-123 in mediating epithelial differentiation through the JNK signaling pathway.
    Title: HPV type 16 E6 and NFX1-123 augment JNK signaling to mediate keratinocyte differentiation and L1 expression.
  6. This study identifies NFX1-123 as a critical host protein partner through which 16E6 is able to subvert the immune response and in turn permit a long-lived high-risk Human papillomavirus infection.
    Title: Human papillomavirus type 16 E6 and NFX1-123 mislocalize immune signaling proteins and downregulate immune gene expression in keratinocytes.
  7. The results showed that a repressor complex composed of NFX1-91, mSin3A and histone deacetylase 1 was involved in the PKC-delta-induced repression of the hTERT promoter, which resulted in the repression of hTERT transcription.
    Title: Involvement of the NFX1-repressor complex in PKC-δ-induced repression of hTERT transcription.
  8. Human papillomavirus 16 E6 (16E6) interacts with the cellular protein NFX1-123, and they collaboratively increase the growth and differentiation master regulator, Notch1.
    Title: Human papillomavirus 16E6 and NFX1-123 potentiate Notch signaling and differentiation without activating cellular arrest.
  9. NFX1-123 and human papillomavirus 16E6 upregulated Notch 1 expression in keratinocytes.
    Title: NFX1-123 and human papillomavirus 16E6 increase Notch expression in keratinocytes.
  10. a mechanism for HPV16 E6 activation of the NFkappaB pathway through NFX1-91
    Title: NFX1 plays a role in human papillomavirus type 16 E6 activation of NFkappaB activity.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC20369, DKFZp779G2416

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in inflammatory response TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of MHC class II biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein autoubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination TAS
Traceable Author Statement
more info
 PubMed 
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
transcriptional repressor NF-X1
Names
nuclear transcription factor, X box-binding protein 1
NP_001305687.1
NP_002495.2
NP_667345.1
XP_047279383.1
XP_047279384.1
XP_047279385.1
XP_054218977.1
XP_054218978.1
XP_054218979.1
XP_054218980.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029578.1 RefSeqGene

    Range
    5097..85738
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001318758.2 → NP_001305687.1  transcriptional repressor NF-X1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in an internal exon, compared to variant 1. It encodes isoform 4 which is longer than isoform 1.
    Source sequence(s)
    AI884552, AL356218, AL356472, AL832342, DA290058
    Conserved Domains (2) summary
    cd02643
    Location:988 → 1061
    R3H_NF-X1; R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown ...
    cd06008
    Location:622 → 674
    NF-X1-zinc-finger; Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger ...

  2. NM_002504.6 → NP_002495.2  transcriptional repressor NF-X1 isoform 1

    See identical proteins and their annotated locations for NP_002495.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    BC012151, BP871782, DB076795
    Consensus CDS
    CCDS6538.1
    UniProtKB/Swiss-Prot
    A8K6H8, Q12986, Q5VXW6, Q96EL5, Q9BXI1
    Related
    ENSP00000368856.3, ENST00000379540.8
    Conserved Domains (3) summary
    cd02643
    Location:987 → 1060
    R3H_NF-X1; R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown ...
    cd06008
    Location:622 → 674
    NF-X1-zinc-finger; Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger ...
    cd16696
    Location:356 → 409
    RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins

  3. NM_147134.4 → NP_667345.1  transcriptional repressor NF-X1 isoform 3

    See identical proteins and their annotated locations for NP_667345.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) utilizes an alternate 3' terminal exon compared to variant 1 and encodes the shortest isoform (3), with a unique C-terminus.
    Source sequence(s)
    AK225750, AL356472, DA290058, DB076795
    Consensus CDS
    CCDS6540.1
    UniProtKB/TrEMBL
    A0JLR2
    Related
    ENSP00000317695.6, ENST00000318524.6
    Conserved Domains (2) summary
    cd06008
    Location:622 → 674
    NF-X1-zinc-finger; Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger ...
    cd16696
    Location:356 → 409
    RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    33290516..33371157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423427.1 → XP_047279383.1  transcriptional repressor NF-X1 isoform X1

  2. XM_047423429.1 → XP_047279385.1  transcriptional repressor NF-X1 isoform X3

    Conserved Domains (2) summary
    cd06008
    Location:622 → 674
    NF-X1-zinc-finger; Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger ...
    cd16696
    Location:356 → 409
    RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins

  3. XM_047423428.1 → XP_047279384.1  transcriptional repressor NF-X1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    33309149..33389758
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363002.1 → XP_054218977.1  transcriptional repressor NF-X1 isoform X1

  2. XM_054363004.1 → XP_054218979.1  transcriptional repressor NF-X1 isoform X3

  3. XM_054363003.1 → XP_054218978.1  transcriptional repressor NF-X1 isoform X2

  4. XM_054363005.1 → XP_054218980.1  transcriptional repressor NF-X1 isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_147133.2: Suppressed sequence

    Description
    NM_147133.2: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q12986.2 GenPept UniProtKB/Swiss-Prot:Q12986

Gene LinkOut

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