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

    Gene ID: 4799, updated on 10-Dec-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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    See NFX1 in Genome Data Viewer
    Location:
    9p13.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (33290516..33371157)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (33309149..33389758)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. 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
    2. 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
    3. A novel cysteine-rich sequence-specific DNA-binding protein interacts with the conserved X-box motif of the human major histocompatibility complex class II genes via a repeated Cys-His domain and functions as a transcriptional repressor. Song Z, et al. J Exp Med, 1994 Nov 1. PMID 7964459, 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 (67) 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)

    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
    located_in 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_2024_08

    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

      UniProtKB/TrEMBL
      A0JLR2

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

      UniProtKB/TrEMBL
      A0JLR2
      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

      UniProtKB/TrEMBL
      A0JLR2

    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

      UniProtKB/TrEMBL
      A0JLR2

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

      UniProtKB/TrEMBL
      A0JLR2

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

      UniProtKB/TrEMBL
      A0JLR2

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

      UniProtKB/TrEMBL
      A0JLR2

    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

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