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

    Gene ID: 4799, updated on 12-Oct-2019

    Summary

    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
    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

    Genomic context

    See NFX1 in Genome Data Viewer
    Location:
    9p13.3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    109.20190905 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (33290475..33371157)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (33290418..33371155)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene charged multivesicular body protein 5 Neighboring gene nucleus accumbens associated 1, BEN and BTB (POZ) domain containing pseudogene Neighboring gene uncharacterized LOC105376018 Neighboring gene uncharacterized LOC105376020 Neighboring gene aquaporin 7 Neighboring gene aquaporin 3 (Gill blood group)

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC20369, DKFZp779G2416

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    inflammatory response TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of MHC class II biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein ubiquitination TAS
    Traceable Author Statement
    more info
    PubMed 
    regulation of transcription, DNA-templated IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    PubMed 
    viral process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    nuclear chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    transcriptional repressor NF-X1
    Names
    nuclear transcription factor, X box-binding protein 1
    NP_001305687.1
    NP_002495.2
    NP_667345.1

    NCBI Reference Sequences (RefSeq)

    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_001318758.2NP_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:9881061
      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:622674
      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_002504.6NP_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
      Q12986
      Related
      ENSP00000368856.3, ENST00000379540.8
      Conserved Domains (3) summary
      cd02643
      Location:9871060
      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:622674
      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:356409
      RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins
    3. NM_147134.4NP_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/Swiss-Prot
      Q12986
      Related
      ENSP00000317695.6, ENST00000318524.6
      Conserved Domains (2) summary
      cd06008
      Location:622674
      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:356409
      RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

      Range
      33290475..33371157
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_001746311.2 RNA Sequence

    2. XR_001746313.2 RNA Sequence

    3. XR_001746310.2 RNA Sequence

    4. XR_001746312.2 RNA Sequence

    5. XR_001746314.2 RNA Sequence

    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.
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