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

Gene ID: 4799, updated on 4-Jun-2020

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
109.20200522 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 PubChem

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 autoubiquitination 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 Updated Annotation Release 109.

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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