U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Nfx1 nuclear transcription factor, X-box binding 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313166, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Nfx1provided by RGD
    Official Full Name
    nuclear transcription factor, X-box binding 1provided by RGD
    Primary source
    RGD:1310277
    See related
    EnsemblRapid:ENSRNOG00000009015 AllianceGenome:RGD:1310277
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and ubiquitin protein ligase activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II and protein autoubiquitination. Predicted to act upstream of or within negative regulation of MHC class II biosynthetic process. Predicted to be located in cytosol; nuclear lumen; and plasma membrane. Predicted to be active in nucleus. Orthologous to human NFX1 (nuclear transcription factor, X-box binding 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 182.0), Liver (RPKM 126.8) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Nfx1 in Genome Data Viewer
    Location:
    5q22
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (60900140..60958889)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (56104945..56162912)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (57290916..57348720)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene BAG cochaperone 1 Neighboring gene charged multivesicular body protein 5 Neighboring gene aquaporin 7 Neighboring gene U6 spliceosomal RNA

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. 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
    2. Murine NFX.1: isolation and characterization of its messenger RNA, mapping of its chromosomal location and assessment of its developmental expression. Arlotta P, et al. Immunology, 2002 Jun. PMID 12047746, Free PMC Article
    3. RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination. Lorick KL, et al. Proc Natl Acad Sci U S A, 1999 Sep 28. PMID 10500182, Free PMC Article
    4. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    5. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of MHC class II biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein autoubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    transcriptional repressor NF-X1
    NP_001019955.2
    XP_008761845.1
    XP_063143670.1
    XP_063143671.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001024784.2 → NP_001019955.2  transcriptional repressor NF-X1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A8I6AMR9, A6IIT2, D4AE50
      Related
      ENSRNOP00000057423.2, ENSRNOT00000060692.6
      Conserved Domains (2) summary
      cd02643
      Location:981 → 1054
      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:616 → 668
      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 ...

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      60900140..60958889
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008763623.4 → XP_008761845.1  transcriptional repressor NF-X1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6ALJ0, Q4V7B3
      Related
      ENSRNOP00000096312.2, ENSRNOT00000105959.2
      Conserved Domains (1) summary
      cd06008
      Location:616 → 668
      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. XM_063287600.1 → XP_063143670.1  transcriptional repressor NF-X1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AMR9
      Related
      ENSRNOP00000108253.1, ENSRNOT00000160551.1

    3. XM_063287601.1 → XP_063143671.1  transcriptional repressor NF-X1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AMR9
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools