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Nfkb1 nuclear factor kappa B subunit 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 81736, updated on 23-Jun-2022

Summary

Official Symbol
Nfkb1provided by RGD
Official Full Name
nuclear factor kappa B subunit 1provided by RGD
Primary source
RGD:70498
See related
Ensembl:ENSRNOG00000023258 AllianceGenome:RGD:70498
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
Also known as
EBP-1; NF-kB
Summary
Enables heat shock protein binding activity; identical protein binding activity; and transcription cis-regulatory region binding activity. Involved in several processes, including cellular response to cytokine stimulus; cellular response to lipid; and regulation of gene expression. Acts upstream of or within cellular response to cytokine stimulus and cellular response to organic cyclic compound. Located in cytosol; neuron projection; and nucleus. Part of protein-containing complex. Used to study fatty liver disease. Biomarker of alcoholic hepatitis; non-alcoholic steatohepatitis; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in several diseases, including carcinoma (multiple); common variable immunodeficiency; melanoma; prostate cancer; and tropical spastic paraparesis. Orthologous to human NFKB1 (nuclear factor kappa B subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Spleen (RPKM 254.0), Lung (RPKM 209.4) and 9 other tissues See more
Orthologs
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Genomic context

See Nfkb1 in Genome Data Viewer
Location:
2q43
Exon count:
25
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (224016214..224132135, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (240773520..240890053, complement)

Chromosome 2 - NC_051337.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120100948 Neighboring gene mannosidase beta Neighboring gene U6 spliceosomal RNA Neighboring gene U2 spliceosomal RNA Neighboring gene 60S ribosomal protein L7 pseudogene Neighboring gene solute carrier family 39 member 8

Genomic regions, transcripts, and products

Expression

  • 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

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

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables actinin binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
 
enables double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
 
enables heat shock protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription coactivator binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in JNK cascade ISO
Inferred from Sequence Orthology
more info
 
involved_in MAPK cascade ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to angiotensin ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to brain-derived neurotrophic factor stimulus IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to carbohydrate stimulus IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within cellular response to cytokine stimulus IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to diterpene IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within cellular response to dsRNA ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to glucoside IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to interleukin-1 IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to interleukin-1 ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to interleukin-6 ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within cellular response to lipopolysaccharide ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to lipopolysaccharide ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to mechanical stimulus ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to nicotine ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cellular response to organic cyclic compound IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to peptide IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to tumor necrosis factor IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to tumor necrosis factor IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within cellular response to tumor necrosis factor ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to virus ISO
Inferred from Sequence Orthology
more info
 
involved_in gene expression ISO
Inferred from Sequence Orthology
more info
 
involved_in leukocyte migration involved in inflammatory response IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in mammary gland involution ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of calcidiol 1-monooxygenase activity ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cytokine production ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of inflammatory response ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of interleukin-12 production ISO
Inferred from Sequence Orthology
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 positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of canonical Wnt signaling pathway ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of hyaluronan biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of miRNA metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of miRNA transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of miRNA-mediated gene silencing IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in response to bacterium IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to copper ion IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to ethanol IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within response to muscle stretch ISO
Inferred from Sequence Orthology
more info
 
involved_in response to organic cyclic compound IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to organic cyclic compound IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in response to oxidative stress IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to xenobiotic stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
 
involved_in system development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of NF-kappaB complex ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
 
located_in neuron projection IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus TAS
Traceable Author Statement
more info
PubMed 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
nuclear factor NF-kappa-B p105 subunit
Names
DNA-binding factor KBF1
nuclear factor of kappa light chain gene enhancer in B-cells 1, p105
nuclear factor of kappa light polypeptide gene enhancer in B-cells 1, p105

NCBI Reference Sequences (RefSeq)

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_001276711.1NP_001263640.1  nuclear factor NF-kappa-B p105 subunit

    Status: VALIDATED

    Source sequence(s)
    JACYVU010000079
    Conserved Domains (8) summary
    cd07935
    Location:40241
    RHD-n_NFkB1; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa B1 (NF-kappa B1)
    cd00204
    Location:573702
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01177
    Location:248349
    IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...
    cd08797
    Location:813887
    Death_NFkB1_p105; Death domain of the Nuclear Factor-KappaB1 precursor protein p105
    pfam12796
    Location:583677
    Ank_2; Ankyrin repeats (3 copies)
    pfam13637
    Location:540599
    Ank_4; Ankyrin repeats (many copies)
    pfam13857
    Location:667723
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:580609
    ANK; ANK repeat [structural motif]

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051337.1 Reference mRatBN7.2 Primary Assembly

    Range
    224016214..224132135 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006233360.4XP_006233422.1  nuclear factor NF-kappa-B p105 subunit isoform X3

    Conserved Domains (8) summary
    cd07935
    Location:41242
    RHD-n_NFkB1; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa B1 (NF-kappa B1)
    cd00204
    Location:574703
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01177
    Location:249350
    IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...
    pfam12796
    Location:584678
    Ank_2; Ankyrin repeats (3 copies)
    pfam13637
    Location:541600
    Ank_4; Ankyrin repeats (many copies)
    pfam13857
    Location:668724
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:581610
    ANK; ANK repeat [structural motif]
    cl14633
    Location:814863
    DD; Death Domain Superfamily of protein-protein interaction domains
  2. XM_006233358.4XP_006233420.1  nuclear factor NF-kappa-B p105 subunit isoform X1

    UniProtKB/TrEMBL
    F1LQH2
    Related
    ENSRNOP00000082290.1, ENSRNOT00000109057.1
    Conserved Domains (8) summary
    cd07935
    Location:41242
    RHD-n_NFkB1; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa B1 (NF-kappa B1)
    cd00204
    Location:574703
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01177
    Location:249350
    IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...
    cd08797
    Location:814888
    Death_NFkB1_p105; Death domain of the Nuclear Factor-KappaB1 precursor protein p105
    pfam12796
    Location:584678
    Ank_2; Ankyrin repeats (3 copies)
    pfam13637
    Location:541600
    Ank_4; Ankyrin repeats (many copies)
    pfam13857
    Location:668724
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:581610
    ANK; ANK repeat [structural motif]
  3. XM_039103225.1XP_038959153.1  nuclear factor NF-kappa-B p105 subunit isoform X2

    Conserved Domains (5) summary
    cd07935
    Location:22223
    RHD-n_NFkB1; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa B1 (NF-kappa B1)
    cd01177
    Location:230331
    IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...
    cd08797
    Location:795869
    Death_NFkB1_p105; Death domain of the Nuclear Factor-KappaB1 precursor protein p105
    sd00045
    Location:562591
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:565659
    Ank_2; Ankyrin repeats (3 copies)
  4. XM_039103226.1XP_038959154.1  nuclear factor NF-kappa-B p105 subunit isoform X4

    Related
    ENSRNOP00000028944.4, ENSRNOT00000036838.5
    Conserved Domains (5) summary
    cd07935
    Location:30231
    RHD-n_NFkB1; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa B1 (NF-kappa B1)
    cd01177
    Location:238339
    IPT_NFkappaB; IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to ...
    cd08797
    Location:803877
    Death_NFkB1_p105; Death domain of the Nuclear Factor-KappaB1 precursor protein p105
    sd00045
    Location:570599
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:573667
    Ank_2; Ankyrin repeats (3 copies)