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nfkb2 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) [ Danio rerio (zebrafish) ]

Gene ID: 415100, updated on 11-Apr-2024

Summary

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Official Symbol
nfkb2provided by ZNC
Official Full Name
nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)provided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-6701
See related
Ensembl:ENSDARG00000038687 AllianceGenome:ZFIN:ZDB-GENE-030131-6701
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
p100; wu:fa03b02; zgc:136693
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within angiogenesis and cholesterol homeostasis. Predicted to be located in cytoplasm and nucleus. Is expressed in male organism and retina. Human ortholog(s) of this gene implicated in common variable immunodeficiency. Orthologous to human NFKB2 (nuclear factor kappa B subunit 2). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 13
Exon count:
25
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (22717355..22735561)
105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (22586916..22605111)

Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene zgc:193505 Neighboring gene glutamate dehydrogenase 1a Neighboring gene shieldin complex subunit 2 Neighboring gene pleckstrin and Sec7 domain containing a Neighboring gene uncharacterized LOC100001713 Neighboring gene DNA replication helicase/nuclease 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. The non-canonical NF-κB pathway promotes NPC2 expression and regulates intracellular cholesterol trafficking. Liao Y, et al. Sci China Life Sci, 2018 Oct. PMID 30091016
  2. Different wild type strains of zebrafish show divergent susceptibility to TNBS-induced intestinal inflammation displaying distinct immune cell profiles. Padovani BN, et al. Curr Res Immunol, 2022. PMID 35496825, Free PMC Article
  3. A CRISPR/Cas9 zebrafish lamin A/C mutant model of muscular laminopathy. Nicolas HA, et al. Dev Dyn, 2022 Apr. PMID 34599606
  4. Sheng-Mai Yin exerts anti-inflammatory effects on RAW 264.7 cells and zebrafish. Zheng Y, et al. J Ethnopharmacol, 2021 Mar 1. PMID 33091492
  5. Identification and innate immunity mechanism of protective immunogens from extracellular proteins of Edwardsiella tarda. Li L, et al. Fish Shellfish Immunol, 2020 Feb. PMID 31830569

See all (89) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Study indicates an essential role of NF-kappaB in gonadal differentiation
    Title: Activation of NF-κB protein prevents the transition from juvenile ovary to testis and promotes ovarian development in zebrafish.
Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Markers

Homology

Clone Names

  • MGC136693

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within angiogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in canonical NF-kappaB signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to stress IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within cholesterol homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in epithelium development IEA
Inferred from Electronic Annotation
more info
  
involved_in inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in non-canonical NF-kappaB signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in response to cytokine IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
nuclear factor NF-kappa-B p100 subunit
Names
NF-kB2-I precursor protein
NF-kB2-II precursor protein
P100/P52 transcription factor

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.

mRNA and Protein(s)

  1. NM_001001840.3 → NP_001001840.2  nuclear factor NF-kappa-B p100 subunit

    See identical proteins and their annotated locations for NP_001001840.2

    Status: VALIDATED

    Source sequence(s)
    BX005174, CR550304
    UniProtKB/TrEMBL
    A0A8M1MZQ8, Q0II00
    Related
    ENSDARP00000121285.1, ENSDART00000134122.3
    Conserved Domains (6) summary
    cd07934
    Location:53 → 238
    RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)
    cd08798
    Location:794 → 867
    Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100
    cd00204
    Location:558 → 687
    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 ...
    pfam12796
    Location:532 → 627
    Ank_2; Ankyrin repeats (3 copies)
    pfam16179
    Location:246 → 344
    RHD_dimer; Rel homology dimerization domain
    sd00045
    Location:599 → 629
    ANK; ANK repeat [structural motif]

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007124.7 Reference GRCz11 Primary Assembly

    Range
    22717355..22735561
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009307306.3 → XP_009305581.1  nuclear factor NF-kappa-B p100 subunit isoform X1

    See identical proteins and their annotated locations for XP_009305581.1

    UniProtKB/TrEMBL
    A0A8M1MZQ8, Q0II00
    Related
    ENSDARP00000154151.1, ENSDART00000188288.1
    Conserved Domains (6) summary
    cd07934
    Location:53 → 238
    RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)
    cd08798
    Location:794 → 867
    Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100
    cd00204
    Location:558 → 687
    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 ...
    pfam12796
    Location:532 → 627
    Ank_2; Ankyrin repeats (3 copies)
    pfam16179
    Location:246 → 344
    RHD_dimer; Rel homology dimerization domain
    sd00045
    Location:599 → 629
    ANK; ANK repeat [structural motif]

  2. XM_005156814.4 → XP_005156871.1  nuclear factor NF-kappa-B p100 subunit isoform X2

    UniProtKB/TrEMBL
    A0A8M2B350
    Conserved Domains (6) summary
    cd07934
    Location:47 → 232
    RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)
    cd08798
    Location:788 → 861
    Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100
    cd00204
    Location:552 → 681
    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 ...
    pfam12796
    Location:526 → 621
    Ank_2; Ankyrin repeats (3 copies)
    pfam16179
    Location:240 → 338
    RHD_dimer; Rel homology dimerization domain
    sd00045
    Location:593 → 623
    ANK; ANK repeat [structural motif]

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394884.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    160820..179030
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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