Nfkb2 nuclear factor kappa B subunit 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nfkb2provided by RGD
Official Full Name: nuclear factor kappa B subunit 2provided by RGD
Primary source: RGD:1307189
See related: EnsemblRapid:ENSRNOG00000019311 AllianceGenome:RGD:1307189
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1307189
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in response to cytokine and response to lipopolysaccharide. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of Bcl3/NF-kappaB2 complex. Predicted to be active in cytoplasm and nucleus. Used to study Parkinsonism. Human ortholog(s) of this gene implicated in common variable immunodeficiency 10. Orthologous to human NFKB2 (nuclear factor kappa B subunit 2). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 124.5), Thymus (RPKM 83.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q54

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (255106010..255114649)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (245164586..245173225)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (266050634..266059277)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TNFalpha-RelB/p52 pathway may be involved in the early stages of renal damage, in part by stimulating COX-2 and inflammatory responses
Title: TNFα up-regulates COX-2 in chronic progressive nephropathy through nuclear accumulation of RelB and NF-κB2.
PACAP promotes both survival and neuritogenesis in PC12 cells by activating NF-kappaB pathway, most likely via classical and alternative signaling cascades involving ERK1/2 kinases, Ca(2+), and c-Rel/p52 dimers.
Title: Pituitary adenylate cyclase-activating polypeptide (PACAP) promotes both survival and neuritogenesis in PC12 cells through activation of nuclear factor κB (NF-κB) pathway: involvement of extracellular signal-regulated kinase (ERK), calcium, and c-REL.
Calbindin-D28K expression induced by glial cell line-derived neurotrophic factor in substantia nigra neurons dependent on PI3K/Akt/NF-kappaB(p65/p52) signaling pathway.
Title: Calbindin-D28K expression induced by glial cell line-derived neurotrophic factor in substantia nigra neurons dependent on PI3K/Akt/NF-kappaB signaling pathway.
results indicate GDNF could activate the NF-kappaB signaling pathway in degenerating dopaminergic neurons; the NF-kappaB noncanonical signaling pathway, which contained the NF-kappaB p65/p52 complex that was involved in the effects of GDNF on DA neurons
Title: The involvement of NF-kappaB p65/p52 in the effects of GDNF on DA neurons in early PD rats.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within extracellular matrix organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within follicular dendritic cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within germinal center formation	ISO Inferred from Sequence Orthology more info
involved_in non-canonical NF-kappaB signal transduction	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 DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in response to cytokine	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within spleen development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of Bcl3/NF-kappaB2 complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	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
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nuclear factor NF-kappa-B p100 subunit

Names: nuclear factor of kappa light polypeptide gene enhancer in B-cells 2, p49/p100

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)

NM_001008349.1 → NP_001008350.1 nuclear factor NF-kappa-B p100 subunit

See identical proteins and their annotated locations for NP_001008350.1

Status: PROVISIONAL

Source sequence(s)

BC085800

UniProtKB/TrEMBL

A0A8I6G6F3, A6JHL7, A6JHL8, Q5U2Z4

Related

ENSRNOP00000080319.1, ENSRNOT00000103016.2

Conserved Domains (7) summary

cd07934
Location:38 → 221

RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)

cd08798
Location:773 → 847

Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100

cd00204
Location:482 → 619

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:228 → 327

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:604 → 697

Ank_2; Ankyrin repeats (3 copies)

pfam13637
Location:487 → 546

Ank_4; Ankyrin repeats (many copies)

sd00045
Location:598 → 629

ANK; ANK repeat [structural motif]

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

NC_086019.1 Reference GRCr8

Range

255106010..255114649

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006231503.4 → XP_006231565.1 nuclear factor NF-kappa-B p100 subunit isoform X1

See identical proteins and their annotated locations for XP_006231565.1

UniProtKB/TrEMBL

A0A8I6G6F3, A6JHL7, A6JHL8, Q5U2Z4

Related

ENSRNOP00000026235.2, ENSRNOT00000026235.5

Conserved Domains (7) summary

cd07934
Location:38 → 221

RHD-n_NFkB2; N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2)

cd08798
Location:773 → 847

Death_NFkB2_p100; Death domain of the Nuclear Factor-KappaB2 precursor protein p100

cd00204
Location:482 → 619

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:228 → 327

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:604 → 697

Ank_2; Ankyrin repeats (3 copies)

pfam13637
Location:487 → 546

Ank_4; Ankyrin repeats (many copies)

sd00045
Location:598 → 629

ANK; ANK repeat [structural motif]