Nfkbid Gene Detail

Summary

• Symbol
  Nfkbid
• Name
  nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor, delta
• Synonyms
  IkappaBNS

• Feature Type
  protein coding gene
• IDs
  MGI:3041243
  NCBI Gene: 243910
• Alliance
  gene page
• Transcription Start Sites
  51 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr7:30121157-30128171 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 7, 17.52 cM
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  368 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_3041243	protein coding gene	Chr7:30121156-30128173 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0032019	protein coding gene	Chr7:29409753-29416765 (+)
A/J	MGP_AJ_G0031996	protein coding gene	Chr7:28625666-28632664 (+)
AKR/J	MGP_AKRJ_G0031929	protein coding gene	Chr7:29356137-29363141 (+)
BALB/cJ	MGP_BALBcJ_G0032003	protein coding gene	Chr7:28804091-28811088 (+)
C3H/HeJ	MGP_C3HHeJ_G0031722	protein coding gene	Chr7:29801692-29807487 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0032469	protein coding gene	Chr7:30367991-30374395 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0029519	protein coding gene	Chr7:29660586-29668080 (+)
CAST/EiJ	MGP_CASTEiJ_G0031056	protein coding gene	Chr7:23057998-23066869 (+)
CBA/J	MGP_CBAJ_G0031688	protein coding gene	Chr7:31817335-31821998 (+)
DBA/2J	MGP_DBA2J_G0031840	protein coding gene	Chr7:28355392-28362389 (+)
FVB/NJ	MGP_FVBNJ_G0031797	protein coding gene	Chr7:28474926-28481912 (+)
LP/J	MGP_LPJ_G0031921	protein coding gene	Chr7:29728283-29735280 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0031833	protein coding gene	Chr7:31068239-31076307 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0032497	protein coding gene	Chr7:28855986-28862992 (+)
PWK/PhJ	MGP_PWKPhJ_G0030782	protein coding gene	Chr7:23392711-23399554 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0030615	protein coding gene	Chr7:19861624-19868992 (+)
WSB/EiJ	MGP_WSBEiJ_G0031166	protein coding gene	Chr7:29239708-29246716 (+)

Homology

• Human Ortholog
  NFKBID, NFKB inhibitor delta

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  NFKBID, NFKB inhibitor delta
  
• Synonyms
  IkappaBNS, IkBNS, TA-NFKBH
• Links
  HGNC:15671

  NCBI Gene ID: 84807

  neXtProt AC: NX_Q8NI38

  UniProt: Q8NI38

  
  
• Chr Location
  19q13.12; chr19:35887630-35902303 (-)  GRCh38

---

• MGI Vertebrate Homology
  Nfkbid stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: NFKBID
• Gene Tree
  Nfkbid
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  26 phenotypes from 4 alleles in 5 genetic backgrounds
  3 phenotypes from multigenic genotypes
  31 phenotype references
  

• All Mutations and Alleles
  11
• Chemically induced (ENU)
  1
• Endonuclease-mediated
  1
• Gene trapped
  2
• Targeted
  6
• Transgenic
  1
• Incidental Mutations
  CvDC
• Find Mice (IMSR)
  22 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for a null allele produce higher levels of IL-6 following stimulation and are more susceptible to chemically induced endotoxin shock and colitis.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  14
• GO References
  4

Expression

• Assay Results
  706
• cDNA Data
  13

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  43
• RefSeq
  9
• UniProt
  2
• CCDS
  CCDS21091.1

• Ensembl
  ENSMUSG00000036931 (Evidence)
• NCBI Gene
  243910

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000036931	Ensembl Gene Model | MGI Sequence Detail	7015	C57BL/6J
transcript	ENSMUST00000108176	Ensembl | MGI Sequence Detail	2014	Not Applicable
polypeptide	ENSMUSP00000103811	Ensembl | MGI Sequence Detail	470	Not Applicable

Protein
Information

• UniProt
  2 Sequences
• Protein Ontology
  PR:000011179 NF-kappa-B inhibitor delta
  (term hierarchy)
• InterPro Domains
  IPR002110 Ankyrin repeat
  IPR036770 Ankyrin repeat-containing domain superfamily

Molecular
Reagents

• All nucleic 13

  cDNA 13

  
  

  Microarray probesets 2

References

• Summaries
  All 56

  Gene Ontology 4

  Phenotypes 31
• Earliest
  J:75807 Fiorini E, et al., Peptide-induced negative selection of thymocytes activates transcription of an NF-kappaB inhibitor. Mol Cell. 2002 Mar;9(3):637-48
• Latest
  J:352110 Daly AE, et al., Selective regulation of a defined subset of inflammatory and immunoregulatory genes by an NF-kappaB p50-IkappaBzeta pathway. Genes Dev. 2024 Jul 19;38(11-12):536-553

TSS for Nfkbid:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr65713	Chr7:30119340-30119374 (+)	-1,800 bp
Tssr65714	Chr7:30121149-30121167 (+)	1 bp
Tssr65715	Chr7:30121697-30121720 (+)	552 bp
Tssr65716	Chr7:30121814-30121856 (+)	678 bp
Tssr65717	Chr7:30121858-30121869 (+)	707 bp
Tssr65718	Chr7:30121886-30121895 (+)	734 bp
Tssr65719	Chr7:30122691-30122718 (+)	1,548 bp
Tssr65720	Chr7:30122730-30122739 (+)	1,578 bp
Tssr2184	Chr7:30122769-30122773 (+)	1,614 bp
Tssr65721	Chr7:30122787-30122796 (+)	1,635 bp
Tssr65722	Chr7:30122806-30122833 (+)	1,663 bp
Tssr65723	Chr7:30122837-30122848 (+)	1,686 bp
Tssr65724	Chr7:30122853-30122902 (+)	1,721 bp
Tssr65725	Chr7:30123025-30123030 (+)	1,871 bp
Tssr65726	Chr7:30123032-30123035 (+)	1,877 bp
Tssr65727	Chr7:30123050-30123069 (+)	1,903 bp
Tssr65728	Chr7:30123345-30123347 (+)	2,189 bp
Tssr65729	Chr7:30123663-30123672 (+)	2,511 bp
Tssr65730	Chr7:30123711-30123727 (+)	2,562 bp
Tssr65731	Chr7:30123737-30123741 (+)	2,582 bp
Tssr65732	Chr7:30123775-30123791 (+)	2,626 bp
Tssr65733	Chr7:30123803-30123810 (+)	2,650 bp
Tssr65734	Chr7:30123844-30123849 (+)	2,690 bp
Tssr65735	Chr7:30124643-30124650 (+)	3,490 bp
Tssr65736	Chr7:30124662-30124670 (+)	3,509 bp
Tssr65737	Chr7:30124696-30124714 (+)	3,548 bp
Tssr65738	Chr7:30124752-30124759 (+)	3,599 bp
Tssr65739	Chr7:30124948-30124973 (+)	3,804 bp
Tssr65740	Chr7:30124975-30124997 (+)	3,829 bp
Tssr65741	Chr7:30125128-30125135 (+)	3,975 bp
Tssr65742	Chr7:30125145-30125151 (+)	3,991 bp
Tssr65743	Chr7:30125197-30125200 (+)	4,042 bp
Tssr65744	Chr7:30125224-30125235 (+)	4,073 bp
Tssr65745	Chr7:30125536-30125551 (+)	4,387 bp
Tssr65746	Chr7:30126494-30126501 (+)	5,341 bp
Tssr65747	Chr7:30126523-30126535 (+)	5,372 bp
Tssr65748	Chr7:30126538-30126547 (+)	5,386 bp
Tssr65749	Chr7:30126550-30126555 (+)	5,396 bp
Tssr65750	Chr7:30126579-30126594 (+)	5,430 bp
Tssr65751	Chr7:30126847-30126866 (+)	5,700 bp
Tssr65752	Chr7:30126883-30126897 (+)	5,733 bp
Tssr65753	Chr7:30126907-30126928 (+)	5,761 bp
Tssr65754	Chr7:30127014-30127018 (+)	5,859 bp
Tssr65755	Chr7:30127045-30127053 (+)	5,892 bp
Tssr65756	Chr7:30127579-30127591 (+)	6,428 bp
Tssr65757	Chr7:30127609-30127613 (+)	6,454 bp
Tssr65758	Chr7:30127785-30127794 (+)	6,633 bp
Tssr65759	Chr7:30127797-30127805 (+)	6,644 bp
Tssr65760	Chr7:30127811-30127822 (+)	6,660 bp
Tssr65761	Chr7:30127883-30127886 (+)	6,728 bp
Tssr65762	Chr7:30127897-30127908 (+)	6,746 bp

Nfkbid is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Tpgi1	Chr7, syntenic		J:316317	Nfkbid (MGI:3041243) is one of the most polymorphic genes within the Tpgi1 QTL region and sits between the genetic markers that flank the highest imputed LOD score. The authors explore Nfkbid at length and find strong support for its role in Toxoplasma gondii immunity.

*cM position of peak correlated region/marker