Kdm5b lysine demethylase 5B [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Kdm5bprovided by MGI
Official Full Name: lysine demethylase 5Bprovided by MGI
Primary source: MGI:MGI:1922855
See related: Ensembl:ENSMUSG00000042207 AllianceGenome:MGI:1922855
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: PUT1; Plu1; PLU-1; Rb-Bp2; Jarid1b; RBBP2H1A; mKIAA4034; D1Ertd202e; 2010009J12Rik; 2210016I17Rik
Summary: This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Homozygous mutant mice display decreased body weight, decreased female fertility, lower uterine weight, and a delay in mammary development. Knockout of this gene has also been associated with embryonic lethality. [provided by RefSeq, Dec 2016]
Expression: Ubiquitous expression in testis adult (RPKM 14.9), CNS E11.5 (RPKM 13.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 E4; 1 58.24 cM

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (134487916..134560621)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (134560178..134632878)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Inhibition of KDM5B participates in immune microenvironment remodeling in pancreatic cancer by inducing STING expression.
Title: Inhibition of KDM5B participates in immune microenvironment remodeling in pancreatic cancer by inducing STING expression.
Histone demethylase KDM5B licenses macrophage-mediated inflammatory responses by repressing Nfkbia transcription.
Title: Histone demethylase KDM5B licenses macrophage-mediated inflammatory responses by repressing Nfkbia transcription.
Lysine demethylase KDM5B down-regulates SIRT3-mediated mitochondrial glucose and lipid metabolism in diabetic neuropathy.
Title: Lysine demethylase KDM5B down-regulates SIRT3-mediated mitochondrial glucose and lipid metabolism in diabetic neuropathy.
Alcohol-associated fibrosis in females is mediated by female-specific activation of lysine demethylases KDM5B and KDM5C.
Title: Alcohol-associated fibrosis in females is mediated by female-specific activation of lysine demethylases KDM5B and KDM5C.
KDM5B protein expressed in viable and fertile DeltaARID mice exhibit no demethylase activity.
Title: KDM5B protein expressed in viable and fertile ΔARID mice exhibit no demethylase activity.
KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements.
Title: KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements.
KDM5B Is Essential for the Hyperactivation of PI3K/AKT Signaling in Prostate Tumorigenesis.
Title: KDM5B Is Essential for the Hyperactivation of PI3K/AKT Signaling in Prostate Tumorigenesis.
In this study, we demonstrate that CD34(+) and CD34(-) subpopulations carrying the BRAF(V600E) mutation confer differential sensitivity to targeted BRAF inhibition. Through elevated KDM5B expression, melanoma cells shift toward a more drug-tolerant, CD34(-) state upon exposure to BRAF inhibitor or combined BRAF inhibitor and MEK inhibitor treatment
Title: KDM5B Promotes Drug Resistance by Regulating Melanoma-Propagating Cell Subpopulations.
A novel role of KDM5B in metabolism, as KDM5B-KO mice display growth retardation and improved insulin sensitivity.
Title: The Lysine Demethylase KDM5B Regulates Islet Function and Glucose Homeostasis.
KDM5B regulates nucleosome positioning in embryonic stem cells.
Title: Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing.

Submit: New GeneRIF Correction See all GeneRIFs (27)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (5) 1 citation
Endonuclease-mediated (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126466 (e-PCR)
- UniSTS:163174

AW556288 (e-PCR)
- UniSTS:185453

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	ISO Inferred from Sequence Orthology more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation 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
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within branching involved in mammary gland duct morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within mammary duct terminal end bud growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of mammary gland epithelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within post-embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of circadian rhythm	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within regulation of estradiol secretion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within single fertilization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within uterus morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lysine-specific demethylase 5B

Names: [histone H3]-trimethyl-L-lysine(4) demethylase 5B; histone demethylase JARID1B; jumonji, AT rich interactive domain 1B (Rbp2 like); jumonji/ARID domain-containing protein 1B; lysine (K)-specific demethylase 5B; putative DNA/chromatin binding motif 1

NP_690855.2

EC 1.14.11.67

XP_011246392.1

EC 1.14.11.67

XP_017168105.1

EC 1.14.11.67

XP_017168106.1

EC 1.14.11.67

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_152895.2 → NP_690855.2 lysine-specific demethylase 5B

See identical proteins and their annotated locations for NP_690855.2

Status: REVIEWED

Source sequence(s)

AK076888, BC048180, CX206086, CX567343, W35764

Consensus CDS

CCDS35716.1

UniProtKB/Swiss-Prot

Q5DTR9, Q80Y84, Q8BLU1, Q8JZL8

Related

ENSMUSP00000038138.8, ENSMUST00000047714.14

Conserved Domains (8) summary

smart00501
Location:98 → 188

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00545
Location:31 → 72

JmjN; Small domain found in the jumonji family of transcription factors

pfam02373
Location:486 → 602

JmjC; JmjC domain, hydroxylase

cd15603
Location:311 → 356

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15687
Location:1486 → 1535

PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)

pfam02928
Location:692 → 744

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:757 → 1086

PLU-1; PLU-1-like protein

cl22851
Location:1178 → 1221

PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

134487916..134560621

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011248090.4 → XP_011246392.1 lysine-specific demethylase 5B isoform X1

Conserved Domains (7) summary

cd15603
Location:153 → 198

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15607
Location:1020 → 1063

PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)

cd15687
Location:1328 → 1377

PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)

pfam02373
Location:328 → 444

JmjC; JmjC domain, hydroxylase

cl28902
Location:1 → 25

ARID; ARID/BRIGHT DNA binding domain family

pfam02928
Location:534 → 586

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:599 → 928

PLU-1; PLU-1-like protein
XM_017312617.3 → XP_017168106.1 lysine-specific demethylase 5B isoform X2

Conserved Domains (7) summary

cd15603
Location:153 → 198

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15607
Location:1020 → 1063

PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)

pfam02373
Location:328 → 444

JmjC; JmjC domain, hydroxylase

cl28902
Location:1 → 25

ARID; ARID/BRIGHT DNA binding domain family

pfam02928
Location:534 → 586

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:599 → 928

PLU-1; PLU-1-like protein

cl22851
Location:1328 → 1345

PHD_SF; PHD finger superfamily
XM_017312616.3 → XP_017168105.1 lysine-specific demethylase 5B isoform X1

Conserved Domains (7) summary

cd15603
Location:153 → 198

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15607
Location:1020 → 1063

PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)

cd15687
Location:1328 → 1377

PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)

pfam02373
Location:328 → 444

JmjC; JmjC domain, hydroxylase

cl28902
Location:1 → 25

ARID; ARID/BRIGHT DNA binding domain family

pfam02928
Location:534 → 586

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:599 → 928

PLU-1; PLU-1-like protein