Kdm5b MGI Mouse Gene Detail - MGI:1922855

Symbol

Kdm5b
Name

lysine demethylase 5B
Synonyms

2010009J12Rik, 2210016I17Rik, D1Ertd202e, Jarid1b, Plu1, PLU-1, Rb-Bp2

Feature Type

protein coding gene
IDs

MGI:1922855
NCBI Gene: 75605
Alliance

gene page
Transcription Start Sites

8 TSS

Sequence Map

Chr1:134487916-134560621 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 58.24 cM, cytoband E4
Mapping Data

5 experiments

SNPs within 2kb

1429 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1922855	protein coding gene	Chr1:134487909-134563023 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0016511	protein coding gene	Chr1:138239941-138325653 (+)
A/J	MGP_AJ_G0016494	protein coding gene	Chr1:133024582-133108412 (+)
AKR/J	MGP_AKRJ_G0016459	protein coding gene	Chr1:137002163-137087663 (+)
BALB/cJ	MGP_BALBcJ_G0016454	protein coding gene	Chr1:133358749-133434718 (+)
C3H/HeJ	MGP_C3HHeJ_G0016280	protein coding gene	Chr1:137089572-137172478 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0016915	protein coding gene	Chr1:143276745-143358736 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014626	protein coding gene	Chr1:126156607-126234857 (+)
CAST/EiJ	MGP_CASTEiJ_G0015860	protein coding gene	Chr1:136153758-136237652 (+)
CBA/J	MGP_CBAJ_G0016253	protein coding gene	Chr1:148221964-148301480 (+)
DBA/2J	MGP_DBA2J_G0016359	protein coding gene	Chr1:132035744-132115890 (+)
FVB/NJ	MGP_FVBNJ_G0016358	protein coding gene	Chr1:130672471-130752543 (+)
LP/J	MGP_LPJ_G0016430	protein coding gene	Chr1:139511131-139587678 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016383	protein coding gene	Chr1:153921497-154001863 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0016951	protein coding gene	Chr1:136740838-136822030 (+)
PWK/PhJ	MGP_PWKPhJ_G0015646	protein coding gene	Chr1:131060456-131137928 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0015433	protein coding gene	Chr1:135696700-135779283 (+)
WSB/EiJ	MGP_WSBEiJ_G0015923	protein coding gene	Chr1:136756329-136844158 (+)

Human Ortholog

KDM5B, lysine demethylase 5B

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

KDM5B, lysine demethylase 5B
Synonyms

CT31, JARID1B, MRT65, PLU-1, PLU1, PPP1R98, PUT1, RBBP2H1A, RBP2-H1
Links

HGNC:18039

NCBI Gene ID: 10765

neXtProt AC: NX_Q9UGL1

UniProt: Q9UGL1
Chr Location

1q32.1; chr1:202724495-202808487 (-) GRCh38

MGI Vertebrate Homology

Kdm5b stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: KDM5B
Gene Tree

Kdm5b

Diseases

3 with human KDM5B associations

				Human Disease	Mouse Models
				autosomal recessive intellectual developmental disorder 65 IDs autosomal recessive intellectual developmental disorder 65 DOID:0081226 OMIM:618109
				breast cancer IDs breast cancer DOID:1612 DOID:1648 DOID:4241 ICD10CM:C50 ICD9CM:174.8 MESH:D001943 NCI:C9335 OMIM:114480 UMLS_CUI:C0006142
				high grade glioma IDs high grade glioma DOID:3070 DOID:2627 KEGG:05214 MESH:D005910 NCI:C3059 NCI:C4822 OMIM:PS137800 ORDO:182067 UMLS_CUI:C0017638 UMLS_CUI:C0555198

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

13 phenotypes from 2 alleles in 4 genetic backgrounds
30 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

213
Chemically induced (other)

2
Endonuclease-mediated

5
Gene trapped

200
Radiation induced

1
Targeted

5
Genomic Mutations

3 involving Kdm5b
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

200 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a gene trapped allele exhibit decreased body weight, background-sensitive premature mortality, decreased female fertility, delayed mammary gland development, decreased serum estradiol levels, and reduced mammary epithelial cell proliferation in early puberty.

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All GO Annotations

41
GO References

11

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

928
Tissues

141
cDNA Data

23
Literature Summary

20

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA KDM5B

Xenbase kdm5b

ZFIN kdm5ba, kdm5bb

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All Sequences

70
RefSeq

8
UniProt

4
CCDS

CCDS35716.1

Ensembl

ENSMUSG00000042207 (Evidence)
NCBI Gene

75605

			Length	Strain/Species	Flank
genomic	75605	NCBI Gene Model \| MGI Sequence Detail	72706	C57BL/6J	± kb
transcript	NM_152895	RefSeq \| MGI Sequence Detail	6300	ZRU/MplStud
polypeptide	Q80Y84	UniProt \| EBI \| MGI Sequence Detail	1544	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000009205 lysine-specific demethylase 5B

(term hierarchy)
PDB

2EQY
EC

1.14.11.67
InterPro Domains

IPR001606 ARID DNA-binding domain

IPR036431 ARID DNA-binding domain superfamily

IPR003347 JmjC domain

IPR003349 JmjN domain

IPR047981 Lysine-specific demethylase 5B, ARID domain

IPR047978 Lysine-specific demethylase 5B, first PHD-finger

IPR047979 Lysine-specific demethylase 5B, third PHD-finger

IPR048615 Lysine-specific demethylase 5, C-terminal helical domain

IPR013637 Lysine-specific demethylase-like domain

IPR037869 Spp1/CFP1

IPR004198 Zinc finger, C5HC2-type

IPR011011 Zinc finger, FYVE/PHD-type

IPR019787 Zinc finger, PHD-finger

IPR001965 Zinc finger, PHD-type

IPR019786 Zinc finger, PHD-type, conserved site

IPR013083 Zinc finger, RING/FYVE/PHD-type
GlyGen

Q80Y84 1 site, 1 N-linked glycan (1 site)

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All nucleic 28

cDNA 23

Primer pair 5

Microarray probesets 7

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MGI:1098818, MGI:1917371, MGI:2138618

Summaries

All 96

Developmental Gene Expression 20

Gene Ontology 11

Phenotypes 30
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

J:352232 Perez-Sisques L, et al., The Intellectual Disability Risk Gene Kdm5b Regulates Long-Term Memory Consolidation in the Hippocampus. J Neurosci. 2024 May 8;44(19)

TSS for Kdm5b:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr8904	Chr1:134487895-134487918 (+)	-9 bp
Tssr8905	Chr1:134487928-134487951 (+)	24 bp
Tssr8906	Chr1:134487952-134487971 (+)	46 bp
Tssr8907	Chr1:134502208-134502212 (+)	14,294 bp
Tssr8908	Chr1:134503096-134503100 (+)	15,182 bp
Tssr8909	Chr1:134504158-134504162 (+)	16,244 bp
Tssr8910	Chr1:134541064-134541094 (+)	53,163 bp
Tssr8911	Chr1:134559867-134559871 (+)	71,953 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/19/2024 MGI 6.24