Kdm6b MGI Mouse Gene Detail - MGI:2448492 - KDM1 lysine (K)-specific demethylase 6B

Symbol

Kdm6b
Name

KDM1 lysine (K)-specific demethylase 6B
Synonyms

Jmjd3, mKIAA0346

Feature Type

protein coding gene
IDs

MGI:2448492
NCBI Gene: 216850
Alliance

gene page
Transcription Start Sites

19 TSS

Sequence Map

Chr11:69289334-69304501 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 11, 42.60 cM
Mapping Data

1 experiment

SNPs within 2kb

294 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2448492	protein coding gene	Chr11:69289334-69311188 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0018534	protein coding gene	Chr11:69827087-69844213 (-)
A/J	MGP_AJ_G0018502	protein coding gene	Chr11:67200038-67215214 (-)
AKR/J	MGP_AKRJ_G0018471	protein coding gene	Chr11:69211532-69221129 (-)
BALB/cJ	MGP_BALBcJ_G0018474	protein coding gene	Chr11:67519041-67534202 (-)
C3H/HeJ	MGP_C3HHeJ_G0018287	protein coding gene	Chr11:69228511-69244945 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0018925	protein coding gene	Chr11:71941015-71957862 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0016570	protein coding gene	Chr11:64128899-64143763 (-)
CAST/EiJ	MGP_CASTEiJ_G0017842	protein coding gene	Chr11:69464461-69487270 (-)
CBA/J	MGP_CBAJ_G0018260	protein coding gene	Chr11:75163302-75180480 (-)
DBA/2J	MGP_DBA2J_G0018369	protein coding gene	Chr11:66790963-66805457 (-)
FVB/NJ	MGP_FVBNJ_G0018359	protein coding gene	Chr11:66417892-66435294 (-)
LP/J	MGP_LPJ_G0018439	protein coding gene	Chr11:70398518-70414702 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0018382	protein coding gene	Chr11:75776100-75801729 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0018967	protein coding gene	Chr11:69461906-69478102 (-)
PWK/PhJ	MGP_PWKPhJ_G0017616	protein coding gene	Chr11:67434074-67456928 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0017406	protein coding gene	Chr11:69281359-69298787 (-)
WSB/EiJ	MGP_WSBEiJ_G0017896	protein coding gene	Chr11:69138567-69159234 (-)

Human Ortholog

KDM6B, lysine demethylase 6B

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

KDM6B, lysine demethylase 6B
Synonyms

JMJD3, NEDCFSA, NEDSST
Links

HGNC:29012

NCBI Gene ID: 23135

UniProt: O15054
Chr Location

17p13.1; chr17:7834217-7854796 (+) GRCh38

MGI Vertebrate Homology

Kdm6b stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: KDM6B
Gene Tree

Kdm6b

Diseases

1 with human KDM6B associations

				Human Disease	Mouse Models
				Stolerman neurodevelopmental syndrome IDs Stolerman neurodevelopmental syndrome DOID:0081443 OMIM:618505

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

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Phenotype Summary

51 phenotypes from 9 alleles in 8 genetic backgrounds
4 phenotypes from multigenic genotypes
1 images
68 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

55
Chemically induced (other)

1
Endonuclease-mediated

8
Gene trapped

19
Targeted

26
Transgenic

1
Genomic Mutations

1 involving Kdm6b
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

65 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a null allele show perinatal death, thick alveolar septum, and absence of air space in the lungs. Mice homozygous for a different null allele die neonatally displaying abnormal lung development, dwarfism, kyphosis, short limbs, and a severe delay in endochondral ossification.

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All GO Annotations

43
GO References

15

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

757
Tissues

30
cDNA Data

11
Literature Summary

25

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase kdm6b

ZFIN kdm6ba, kdm6bb

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All Sequences

65
RefSeq

28
UniProt

3
CCDS

CCDS24895.1

Ensembl

ENSMUSG00000018476 (Evidence)
NCBI Gene

216850

			Length	Strain/Species	Flank
genomic	ENSMUSG00000018476	Ensembl Gene Model \| MGI Sequence Detail	15168	C57BL/6J	± kb
transcript	ENSMUST00000094077	Ensembl \| MGI Sequence Detail	6654	Not Applicable
polypeptide	ENSMUSP00000091620	Ensembl \| MGI Sequence Detail	1641	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000009217 lysine-specific demethylase 6B

(term hierarchy)
PDB

4EYU, 4EZ4, 4EZH
EC

1.14.11.68
InterPro Domains

IPR003347 JmjC domain

IPR048562 Lysine-specific demethylase 6A/B-like, C-terminal helical domain

IPR048560 Lysine-specific demethylase 6A/B-like, GATA-like

IPR046941 Lysine-specific demethylase 6, GATA-like domain superfamily

IPR051630 Transcriptional Corepressor and Histone Demethylase
GlyGen

Q5NCY0 6 sites, 1 O-linked glycan (1 site)

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All nucleic 14

cDNA 11

Primer pair 2

Other 1

Microarray probesets 4

Summaries

All 150

Developmental Gene Expression 25

Gene Ontology 15

Phenotypes 68
Earliest

J:137335 Roderick TH, Chromosomal inversions in studies of mammalian mutagenesis. Genetics. 1979 May;92(1 Pt 1 Suppl):s121-6
Latest

J:365121 McIntyre TI, et al., KDM6B-dependent epigenetic programming of uterine fibroblasts in early pregnancy regulates parturition timing in mice. Cell. 2025 Jan 13;

TSS for Kdm6b:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr108684	Chr11:69304932-69304938 (-)	-434 bp
Tssr108683	Chr11:69304083-69304124 (-)	397 bp
Tssr108670	Chr11:69300373-69300395 (-)	4,117 bp
Tssr108669	Chr11:69300254-69300271 (-)	4,238 bp
Tssr108668	Chr11:69300239-69300248 (-)	4,257 bp
Tssr108667	Chr11:69300218-69300237 (-)	4,273 bp
Tssr108666	Chr11:69299972-69299986 (-)	4,522 bp
Tssr3543	Chr11:69299506-69299550 (-)	4,973 bp
Tssr108665	Chr11:69299384-69299388 (-)	5,115 bp
Tssr108664	Chr11:69298639-69298657 (-)	5,853 bp
Tssr108663	Chr11:69298463-69298475 (-)	6,032 bp
Tssr108662	Chr11:69298432-69298446 (-)	6,062 bp
Tssr108661	Chr11:69297581-69297596 (-)	6,912 bp
Tssr108660	Chr11:69296699-69296737 (-)	7,783 bp
Tssr108659	Chr11:69296268-69296287 (-)	8,223 bp
Tssr108658	Chr11:69296094-69296112 (-)	8,398 bp
Tssr108657	Chr11:69296057-69296085 (-)	8,430 bp
Tssr108656	Chr11:69295798-69295822 (-)	8,691 bp
Tssr108655	Chr11:69292164-69292193 (-)	12,322 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 03/18/2025 MGI 6.24