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

16 TSS

Sequence Map

Chr11:69398508-69413675 bp, - strand
From Ensembl annotation of GRCm38

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 11, 42.60 cM
Mapping Data

1 experiment

SNPs within 2kb

78 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	Chr11:69398508-69418147 (-)
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

7

Human Ortholog

KDM6B, lysine demethylase 6B
Orthology source: HomoloGene, HGNC
Synonyms

JMJD3, NEDCFSA
Links

HGNC:29012

NCBI Gene ID: 23135

neXtProt AC: NX_O15054

UniProt: O15054
Chr Location

17p13.1; chr17:7834210-7854800 (+) GRCh38.p7

HomoloGene

Vertebrate Homology Class 18945
1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 macaque, rhesus
HCOP

human homology predictions: KDM6B
Gene Tree

Kdm6b

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Phenotype Summary

38 phenotypes from 8 alleles in 6 genetic backgrounds
2 phenotypes from multigenic genotypes
1 images
33 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	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

44
Chemically induced (other)

1
Endonuclease-mediated

1
Gene trapped

21
Targeted

20
Transgenic

1
Genomic Mutations

1 involving Kdm6b
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

47 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

38
GO References

11

External Resources

FuncBase

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 death	cell differentiation	cell population proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	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	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	synapse	vacuole

Click cells to view annotations.

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Assay Results

1
Tissues

1
cDNA Data

8
Literature Summary

15

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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Kdm6b interacts with 204 markers (Mir7-2, Mir7b, Mir9-1, ...) View All

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All Sequences

49
RefSeq

12
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.-
InterPro Domains

IPR003347 JmjC domain

IPR029518 Lysine-specific demethylase 6B

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All nucleic 9

cDNA 8

Other 1

Microarray probesets 4

Summaries

All 96

Developmental Gene Expression 15

Gene Ontology 11

Phenotypes 33
Earliest

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

J:274280 Jia W, et al., Histone demethylase JMJD3 regulates fibroblast-like synoviocyte-mediated proliferation and joint destruction in rheumatoid arthritis. FASEB J. 2018 Jul;32(7):4031-4042

TSS for Kdm6b:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr108686	Chr11:69416188-69416227 (-)	-2,533 bp
Tssr108685	Chr11:69416145-69416167 (-)	-2,481 bp
Tssr108684	Chr11:69414106-69414112 (-)	-434 bp
Tssr108683	Chr11:69413257-69413298 (-)	397 bp
Tssr108660	Chr11:69405873-69405911 (-)	7,783 bp
Tssr108659	Chr11:69405442-69405461 (-)	8,223 bp
Tssr108658	Chr11:69405268-69405286 (-)	8,398 bp
Tssr108657	Chr11:69405231-69405259 (-)	8,430 bp
Tssr108656	Chr11:69404972-69404996 (-)	8,691 bp
Tssr108655	Chr11:69401338-69401367 (-)	12,322 bp
Tssr108654	Chr11:69399602-69399606 (-)	14,071 bp
Tssr108653	Chr11:69399421-69399445 (-)	14,242 bp
Tssr108652	Chr11:69399320-69399338 (-)	14,346 bp
Tssr108651	Chr11:69399307-69399313 (-)	14,365 bp
Tssr108650	Chr11:69399177-69399192 (-)	14,490 bp
Tssr108649	Chr11:69398945-69398999 (-)	14,703 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 & Copyright Notice Send questions and comments to User Support.	last database update 08/13/2019 MGI 6.14