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KDM6B Gene

protein-coding GIFtS: 40

GC17P007686

lysine (K)-specific demethylase 6B
(Previous names: jumonji domain containing 3, jumonji domain containing 3, histone lysine demethylase )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: JMJD3)

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases
EC 1.14.11.- ^³
JMJD3 ^², ³
KIAA0346 ^¹, ², ³

Descriptions
JmjC domain-containing protein 3 ^³
Jumonji domain-containing protein 3 ^³
Lysine demethylase 6B ^³
jumonji domain containing 3 ^¹
jumonji domain containing 3, histone lysine demethylase ^¹, ²
lysine (K)-specific demethylase 6B ^²
lysine-specific demethylase 6B ^¹

External Ids
HGNC: 29012¹
Entrez Gene: 23135²
UniProtKB: O15054³

Search outside databases for aliases for KDM6B gene

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: KDM6B_HUMAN, O15054

Function: Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby

playing a central role in histone code. Demethylates trimethylated and dimethylated H3 'Lys-27'.

Plays a central role in regulation of posterior development, by regulating HOX gene expression.

Involved in inflammatory response by participating in macrophage differentiation in case of

inflammation by regulating gene expression and macrophage differentiation

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17p13.1 HGNC cytogenetic band: 17p13.1

KDM6B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 17 GeneLoc Exon Structure

GeneLoc location for GC17P007686: (about GC identifiers)

Start:	7,683,960 bp from pter
End:	7,698,843 bp from pter
Size:	14,884 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000017.9 NT_010718.15

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: KDM6B_HUMAN, O15054 (See protein sequence)

Recommended Name: Lysine-specific demethylase 6B

Size: 1679 amino acids; 180411 Da

Cofactor: Ascorbate (By similarity)

Cofactor: Fe(2+)

Subunit: Interacts with TLE1 (By similarity). Component of the MLL4 complex, at least composed of

MLL4, ASH2L, RBBP5, WDR5, and KDM6B

Subcellular location: Nucleus (Probable)

Secondary accessions: Q96G33

Alternative splicing: 2 isoforms: O15054-1 O15054-2

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_001073893.1
Human Recombinant Proteins

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	Recombinant Proteins from Abcam (KDM6B / JMJD3)
	Browse Abnova for Human Recombinant Proteins

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

1 Gene Ontology (GO) cellular component term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	IEA	--

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Antibodies for KDM6B:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for KDM6B
	Browse R&D Systems for Antibodies
	Cell Signaling Technology (CST) Antibodies for KDM6B (JMJD3)
	Antibodies from Abcam (KDM6B / JMJD3), each with their Abpromise^SM
	Browse Abnova for Monoclonal and Polyclonal Antibodies
	Search Novus for antibodies for KDM6B

Assays for KDM6B:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

Graphical View of Domain Structure for InterPro Entry O15054

ProtoNet protein and cluster: O15054

1 Blocks protein family: IPB003347 Transcription factor jumonji

UniProtKB/Swiss-Prot: KDM6B_HUMAN, O15054

Similarity: Belongs to the UTX family

Similarity: Contains 1 JmjC domain

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (KDM6B)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

Browse Origene for 29mer shRNA kit in GFP-retroviral vector

Applied Biosystems Silencer® siRNAs for KDM6B

Sigma-Aldrich siRNA for KDM6B

Browse shRNA at Sigma-Aldrich

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Browse Clone Ranger at Invitrogen for clones
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_001080424
Myc/DDK tagged cDNA clone in CMV expression vector: NM_001080424
untagged cDNA clone in CMV expression vector: NM_001080424

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_001080424

UniProtKB/Swiss-Prot: KDM6B_HUMAN, O15054

Function: Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby

playing a central role in histone code. Demethylates trimethylated and dimethylated H3 'Lys-27'.

Plays a central role in regulation of posterior development, by regulating HOX gene expression.

Involved in inflammatory response by participating in macrophage differentiation in case of

inflammation by regulating gene expression and macrophage differentiation

Induction: By 12-O-tetradecanoylphorbol-13-acetate (TPA) in myeloid leukemia cells

Enzyme Number (IUBMB): EC 1.14.11.-

5/6 Gene Ontology (GO) molecular function terms (links to tree view) (see all 6 ):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005488	binding	IEA	--
GO:0005506	iron ion binding	IEA	--
GO:0016491	oxidoreductase activity	IEA	--
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	IEA	--
GO:0043565	sequence-specific DNA binding	IEA	--

About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

5 Gene Ontology (GO) biological process terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IEA	--
GO:0006954	inflammatory response	IEA	--
GO:0016568	chromatin modification	IEA	--
GO:0016577	histone demethylation	IEA	--
GO:0055114	oxidation reduction	IEA	--

About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for KDM6B

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (KDM6B)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

Browse Origene for 29mer shRNA kit in GFP-retroviral vector

Sigma-Aldrich siRNA for KDM6B

Browse shRNA at Sigma-Aldrich

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_001080424

REFSEQ mRNAs for KDM6B gene:

NM_001080424.1

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_001080424

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_001080424
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_001080424
                                 untagged cDNA clone in CMV expression vector: NM_001080424

Additional cDNA sequence:

AB002344.2 BC009994.1 BC035897.1 BC067879.1

9 DOTS entries:

DT.85105311 DT.95162298 DT.120930861 DT.410301 DT.100689210 DT.100673297 DT.100696592 DT.95114142

DT.95359014

24/255 AceView cDNA sequences (see all 255 ):

BQ649062 BQ721168 BE503406 BQ438795 BG222892 BC009994 NM_203411 BQ013215

BQ013626 C00123 BM696116 AA355717 AI394006 BC057812 AA736517 CD365458

BU734395 BC035897 BM968430 BM849688 AA594247 BE219729 BQ063399 AI671664

Unigene Cluster for KDM6B:

Lysine (K)-specific demethylase 6B

Hs.223678 [show with all ESTs]

Unigene Representative Sequence: NM_001080424

GeneLoc Exon Structure

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

KDM6B expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for KDM6B

¹ / ²

10 probe-sets matching KDM6B gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
41386_i_at²	U95-A	2	1.00	0.50	0.91	1.04	--	--	--	--	--
41387_r_at²	U95-A	2	1.00	0.50	0.71	0.96	--	--	--	--	--
41386_i_at²	U133-A	2	1.00	0.50	--	--	--	--	--	--	--
41387_r_at²	U133-A	2	1.00	0.50	--	--	--	--	--	--	--
213146_at²	U133-A	2	1.00	0.50	--	--	--	--	--	--	--
41386_i_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
41387_r_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
1556067_a_at²	U133Plus2	2	1.00	0.50	--	--	--	--	--	--	--
1556066_at²	U133Plus2	2	1.00	0.50	--	--	--	--	--	--	--
213146_at²	U133Plus2	2	1.00	0.50	--	--	--	--	--	--	--

GeneDecks KDM6B for binary patterns associated with the probe-sets selected above

About GeneDecksing

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Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: GTGCTCAAAC

SOURCE GeneReport for Unigene cluster: Hs.223678

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for KDM6B gene from 4 species

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	JMJD3¹	--	jumonji domain containing 3	91.12(n) 94.18(a)	489481 XM_546599.2 XP_546599.2
rat (Rattus norvegicus)	Jmjd3¹	--	jumonji domain containing 3	86.79(n) 90.64(a)	363630 XM_343919.3 XP_343920.3
mouse (Mus musculus)	Kdm6b⁵ Jmjd3¹	11⁵	KDM1 lysine (K)-specific demethylase 6B⁵ jumonji domain containing 3¹	88.57(n)¹ 92.65(a)¹	216850¹ NM_001017426.1¹ NP_001017426.1¹ AI849352⁵ AK129121⁵ (see all 14)
zebrafish (Danio rerio)	jmjd3¹	--	jumonji domain containing 3, histone lysine demethylase	58.53(n) 58.69(a)	563644 NM_001030178.1 NP_001025349.1

About this table Species with no ortholog for KDM6B

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/69 NCBI SNPs in KDM6B are shown (see all 69 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 42)

AB	SNP ID	Valid	Chr 17 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs2270516^1,2	C,F,H	7691161(+)	`GCACTC/TGCTGC`	1	S/L	mis¹		9		EA EU WA	2298
	rs11078709^1,2	A,C	7690957(+)	`CTGGCC/TACCAG`	1	A/A	syn¹		0	--	--	--	--
	rs3736306^1,2	F,H	7695185(-)	`GGCCAG/TATCTG`	1	I/I	syn¹		5		EA EU WA	1912
--	rs3744249^1,2	C	7692503(+)	`CCCCCA/GCTGAA`	1	P/P	syn¹		0	--	--	--	--
--	rs3744248^1,2	F	7692476(+)	`CAACAC/TGAAGC`	1	H/H	syn¹		1		EA	1482
	rs3744247^1,2	F	7692113(+)	`AACCCC/ACAGGA`	1	P/P	syn¹		1		EA	750
	rs4791840^1,2	A,C,F,H	7684918(+)	`ACTTTC/ATCCTC`	1	--	int¹		4		EU EA WA	406
	rs11871032^1,2	C,F,H	7686336(+)	`TTCGCC/TGGGAG`	1	--	int¹		4		EU EA WA	416
--	rs11657063^1,2	A,C	7686023(+)	`TGCGAC/TGAGGG`	1	--	int¹		0	--	--	--	--
	rs2270517^1,2	F,H	7691572(+)	`CCACCC/TGCTTC`	1	--	int¹		5		EA EU WA	1904

About this table

HapMap Linkage Disequilibrium images for KDM6B (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 611577

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

10/12 PubMed articles for KDM6B gene (see all 12 ):

Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9205841)^{2, 3, 4} Nagase T....Ohara O. (1997)
Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. (PubMed id 18003914)^{3, 4} Hong S....Ge K. (2007)
Physical map of 17p13 and the genes adjacent to p53. (PubMed id 10662545)^{2, 3} Cousin P....Shaw P. (2000)
Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. (PubMed id 18628393)³ Sen G.L....Khavari P.A. (2008)
UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. (PubMed id 17713478)³ Agger K....Helin K. (2007)
The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. (PubMed id 17825402)⁴ De Santa F....Natoli G. (2007)
JMJD3 is a histone H3K27 demethylase. (PubMed id 17923864)³ Xiang Y....Chen C.D. (2007)
A histone H3 lysine 27 demethylase regulates animal posterior development. (PubMed id 17851529)⁴ Lan F....Shi Y. (2007)
An efficient strategy to identify early TPA-responsive genes during differentiation of HL-60 cells. (PubMed id 17193924)⁴ Hu L.Y.... Lin W.C. (2006)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)⁴ Gerhard D.S....Malek J. (2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 23135	HGNC: 29012	AceView: FLJ32499andLOC92162andJMJD3	euGenes: HUgn23135	ECgene: KDM6B
H-InvDB: KDM6B

(According to HUGE)
About This Section

HUGE: KIAA0346

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Licensable Technologies for KDM6B
(Available from WIS Yeda, Salk, Tufts)

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(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
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Products for KDM6B:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for KDM6B-related products

	Millipore Custom Antibody & Bulk Services
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	Antibodies (KDM6B / JMJD3)

Search OriGene for KDM6B

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KDM6B Gene

protein-coding GIFtS: 40

Aliases &
Descriptions
for KDM6B

Summaries
for KDM6B

Genomic Location
for KDM6B

Proteins
for KDM6B

Protein Domains/
Families
for KDM6B

Gene Function
for KDM6B

Pathways & Interactions
for KDM6B

Drugs & Compounds
for KDM6B

Transcripts
for KDM6B

Expression
for KDM6B

Orthologs
for KDM6B

Paralogs
for KDM6B

SNPs/Variants
for KDM6B

Disorders & Mutations
for KDM6B

Medical News
for KDM6B

Publications
for KDM6B

Search for KDM6B

Genome Databases showing KDM6B

Other Databases showing KDM6B

Specialized Databases showing KDM6B

Licensable Technologies
for KDM6B

Services
for KDM6B

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

KDM6B Gene

protein-coding GIFtS: 40

Aliases & Descriptionsfor KDM6B

Summariesfor KDM6B

Genomic Locationfor KDM6B

Proteinsfor KDM6B

Protein Domains/Familiesfor KDM6B

Gene Functionfor KDM6B

Pathways & Interactionsfor KDM6B

Drugs & Compoundsfor KDM6B

Transcriptsfor KDM6B

Expression for KDM6B

Orthologsfor KDM6B

Paralogsfor KDM6B

SNPs/Variantsfor KDM6B

Disorders & Mutationsfor KDM6B

Medical Newsfor KDM6B

Publicationsfor KDM6B

Search for KDM6B

Genome Databases showing KDM6B

Other Databases showing KDM6B

Specialized Databases showing KDM6B

Licensable Technologiesfor KDM6B

Servicesfor KDM6B

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for KDM6B

Summaries
for KDM6B

Genomic Location
for KDM6B

Proteins
for KDM6B

Protein Domains/
Families
for KDM6B

Gene Function
for KDM6B

Pathways & Interactions
for KDM6B

Drugs & Compounds
for KDM6B

Transcripts
for KDM6B

Expression
for KDM6B

Orthologs
for KDM6B

Paralogs
for KDM6B

SNPs/Variants
for KDM6B

Disorders & Mutations
for KDM6B

Medical News
for KDM6B

Publications
for KDM6B

Licensable Technologies
for KDM6B

Services
for KDM6B