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VCPKMT Gene

protein-coding GIFtS: 36
GCID: GC14M050577

Valosin Containing Protein Lysine (K) Methyltransferase

(Previous names: chromosome 14 open reading frame 138, methyltransferase...)
(Previous symbols: C14orf138, METTL21D)

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
Valosin Containing Protein Lysine (K) Methyltransferase¹ ²		VCP-KMT² ³
C14orf138¹ ² ³ ⁵		VCP Lysine Methyltransferase² ³
METTL21D¹ ² ³ ⁵		Chromosome 14 Open Reading Frame 138¹
Methyltransferase Like 21D¹ ²		Protein-Lysine Methyltransferase METTL21D²
Methyltransferase-Like Protein 21D² ³		EC 2.1.1.-³
Valosin-Containing Protein Lysine Methyltransferase² ³

External Ids:	HGNC: 20352¹	Entrez Gene: 79609²	Ensembl: ENSG00000100483⁷	OMIM: 615260⁵	UniProtKB: Q9H867³

Export aliases for VCPKMT gene to outside databases

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for VCPKMT Gene:

VCPKMT (valosin containing protein lysine (K) methyltransferase) is a protein-coding gene. GO annotations related to this gene include protein-lysine N-methyltransferase activity. An important paralog of this gene is METTL21B.

UniProtKB/Swiss-Prot: MT21D_HUMAN, Q9H867

Function: Protein-lysine N-methyltransferase that specifically trimethylates 'Lys-315' of VCP/p97; this

modification may decrease VCP ATPase activity

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:

Search for regulatory transcription factor binding sites for VCPKMT
Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

Search Chromatin IP Primers for VCPKMT

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VCPKMT

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 14q21.3 Ensembl cytogenetic band: 14q21.3 HGNC cytogenetic band: 14q21.3

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

GeneLoc information about chromosome 14 GeneLoc Exon Structure

GeneLoc location for GC14M050577: view genomic region (about GC identifiers)

Start:	50,575,350 bp from pter	End:	50,583,318 bp from pter
Size:	7,969 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: MT21D_HUMAN, Q9H867 (See protein sequence)

Recommended Name: Protein-lysine methyltransferase METTL21D

Size: 229 amino acids; 25807 Da

Subunit: Interacts with ALKBH6. Interacts with ASPSCR1 and UBXN6; interaction with ASPSCR1, but not with UBXN6,

enhances VCP methylation

Sequence caution: Sequence=CAD62329.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

1 PDB 3D structure from and Proteopedia for VCPKMT:

4LG1 (3D)

Secondary accessions: B7ZLA3 B7ZLA4 Q2M2X3 Q86T12

Alternative splicing: 5 isoforms: Q9H867-4 Q9H867-1 Q9H867-2 Q9H867-3 Q9H867-5 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VCPKMT: NX_Q9H867

Explore proteomics data for VCPKMT at MOPED

Post-translational modifications:

Ubiquitination² at Lys122

Modification sites at PhosphoSitePlus

See VCPKMT Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts):

NP_001035752.1 NP_078834.2

ENSEMBL proteins:

ENSP00000379201 ENSP00000437113 ENSP00000379200

VCPKMT Human Recombinant Protein Products:

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	antibodies-online proteins for VCPKMT
	antibodies-online peptides for VCPKMT

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	antibodies-online kits for VCPKMT (2 products)

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:

IPR019410 Nicotinamide_N-MeTfrase-like

Graphical View of Domain Structure for InterPro Entry Q9H867

ProtoNet protein and cluster: Q9H867

UniProtKB/Swiss-Prot: MT21D_HUMAN, Q9H867

Similarity: Belongs to the methyltransferase superfamily. METTL21 family

Find genes that share domains with VCPKMT About GenesLikeMe

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: MT21D_HUMAN, Q9H867

Function: Protein-lysine N-methyltransferase that specifically trimethylates 'Lys-315' of VCP/p97; this

modification may decrease VCP ATPase activity

Enzyme Number (IUBMB): EC 2.1.1.-¹

Gene Ontology (GO): 2 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	IPI	--
GO:0016279	protein-lysine N-methyltransferase activity	IDA	--

Find genes that share ontologies with VCPKMT About GenesLikeMe

Phenotypes:
1 MGI phenotypic allele

for Mettl21d (no phenotypes)

Find genes that share phenotypes with VCPKMT About GenesLikeMe

Animal Models:
MGI mouse knock-out Vcpkmt^{tm1(KOMP)Vlcg} for VCPKMT

genOway: Develop your customized and physiologically relevant rodent model for VCPKMT

miRNA Products:		miRTarBase miRNAs that target VCPKMT: hsa-mir-130b-3p (MIRT020242), hsa-mir-30b-5p (MIRT023432), hsa-mir-331-3p (MIRT019242), hsa-mir-32-5p (MIRT028304)

		Block miRNA regulation of human, mouse, rat VCPKMT using miScript Target Protectors
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In Situ Assay
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

MT21D_HUMAN, Q9H867: Cytoplasm

Gene Ontology (GO): 2 cellular component terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005575	cellular_component	ND	--
GO:0005737	cytoplasm	IEA	--

Find genes that share ontologies with VCPKMT About GenesLikeMe

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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Custom Pathway & Disease-focused RT² Profiler PCR Arrays for VCPKMT
Interactions:

Search GeneGlobe Interaction Network for VCPKMT

STRING Interaction Network Preview (showing 5 interactants - click image to see 10)

Selected Interacting proteins for VCPKMT (ENSP00000379201⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 10)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
MUS81	ENSP00000307853⁴	STRING: ENSP00000307853
TMA16	ENSP00000351380⁴	STRING: ENSP00000351380
FARS2	ENSP00000274680⁴	STRING: ENSP00000274680
SLC26A11	ENSP00000355384⁴	STRING: ENSP00000355384
SNRPD2	ENSP00000342374⁴	STRING: ENSP00000342374

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Gene Ontology (GO): 1 biological process term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0018023	peptidyl-lysine trimethylation	IDA	--

Find genes that share ontologies with VCPKMT About GenesLikeMe

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for VCPKMT (MT21D)

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for VCPKMT gene (2 alternative transcripts):

NM_001040662.1 NM_024558.2

5 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000569518(uc001wxn.1) ENST00000395860 ENST00000491402(uc001wxo.1 uc001wxp.1 uc001wxq.1)

ENST00000484763 ENST00000395859

miRNA Products:		Block miRNA regulation of human, mouse, rat VCPKMT using miScript Target Protectors
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Selected AceView cDNA sequences (see all 289):

CA447489 BI767189 CB157850 BM542870 BE675872 N54093 AA846566 BG617243

AI419975 BQ023799 AA262031 CR601939 BM263987 N54196 BQ023936 BI758040

BE675871 BM127111 N56889 AL135612 AA809852 AI272033 BI324870 AA256544

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for VCPKMT (see all 8) About this scheme

ExUns:	1a	·	1b	^	2a	·	2b	·	2c	^	3a	·	3b	^	4	^	5a	·	5b	^	6	^	7	^	8	^	9a	·	9b	·	9c	·	9d
SP1:					-				-		-								-		-				-
SP2:					-						-								-		-				-
SP3:									-		-								-		-				-
SP4:					-						-								-		-		-		-
SP5:											-								-				-		-

ECgene alternative splicing isoforms for VCPKMT

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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VCPKMT expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

VCPKMT Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

VCPKMT Protein Expression

Custom PCR Arrays for VCPKMT

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of eukaryotes.

Orthologs for VCPKMT gene from Selected species (see all 15) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Mettl21d⁵ Vcpkmt¹	methyltransferase like 21D⁵ valosin containing protein lysine (K) methyltransferase¹	87.43(n)¹ 89.91(a)¹		12 (28.92 cM)⁵ 207965¹ NM_001033236.2¹ NP_001028408.2¹ 69577628⁵
chicken (Gallus gallus)	Aves	METTL21D¹	methyltransferase like 21D	66.67(n) 67.44(a)		423571 XM_421460.4 XP_421460.3
lizard (Anolis carolinensis)	Reptilia	VCPKMT⁶	valosin containing protein lysine (K) methyltransf...	76(a)	1 ↔ 1	AAWZ02039455(2395-8359)
tropical clawed frog (Xenopus tropicalis)	Amphibia	Str.15857²	Transcribed sequence with weak similarity to protein more	73.77(n)		CF591215.1
zebrafish (Danio rerio)	Actinopterygii	vcpkmt¹	valosin containing protein lysine (K) methyltransferase	61.05(n) 61.8(a)		751625 NM_001045345.1 NP_001038810.1
worm (Caenorhabditis elegans)	Secernentea	C42C1.13¹	C42C1.13	47.37(n) 36.84(a)		178175 NM_001129287.2 NP_001122759.1
baker's yeast (Saccharomyces cerevisiae)	Saccharomycetes	--	Putative protein of unknown function with seven be...	28(a)	1 → many	XIV(587107-587847) YNL024C
thale cress (Arabidopsis thaliana)	eudicotyledons	AT1G73320¹	AT1G73320	48.82(n) 38.8(a)		843666 NM_105991.4 NP_177475.3
rice (Oryza sativa)	Liliopsida	Os06g0101100¹	Os06g0101100	47.62(n) 36.51(a)		4339829 NM_001063063.1 NP_001056528.1

ENSEMBL Gene Tree for VCPKMT (if available)
TreeFam Gene Tree for VCPKMT (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for VCPKMT gene

METTL21B² METTL21C² METTL21A²

1 SIMAP similar gene for VCPKMT using alignment to 1 protein entry: MT21D_HUMAN:

METTL21A

Find genes that share paralogs with VCPKMT About GenesLikeMe

1 Pseudogenes.org Pseudogene for VCPKMT
PGOHUM00000243970

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 14 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs11455635^1,2	C	--	50574928(+)	`AAAAA-/A/A A/AAAGAGAA`	6	--	ds500¹ cds¹		1		NA	2
rs117792549^1,2	F	--	50574930(+)	`AAAAGA/GGAAAG`	4	--	ds500¹		1		NA	120
rs76624508^1,2	C	--	50575083(+)	`AACAGC/TTAGCA`	4	--	ds500¹		5		NA CSA WA EA	362
rs60842462^1,2	C,F	--	50575110(+)	`AAGCAC/TCACAG`	4	--	ds500¹		2		WA	120
rs7156871^1,2	C,F,H	--	50575160(+)	`CTAAGG/AACAGT`	4	--	ds500¹		10		NS EA NA WA	1200
rs117557401^1,2	F	--	50575199(+)	`ACCAGC/GAAAGG`	4	--	ds500¹		1		NA	120
rs56191746^1,2	C,F	--	50575253(+)	`TCTTGA/GCTTGT`	4	--	ds500¹		2		WA	120
rs79692900^1,2	C,F	--	50575280(+)	`AATAGG/CGCTGC`	4	--	ds500¹		1		WA	118
rs17122134^1,2	C,F,H	--	50575302(+)	`TTAACT/GGTTTA`	4	--	ds500¹		8		NA NS EA	672
rs188325493^1,2		--	50575392(+)	`ATGTAC/GCATCT`	4	--	ut3¹ nc-transcript-variant		0	--	--	--	--

HapMap Linkage Disequilibrium report for VCPKMT (50575350 - 50583318 bp)

Structural Variations
Database of Genomic Variants (DGV) variations for VCPKMT: --

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing VCPKMT

DNA2.0 Custom Variant and Variant Library Synthesis for VCPKMT

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 615260 OMIM disorders: --

Find genes that share disorders with VCPKMT About GenesLikeMe

Export disorders for VCPKMT gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for VCPKMT gene integrated from 10 sources:
(articles sorted by number of sources associating them with VCPKMT)

Utopia: connect your pdf to the dynamic
world of online information

Lysine methylation of VCP by a member of a novel human protein methyltransferase family. (PubMed id 22948820)^{1, 2, 3} Kernstock S.... Falnes P.O. (Nat. Commun. 2012)
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. (PubMed id 23349634)^{1, 2} Cloutier P.... Coulombe B. (PLoS Genet. 2013)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S.... Malek J. (Genome Res. 2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (Nat. Genet. 2004)
N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)² Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
The DNA sequence and analysis of human chromosome 14. (PubMed id 12508121)² Heilig R.... Weissenbach J. (Nature 2003)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(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, Kegg, and/or H-InvDB)
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Entrez Gene: 79609	HGNC: 20352	AceView: SOS2andC14orf138	Ensembl:ENSG00000100483	euGenes: HUgn79609
ECgene: VCPKMT	H-InvDB: VCPKMT

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for VCPKMT	Pharmacogenomics, SNPs, Pathways

Intellectual Property for VCPKMT gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for VCPKMT gene:
Search GeneIP for patents involving VCPKMT

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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VCPKMT Gene

Valosin Containing Protein Lysine (K) Methyltransferase

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VCPKMT Gene

Valosin Containing Protein Lysine (K) Methyltransferase

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for VCPKMT gene

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Intellectual Property
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