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VCPKMT Gene(Protein Coding)

Valosin Containing Protein Lysine Methyltransferase

GCID:
GC14M050106
GIFtS:
43
Genes Participants
UDN Logo

Aliases for VCPKMT Gene

Aliases for VCPKMT Gene

  • Valosin Containing Protein Lysine Methyltransferase 2 3 5
  • Valosin Containing Protein Lysine (K) Methyltransferase 2 3
  • Methyltransferase-Like Protein 21D 3 4
  • VCP Lysine Methyltransferase 3 4
  • Methyltransferase Like 21D 2 3
  • C14orf138 3 4
  • METTL21D 3 4
  • VCP-KMT 3 4
  • Valosin-Containing Protein Lysine Methyltransferase 4
  • Protein-Lysine Methyltransferase METTL21D 3
  • Chromosome 14 Open Reading Frame 138 2
  • EC 2.1.1.- 4

External Ids for VCPKMT Gene

Previous HGNC Symbols for VCPKMT Gene

  • C14orf138
  • METTL21D

Previous GeneCards Identifiers for VCPKMT Gene

  • GC14M050577

Summaries for VCPKMT Gene

GeneCards Summary for VCPKMT Gene

VCPKMT (Valosin Containing Protein Lysine Methyltransferase) is a Protein Coding gene. Among its related pathways are Metabolism of proteins. GO annotations related to this gene include protein-lysine N-methyltransferase activity. An important paralog of this gene is METTL21A.

UniProtKB/Swiss-Prot for VCPKMT Gene

  • Protein-lysine N-methyltransferase that specifically trimethylates Lys-315 of VCP/p97; this modification may decrease VCP ATPase activity.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VCPKMT Gene

Genomics for VCPKMT Gene

Products:

  1. Regulatory Element

Regulatory Elements for VCPKMT Gene

Enhancers for VCPKMT Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14F050080 1.6 FANTOM5 Ensembl ENCODE 40.3 +31.5 31472 8.9 HDGF TBP PKNOX1 TBL1XR1 WRNIP1 BMI1 ZBTB40 EGR1 ELK1 CBX5 VCPKMT RNU6-189P DNAAF2 ATL1 ATP5S LINC01588 ARF6 KLHDC2 NEMF SOS2
GH14F050055 1.8 FANTOM5 Ensembl ENCODE 32.4 +55.5 55539 10.9 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 VCPKMT LINC01588 POLE2 KLHDC2 RNU6-189P ATP5S RHOQP1 RPS29 SOS2 ARF6
GH14F050017 1.2 Ensembl ENCODE 30.1 +97.9 97872 3.1 PKNOX1 MLX ZFP64 ARID4B SIN3A YY1 CBX5 FOS ZNF202 PPARG VCPKMT KLHDC2 POLE2 RNU6-189P LINC01588 GC14M050001 PDLIM1P1
GH14F049860 1.5 FANTOM5 ENCODE 23.9 +254.3 254306 4.6 HDGF PKNOX1 CREB3L1 MLX WRNIP1 ARID4B SIN3A FEZF1 DMAP1 YY1 POLE2 VCPKMT RHOQP1 RPS29 MGAT2 KLHDC1 RPL36AL LINC01588 MAP4K5 LRR1
GH14F050229 1.3 Ensembl ENCODE 24.3 -115.0 -115038 4.3 PKNOX1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF48 YY1 SLC30A9 VCPKMT ATP5S SOS2 LOC105370486
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VCPKMT on UCSC Golden Path with GeneCards custom track

Promoters for VCPKMT Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000097592 300 1801 PKNOX1 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF207

Genomic Location for VCPKMT Gene

Chromosome:
14
Start:
50,108,632 bp from pter
End:
50,116,600 bp from pter
Size:
7,969 bases
Orientation:
Minus strand

Genomic View for VCPKMT Gene

Genes around VCPKMT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VCPKMT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VCPKMT Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for VCPKMT Gene

Proteins for VCPKMT Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for VCPKMT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H867-MT21D_HUMAN
    Recommended name:
    Protein-lysine methyltransferase METTL21D
    Protein Accession:
    Q9H867
    Secondary Accessions:
    • B7ZLA3
    • B7ZLA4
    • Q2M2X3
    • Q86T12

    Protein attributes for VCPKMT Gene

    Size:
    229 amino acids
    Molecular mass:
    25807 Da
    Quaternary structure:
    • Interacts with ALKBH6. Interacts with ASPSCR1 and UBXN6; interaction with ASPSCR1, but not with UBXN6, enhances VCP methylation.
    SequenceCaution:
    • Sequence=CAD62329.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for VCPKMT Gene

    Alternative splice isoforms for VCPKMT Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VCPKMT Gene

Protein Expression for VCPKMT Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for VCPKMT Gene

  • Ubiquitination at Lys 122
  • Modification sites at PhosphoSitePlus

Other Protein References for VCPKMT Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VCPKMT Gene

Domains & Families for VCPKMT Gene

Gene Families for VCPKMT Gene

HGNC:

Protein Domains for VCPKMT Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VCPKMT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H867

UniProtKB/Swiss-Prot:

MT21D_HUMAN :
  • Belongs to the methyltransferase superfamily. METTL21 family.
Family:
  • Belongs to the methyltransferase superfamily. METTL21 family.
genes like me logo Genes that share domains with VCPKMT: view

Function for VCPKMT Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for VCPKMT Gene

UniProtKB/Swiss-Prot Function:
Protein-lysine N-methyltransferase that specifically trimethylates Lys-315 of VCP/p97; this modification may decrease VCP ATPase activity.

Enzyme Numbers (IUBMB) for VCPKMT Gene

Gene Ontology (GO) - Molecular Function for VCPKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22948820
GO:0008168 methyltransferase activity IEA --
GO:0016279 protein-lysine N-methyltransferase activity IDA 22948820
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with VCPKMT: view
genes like me logo Genes that share phenotypes with VCPKMT: view

Animal Models for VCPKMT Gene

MGI Knock Outs for VCPKMT:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VCPKMT Gene

Localization for VCPKMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for VCPKMT Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VCPKMT gene
Compartment Confidence
cytosol 5
nucleus 2

Gene Ontology (GO) - Cellular Components for VCPKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with VCPKMT: view

Pathways & Interactions for VCPKMT Gene

genes like me logo Genes that share pathways with VCPKMT: view

Pathways by source for VCPKMT Gene

SIGNOR curated interactions for VCPKMT Gene

Is activated by:

Gene Ontology (GO) - Biological Process for VCPKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0018023 peptidyl-lysine trimethylation IDA 22948820
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with VCPKMT: view

Drugs & Compounds for VCPKMT Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for VCPKMT Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for VCPKMT Gene

(6) REFSEQ mRNAs :
(289) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VCPKMT Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c · 9d
SP1: - - - - - -
SP2: - - - - -
SP3: - - - - -
SP4: - - - - - -
SP5: - - - -
SP6: - -
SP7: -
SP8:

Relevant External Links for VCPKMT Gene

GeneLoc Exon Structure for
VCPKMT
ECgene alternative splicing isoforms for
VCPKMT

Expression for VCPKMT Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VCPKMT Gene

mRNA expression in normal human tissues for VCPKMT Gene
mRNA expression by BioGPS for VCPKMT GenemRNA expression by GTEx for VCPKMT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VCPKMT Gene

This gene is overexpressed in Oral epithelium (44.3), Lymph node (15.3), and Fetal ovary (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VCPKMT Gene



NURSA nuclear receptor signaling pathways regulating expression of VCPKMT Gene:

VCPKMT
genes like me logo Genes that share expression patterns with VCPKMT: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for VCPKMT Gene

Orthologs for VCPKMT Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VCPKMT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia METTL21D 34
  • 100 (n)
VCPKMT 35
  • 100 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia VCPKMT 35
  • 95 (a)
 OneToOne
METTL21D 34
  • 91.85 (n)
cow
(Bos Taurus)
 Mammalia VCPKMT 35
  • 94 (a)
 OneToOne
METTL21D 34
  • 91.8 (n)
mouse
(Mus musculus)
 Mammalia Mettl21d 35
  • 90 (a)
 OneToOne
Vcpkmt 34 16
  • 87.43 (n)
rat
(Rattus norvegicus)
 Mammalia LOC102548559 34
  • 86.55 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia VCPKMT 35
  • 78 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia VCPKMT 35
  • 65 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves METTL21D 34
  • 66.67 (n)
VCPKMT 35
  • 64 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia VCPKMT 35
  • 76 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia vcpkmt 34
  • 66.98 (n)
Str.15857 34
zebrafish
(Danio rerio)
 Actinopterygii vcpkmt 34 35
  • 61.05 (n)
worm
(Caenorhabditis elegans)
 Secernentea C42C1.13 34 35
  • 47.37 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes -- 35
  • 28 (a)
 OneToMany
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT1G73320 34
  • 48.82 (n)
rice
(Oryza sativa)
 Liliopsida Os06g0101100 34
  • 47.62 (n)
Species where no ortholog for VCPKMT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VCPKMT Gene

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

Paralogs for VCPKMT Gene

Paralogs for VCPKMT Gene

(1) SIMAP similar genes for VCPKMT Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for VCPKMT Gene

genes like me logo Genes that share paralogs with VCPKMT: view

Variants for VCPKMT Gene

Sequence variations from dbSNP and Humsavar for VCPKMT Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs10047927 -- 50,114,823(+) ACAAC(A/C)TGTGT intron-variant
rs10144333 -- 50,110,317(+) caacc(C/T)acaga intron-variant
rs10150798 -- 50,109,121(+) TTGGC(C/T)AATAT intron-variant, nc-transcript-variant, utr-variant-3-prime
rs1044751 -- 50,108,703(-) GAATT(C/T)TGGTA intron-variant, nc-transcript-variant, utr-variant-3-prime
rs1044754 -- 50,108,693(-) ATTTA(C/T)AGGCA intron-variant, nc-transcript-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for VCPKMT Gene

Variant ID Type Subtype PubMed ID
esv28926 CNV gain+loss 19812545
nsv564835 CNV gain 21841781

Variation tolerance for VCPKMT Gene

Residual Variation Intolerance Score: 55% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.13; 84.61% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VCPKMT Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VCPKMT

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VCPKMT Gene

Disorders for VCPKMT Gene

Relevant External Links for VCPKMT

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VCPKMT

No disorders were found for VCPKMT Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VCPKMT Gene

Publications for VCPKMT Gene

  1. Lysine methylation of VCP by a member of a novel human protein methyltransferase family. (PMID: 22948820) Kernstock S. … Falnes P.O. (Nat. Commun. 2012) 2 3 4 64
  2. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. (PMID: 23349634) Cloutier P. … Coulombe B. (PLoS Genet. 2013) 3 4 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for VCPKMT Gene

Sources for VCPKMT Gene

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