Human Gene VCPKMT (uc001wxo.1)
  Description: Homo sapiens methyltransferase like 21D (VCPKMT), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr14:50,575,350-50,583,297 Size: 7,948 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr14:50,576,417-50,583,270 Size: 6,854 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:50,575,350-50,583,297)mRNA (may differ from genome)Protein (229 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMGIneXtProtOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MT21D_HUMAN
DESCRIPTION: RecName: Full=Methyltransferase-like protein 21D; EC=2.1.1.-;
FUNCTION: Probable methyltransferase (By similarity).
SIMILARITY: Belongs to the methyltransferase superfamily. METTL21 family.
SEQUENCE CAUTION: Sequence=CAD62329.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.41 RPKM in Spleen
Total median expression: 306.26 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.1027-0.448 Picture PostScript Text
3' UTR -253.471067-0.238 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019410 - Nicotinamide_N-MeTfrase-like

Pfam Domains:
PF10294 - Lysine methyltransferase

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases

ModBase Predicted Comparative 3D Structure on Q9H867
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0016279 protein-lysine N-methyltransferase activity
GO:0016740 transferase activity
GO:0051117 ATPase binding

Biological Process:
GO:0006479 protein methylation
GO:0018022 peptidyl-lysine methylation
GO:0018023 peptidyl-lysine trimethylation
GO:0032259 methylation
GO:0032780 negative regulation of ATPase activity

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  BC027585 - Homo sapiens chromosome 14 open reading frame 138, mRNA (cDNA clone IMAGE:4831331), partial cds.
AK129564 - Homo sapiens cDNA FLJ26053 fis, clone PRS03169.
LP895299 - Sequence 163 from Patent EP3253886.
JD299673 - Sequence 280697 from Patent EP1572962.
AK023982 - Homo sapiens cDNA FLJ13920 fis, clone Y79AA1000420.
BX247997 - human full-length cDNA clone CS0DH005YM12 of T cells (Jurkat cell line) of Homo sapiens (human).
JD207258 - Sequence 188282 from Patent EP1572962.
JD511904 - Sequence 492928 from Patent EP1572962.
JD463716 - Sequence 444740 from Patent EP1572962.
JD206246 - Sequence 187270 from Patent EP1572962.
JD510714 - Sequence 491738 from Patent EP1572962.
JD552860 - Sequence 533884 from Patent EP1572962.
LF209550 - JP 2014500723-A/17053: Polycomb-Associated Non-Coding RNAs.
JD184428 - Sequence 165452 from Patent EP1572962.
JD422768 - Sequence 403792 from Patent EP1572962.
JD358102 - Sequence 339126 from Patent EP1572962.
JD301492 - Sequence 282516 from Patent EP1572962.
BC105118 - Homo sapiens chromosome 14 open reading frame 138, mRNA (cDNA clone MGC:132778 IMAGE:8144121), complete cds.
BC143673 - Homo sapiens chromosome 14 open reading frame 138, mRNA (cDNA clone MGC:177204 IMAGE:9052187), complete cds.
JD053983 - Sequence 35007 from Patent EP1572962.
BC143674 - Homo sapiens chromosome 14 open reading frame 138, mRNA (cDNA clone MGC:177205 IMAGE:9052188), complete cds.
JD554337 - Sequence 535361 from Patent EP1572962.
JD058269 - Sequence 39293 from Patent EP1572962.
JD263278 - Sequence 244302 from Patent EP1572962.
JD080626 - Sequence 61650 from Patent EP1572962.
LF329421 - JP 2014500723-A/136924: Polycomb-Associated Non-Coding RNAs.
MA564998 - JP 2018138019-A/136924: Polycomb-Associated Non-Coding RNAs.
MA445127 - JP 2018138019-A/17053: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H867 (Reactome details) participates in the following event(s):

R-HSA-8932276 VCPKMT (METTL21D) transfers 3xCH3 from 3xAdoMet to VCP
R-HSA-8876725 Protein methylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZLA3, B7ZLA4, C14orf138, METTL21D, MT21D_HUMAN, NM_024558, NP_078834, Q2M2X3, Q86T12, Q9H867
UCSC ID: uc001wxo.1
RefSeq Accession: NM_024558
Protein: Q9H867 (aka MT21D_HUMAN)
CCDS: CCDS9696.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024558.2
exon count: 6CDS single in 3' UTR: no RNA size: 1784
ORF size: 690CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1580.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.