Vcpkmt (valosin containing protein lysine (K) methyltransferase) - Rat Genome Database

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Gene: Vcpkmt (valosin containing protein lysine (K) methyltransferase) Mus musculus
Analyze
Symbol: Vcpkmt
Name: valosin containing protein lysine (K) methyltransferase
RGD ID: 1614212
MGI Page MGI
Description: Enables protein methyltransferase activity. Predicted to act upstream of or within methylation. Located in cytoplasm. Orthologous to human VCPKMT (valosin containing protein lysine methyltransferase).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Gm71; hypothetical protein LOC207965; methyltransferase like 21D; methyltransferase-like protein 21D; Mettl21; Mettl21d; Mettl221d; protein-lysine methyltransferase METTL21D; valosin-containing protein lysine methyltransferase; VCP lysine methyltransferase; VCP-KMT
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391269,623,504 - 69,629,883 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1269,624,402 - 69,629,884 (-)EnsemblGRCm39 Ensembl
GRCm381269,576,735 - 69,583,017 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1269,577,628 - 69,583,110 (-)EnsemblGRCm38mm10GRCm38
MGSCv371270,678,615 - 70,684,015 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361270,498,281 - 70,501,620 (-)NCBIMGSCv36mm8
Celera1270,666,463 - 70,671,887 (-)NCBICelera
Cytogenetic Map12C2NCBI
cM Map1228.92NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
methylation  (IEA)

Cellular Component
cytoplasm  (IDA,ISO)
cytosol  (IBA,ISO)
protein-containing complex  (IBA,ISO)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:16141072   PMID:16141073   PMID:18799693   PMID:21677750   PMID:21873635  
PMID:24194600   PMID:26544960   PMID:27626380   PMID:32325033   PMID:38355793  


Genomics

Comparative Map Data
Vcpkmt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391269,623,504 - 69,629,883 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1269,624,402 - 69,629,884 (-)EnsemblGRCm39 Ensembl
GRCm381269,576,735 - 69,583,017 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1269,577,628 - 69,583,110 (-)EnsemblGRCm38mm10GRCm38
MGSCv371270,678,615 - 70,684,015 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361270,498,281 - 70,501,620 (-)NCBIMGSCv36mm8
Celera1270,666,463 - 70,671,887 (-)NCBICelera
Cytogenetic Map12C2NCBI
cM Map1228.92NCBI
VCPKMT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381450,102,716 - 50,116,572 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1450,108,632 - 50,116,600 (-)EnsemblGRCh38hg38GRCh38
GRCh371450,575,355 - 50,583,290 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361449,645,100 - 49,653,047 (-)NCBINCBI36Build 36hg18NCBI36
Build 341449,645,105 - 49,653,047NCBI
Celera1430,442,491 - 30,450,433 (-)NCBICelera
Cytogenetic Map14q21.3NCBI
HuRef1430,700,814 - 30,708,767 (-)NCBIHuRef
CHM1_11450,514,037 - 50,522,000 (-)NCBICHM1_1
T2T-CHM13v2.01444,309,674 - 44,322,811 (-)NCBIT2T-CHM13v2.0
Vcpkmt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8693,772,558 - 93,778,400 (-)NCBIGRCr8
mRatBN7.2688,036,485 - 88,042,151 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl688,036,494 - 88,042,000 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0691,880,342 - 91,884,336 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06101,330,561 - 101,336,079 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4691,602,980 - 91,610,509 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera686,533,202 - 86,537,196 (-)NCBICelera
Cytogenetic Map6q24NCBI
Vcpkmt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540912,622,259 - 12,632,246 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540912,622,259 - 12,632,246 (+)NCBIChiLan1.0ChiLan1.0
VCPKMT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21551,245,296 - 51,257,054 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11450,461,800 - 50,473,274 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01430,695,992 - 30,707,327 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11449,002,181 - 49,013,187 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1449,002,181 - 49,013,187 (-)Ensemblpanpan1.1panPan2
VCPKMT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1826,611,333 - 26,636,700 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl826,625,677 - 26,636,316 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha826,364,923 - 26,390,315 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0826,789,131 - 26,814,525 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl826,807,761 - 26,814,116 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1826,444,053 - 26,469,453 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0826,516,540 - 26,541,946 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0826,835,201 - 26,860,599 (-)NCBIUU_Cfam_GSD_1.0
Vcpkmt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405947353 - 5,484 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049401971,070 - 5,090 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004940197408 - 5,645 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VCPKMT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1179,899,646 - 179,906,967 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11179,899,642 - 179,907,439 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21200,260,935 - 200,262,345 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VCPKMT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12427,173,859 - 27,182,941 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2427,173,840 - 27,182,924 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605315,504,133 - 15,512,575 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vcpkmt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473118,694,647 - 18,704,199 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473118,694,765 - 18,704,199 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Vcpkmt
208 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:148
Count of miRNA genes:125
Interacting mature miRNAs:131
Transcripts:ENSMUST00000058639
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12541844077031203Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12955000084146774Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121166000197176774Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121534102679040364Mouse
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121759644780956883Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
1357479Splwt1_mspleen weight 1 (mouse)Not determined124169317590887526Mouse
1357757Lnopy2_mlens opacity 2 (mouse)Not determined125284662686846796Mouse
1357749Vtbt13_mvertebral trabecular bone trait 13 (mouse)Not determined125313200287132145Mouse
12832727Ahrq1_mairway hyperresponsiveness QTL 1 (mouse)125469591082665939Mouse
13504832Bacszq2_mbaculum size QTL 2 (mouse)125694579875345787Mouse
27226728Tibl20_mtibia length 20, 16 week (mouse)125914678693866774Mouse
27226776Tibl6_mtibia length 6, 5 week (mouse)126064678692666774Mouse
10043948Pbft6_mpercent body fat 6 (mouse)Not determined126120542795205427Mouse
1301476Pbwg12_mpostnatal body weight growth 12 (mouse)Not determined126204016496040364Mouse
27226797Scvln19_msacral vertebrae length 2, 16 week (mouse)126214678699466259Mouse
10043895Bw20_mbody weight QTL 20 (mouse)Not determined126230825296308252Mouse
1301046Par3_mpulmonary adenoma resistance 3 (mouse)Not determined126395670897956883Mouse
1301337Cdcs8_mcytokine deficiency colitis susceptibility 8 (mouse)Not determined126468908398689229Mouse
1300633Cdcs7_mcytokine deficiency colitis susceptibility 7 (mouse)Not determined126468908398689229Mouse
14746976Manh73_mmandible shape 73 (mouse)126585713199857131Mouse
27226771Tibl14_mtibia length 14, 10 week (mouse)126834677498766259Mouse
27226793Feml10_mfemur length 10, 5 week (mouse)1268346774113363620Mouse

Markers in Region
Z11664  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381269,584,425 - 69,584,590UniSTSGRCm38
MGSCv371270,685,412 - 70,685,577UniSTSGRCm37
Celera1270,673,278 - 70,673,443UniSTS
Cytogenetic Map12C2UniSTS
Cytogenetic Map12C3-DUniSTS
Whitehead_YAC12 UniSTS
UniSTS:235512  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381269,582,529 - 69,582,851UniSTSGRCm38
MGSCv371270,683,516 - 70,683,838UniSTSGRCm37
Celera1270,671,388 - 70,671,710UniSTS
Celera6107,106,759 - 107,106,991UniSTS
Cytogenetic Map12C2UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000058639   ⟹   ENSMUSP00000055002
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1269,624,402 - 69,629,884 (-)Ensembl
GRCm38.p6 Ensembl1269,577,628 - 69,583,110 (-)Ensembl
RefSeq Acc Id: ENSMUST00000238220   ⟹   ENSMUSP00000158858
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1269,624,456 - 69,629,791 (-)Ensembl
GRCm38.p6 Ensembl1269,577,682 - 69,583,017 (-)Ensembl
RefSeq Acc Id: ENSMUST00000238319
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1269,626,450 - 69,629,789 (-)Ensembl
GRCm38.p6 Ensembl1269,579,676 - 69,583,015 (-)Ensembl
RefSeq Acc Id: ENSMUST00000238563
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1269,629,050 - 69,629,709 (-)Ensembl
GRCm38.p6 Ensembl1269,582,276 - 69,582,935 (-)Ensembl
RefSeq Acc Id: ENSMUST00000238784   ⟹   ENSMUSP00000158802
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1269,624,625 - 69,629,884 (-)Ensembl
GRCm38.p6 Ensembl1269,577,851 - 69,583,110 (-)Ensembl
RefSeq Acc Id: NM_001033236   ⟹   NP_001028408
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391269,623,509 - 69,629,791 (-)NCBI
GRCm381269,576,735 - 69,583,017 (-)NCBI
MGSCv371270,678,615 - 70,684,015 (-)RGD
Celera1270,666,463 - 70,671,887 (-)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001379044   ⟹   NP_001365973
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391269,623,509 - 69,629,791 (-)NCBI
GRCm381269,576,735 - 69,583,017 (-)NCBI
Sequence:
RefSeq Acc Id: NR_166433
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391269,623,509 - 69,629,791 (-)NCBI
GRCm381269,576,735 - 69,583,017 (-)NCBI
Sequence:
RefSeq Acc Id: NR_166434
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391269,623,509 - 69,629,791 (-)NCBI
GRCm381269,576,735 - 69,583,017 (-)NCBI
Sequence:
RefSeq Acc Id: NR_166435
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391269,623,509 - 69,629,791 (-)NCBI
GRCm381269,576,735 - 69,583,017 (-)NCBI
Sequence:
RefSeq Acc Id: NR_166437
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391269,623,509 - 69,629,791 (-)NCBI
GRCm381269,576,735 - 69,583,017 (-)NCBI
Sequence:
RefSeq Acc Id: XM_036157295   ⟹   XP_036013188
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391269,623,504 - 69,629,883 (-)NCBI
Sequence:
RefSeq Acc Id: XR_004937479
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391269,624,408 - 69,629,883 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001028408   ⟸   NM_001033236
- Peptide Label: isoform 2
- UniProtKB: B2RSP0 (UniProtKB/Swiss-Prot),   Q3UML0 (UniProtKB/Swiss-Prot),   Q8C436 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001365973   ⟸   NM_001379044
- Peptide Label: isoform 1
RefSeq Acc Id: ENSMUSP00000158858   ⟸   ENSMUST00000238220
RefSeq Acc Id: ENSMUSP00000158802   ⟸   ENSMUST00000238784
RefSeq Acc Id: ENSMUSP00000055002   ⟸   ENSMUST00000058639
RefSeq Acc Id: XP_036013188   ⟸   XM_036157295
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8C436-F1-model_v2 AlphaFold Q8C436 1-228 view protein structure

Promoters
RGD ID:8678412
Promoter ID:EPDNEW_M17236
Type:multiple initiation site
Name:Vcpkmt_1
Description:Mus musculus valosin containing protein lysine methyltransferase, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381269,583,017 - 69,583,077EPDNEW
RGD ID:6823028
Promoter ID:MM_KWN:11815
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_001033236,   UC007NSM.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361270,683,581 - 70,684,242 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2684917 AgrOrtholog
Ensembl Genes ENSMUSG00000049882 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000058639 ENTREZGENE
  ENSMUST00000058639.11 UniProtKB/Swiss-Prot
  ENSMUST00000238220 ENTREZGENE
  ENSMUST00000238220.2 UniProtKB/TrEMBL
  ENSMUST00000238784.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Methyltransf_16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM-dependent_MTases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:207965 UniProtKB/Swiss-Prot
MGD MGI:2684917 ENTREZGENE
NCBI Gene 207965 ENTREZGENE
PANTHER PROTEIN-LYSINE METHYLTRANSFERASE METTL21D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR14614 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Methyltransf_16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Vcpkmt PhenoGen
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A571BDP3_MOUSE UniProtKB/TrEMBL
  A0A571BDU2_MOUSE UniProtKB/TrEMBL
  B2RSP0 ENTREZGENE
  MT21D_MOUSE UniProtKB/Swiss-Prot
  Q3UML0 ENTREZGENE
  Q8C436 ENTREZGENE
UniProt Secondary B2RSP0 UniProtKB/Swiss-Prot
  Q3UML0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Vcpkmt  valosin containing protein lysine (K) methyltransferase  Mettl21d  methyltransferase like 21D  Symbol and/or name change 5135510 APPROVED
2011-07-27 Mettl21d  methyltransferase like 21D  Gm71  predicted gene 71  Symbol and/or name change 5135510 APPROVED