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HEMK1 Gene

protein-coding   GIFtS: 53
GCID: GC03P050606

HemK Methyltransferase Family Member 1

  See HEMK1-related disease
at  

(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
HemK Methyltransferase Family Member 11 2     m.HsaHemKP2
HEMK2 3     EC 2.1.1.-3
MTQ12     M.HsaHemKP3
HEMK Homolog 7kb2     

External Ids:    HGNC: 249231   Entrez Gene: 514092   Ensembl: ENSG000001147357   UniProtKB: Q9Y5R43   

Export aliases for HEMK1 gene to outside databases

Previous GC identifer: GC03P050581


(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 HEMK1 Gene:
HEMK1 (HemK methyltransferase family member 1) is a protein-coding gene. Diseases associated with HEMK1 include acrocephalosyndactylia. GO annotations related to this gene include protein methyltransferase activity and N-methyltransferase activity.

UniProtKB/Swiss-Prot: HEMK1_HUMAN, Q9Y5R4
Function: N5-glutamine methyltransferase responsible for the methylation of the GGQ triplet of the mitochondrial
translation release factor MTRF1L




(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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RefSeq DNA sequence at NCBI GenBank:
NC_000003.11  NT_022517.19  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HEMK1 gene promoter:
         NF-1   AML1a   HTF   FOXD1   LCR-F1   GATA-1   PPAR-gamma1   COMP1   PPAR-gamma2   Zic3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHEMK1 promoter sequence
   Search Chromatin IP Primers for HEMK1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HEMK1


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

Entrez Gene cytogenetic band: 3p21.3   Ensembl cytogenetic band:  3p21.2   HGNC cytogenetic band: 3p21

HEMK1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HEMK1 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P050606:  view genomic region     (about GC identifiers)

Start:
50,606,583 bp from pter      End:
50,622,422 bp from pter
Size:
15,840 bases      Orientation:
plus 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: HEMK1_HUMAN, Q9Y5R4 (See protein sequence)
Recommended Name: HemK methyltransferase family member 1  
Size: 338 amino acids; 38231 Da

Explore the universe of human proteins at neXtProt for HEMK1: NX_Q9Y5R4

Explore proteomics data for HEMK1 at MOPED


See HEMK1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_057257.1  
ENSEMBL proteins: 
 ENSP00000404843   ENSP00000232854   ENSP00000397966   ENSP00000404334   ENSP00000394027  
 ENSP00000404168  

HEMK1 Human Recombinant Protein Products:

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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4 InterPro protein domains:
 IPR004556 Modification_methylase_HemK
 IPR002295 D21N6_MeTrfase
 IPR019874 Release_fac_Glu-N5_MeTfrase
 IPR002052 DNA_methylase_N6_adenine_CS

Graphical View of Domain Structure for InterPro Entry Q9Y5R4

ProtoNet protein and cluster: Q9Y5R4

2 Blocks protein domains:
IPB002052 N-6 Adenine-specific DNA methylase
IPB002296 N12 class N6 adenine-specific DNA methyltransferase signature


UniProtKB/Swiss-Prot: HEMK1_HUMAN, Q9Y5R4
Similarity: Belongs to the protein N5-glutamine methyltransferase family


Find genes that share domains with HEMK1           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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: HEMK1_HUMAN, Q9Y5R4
Function: N5-glutamine methyltransferase responsible for the methylation of the GGQ triplet of the mitochondrial
translation release factor MTRF1L

     Enzyme Number (IUBMB): EC 2.1.1.-1

     Gene Ontology (GO): 4 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IEA--
GO:0008168methyltransferase activity ----
GO:0008170N-methyltransferase activity IEA--
GO:0008276protein methyltransferase activity IEA--
     
Find genes that share ontologies with HEMK1           About GenesLikeMe


Phenotypes:
     4 GenomeRNAi human phenotypes for HEMK1:
 Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e  Synthetic lethal with Ras 

Animal Models:
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Selected qRT-PCR Assays for microRNAs that regulate HEMK1 (see all 21):
hsa-miR-3934 hsa-miR-4291 hsa-miR-892b hsa-miR-185* hsa-miR-125a-3p hsa-miR-764 hsa-miR-1304 hsa-miR-4325
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HEMK1

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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
HEMK1_HUMAN, Q9Y5R4: Mitochondrion
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
mitochondrion5
cytosol2
nucleus1
peroxisome1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm ----
GO:0005739mitochondrion IEA--

Find genes that share ontologies with HEMK1           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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SuperPaths for HEMK1 About    
See pathways by source

SuperPathContained pathways About
1Phenylalanine metabolism
Tyrosine metabolism0.36
2Histidine metabolism
Histidine metabolism


Find genes that share SuperPaths with HEMK1           About GenesLikeMe

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



2 Kegg Pathways  (Kegg details for HEMK1):
    Histidine metabolism
Tyrosine metabolism

    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HEMK1
Interactions:

    Search GeneGlobe Interaction Network for HEMK1

STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

Selected Interacting proteins for HEMK1 (Q9Y5R43 ENSP000002328544) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
InteractantInteraction Details
GeneCardExternal ID(s)
MTRF1LQ9UGC73, ENSP000003562024I2D: score=5 STRING: ENSP00000356202
CARNS1ENSP000003082684STRING: ENSP00000308268
CNDP1ENSP000003516824STRING: ENSP00000351682
DDCENSP000003506164STRING: ENSP00000350616
HALENSP000002612084STRING: ENSP00000261208
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Gene Ontology (GO): 4 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006306DNA methylation IEA--
GO:0006479protein methylation ----
GO:0008152metabolic process ----
GO:0031167rRNA methylation ----

Find genes that share ontologies with HEMK1           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 HEMK1



(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 HEMK1 gene: 
NM_016173.3  

Unigene Clusters for HEMK1:

HemK methyltransferase family member 1
Hs.517987  [show with all ESTs], Hs.599362  [show with all ESTs]
Unigene Representative Sequences: NM_016173, AL137466
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000434410 ENST00000232854(uc003dau.3 uc003dav.3) ENST00000448997
ENST00000455834 ENST00000482974 ENST00000424388 ENST00000443894
miRNA
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Selected qRT-PCR Assays for microRNAs that regulate HEMK1 (see all 21):
hsa-miR-3934 hsa-miR-4291 hsa-miR-892b hsa-miR-185* hsa-miR-125a-3p hsa-miR-764 hsa-miR-1304 hsa-miR-4325
Browse SwitchGear 3'UTR luciferase reporter plasmids
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat HEMK1
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GenScript: all cDNA clones in your preferred vector: HEMK1 (NM_016173)
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HEMK1
Primer
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OriGene qPCR primer pairs and template standards for HEMK1
OriGene qSTAR qPCR primer pairs in human, mouse for HEMK1
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HEMK1
  QuantiTect SYBR Green Assays in human, mouse, rat HEMK1
  QuantiFast Probe-based Assays in human, mouse, rat HEMK1

Additional mRNA sequence: 

AF074992.1 AL137466.1 

14 DOTS entries:

DT.313880  DT.91743474  DT.309809  DT.40112791  DT.100840006  DT.99997729  DT.120896470  DT.436825 
DT.100778542  DT.102831881  DT.120896473  DT.95069566  DT.99997730  DT.91859463 

Selected AceView cDNA sequences (see all 168):

AA292772 AK025973 AI079554 BQ005588 BQ772019 AI281191 AI915274 BQ013117 
BQ183021 AK124369 BQ015610 BU620766 AA279011 AU099261 BC000781 AA731007 
BM671111 AA293435 AW629265 BG105120 CA308706 AI143776 BU529084 AA742191 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for HEMK1    About this scheme

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b
SP1:                                                                                          
SP2:              -                                                                           
SP3:                                                                                          
SP4:                                            -     -     -                                 


ECgene alternative splicing isoforms for HEMK1

(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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HEMK1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CTCTGCATTT
HEMK1 Expression
About this image

HEMK1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

HEMK1 Protein Expression

SOURCE GeneReport for Unigene clusters: Hs.517987 Hs.599362
    Custom PCR Arrays for HEMK1
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HEMK1

(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 animals and fungi.

Orthologs for HEMK1 gene from Selected species (see all 14)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Hemk11 , 5 HemK methyltransferase family member 11, 5 82.94(n)1
78.99(a)1
  9 (58.00 cM)5
695361  NM_133984.21  NP_598745.21 
 1073276925 
chicken
(Gallus gallus)
Aves HEMK11 HemK methyltransferase family member 1 61.36(n)
58.26(a)
  415915  XM_004944400.1  XP_004944457.1 
lizard
(Anolis carolinensis)
Reptilia HEMK16
HemK methyltransferase family member 1
52(a)
1 ↔ 1
2(151400675-151460583)
tropical clawed frog
(Xenopus tropicalis)
Amphibia hemk11 HemK methyltransferase family member 1 54.88(n)
52.19(a)
  101732423  XM_004914073.1  XP_004914130.1 
zebrafish
(Danio rerio)
Actinopterygii hemk11 HemK methyltransferase family member 1 54.76(n)
47.28(a)
  560620  NM_001114419.1  NP_001107891.1 
fruit fly
(Drosophila melanogaster)
Insecta CG95311 CG9531 48.9(n)
36.33(a)
  33902  NM_001273205.1  NP_001260134.1 
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MTQ1(YNL063W)4 S-adenosylmethionine-dependent methyltransferase; methylates more   --   14(507758-508702) 855662  NP_014336.1 


ENSEMBL Gene Tree for HEMK1 (if available)
TreeFam Gene Tree for HEMK1 (if available)

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

(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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Selected SNPs for HEMK1 (see all 332)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 3 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1165351421,2
C,F--50537869(+) TGGCCA/GGGCCC 1 -- us2k11Minor allele frequency- G:0.23WA 118
rs753117161,2
C,F--50538271(+) AAAACG/ACGGAT 1 -- us2k12Minor allele frequency- A:0.21CSA WA 119
rs1458527741,2
C--50538445(+) GGAATA/CTTCGT 1 -- us2k10--------
rs1466349681,2
--50538628(+) TGGTAA/CAAATG 1 -- us2k10--------
rs341669571,2
C,F,H--50538700(+) TTTAAG/AGCCGG 1 -- us2k110Minor allele frequency- A:0.02NS NA 1120
rs1411155431,2
--50538723(+) ACTCCC/TGTAAT 1 -- us2k10--------
rs1501870751,2
--50538763(+) ATCACC/TTGAAG 1 -- us2k10--------
rs1141385271,2
C--50538922(+) TGCAGG/TGAGCA 1 -- us2k10--------
rs758002791,2
--50538991(+) AAAAAG/AAAAAA 1 -- us2k11Minor allele frequency- A:0.00NA 2
rs1445681561,2
--50538998(+) AAAAA-/GAAAAA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for HEMK1 (50606583 - 50622422 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for HEMK1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv460532CNV Loss19166990
nsv876770CNV Loss21882294
nsv460533CNV Loss19166990

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing HEMK1
DNA2.0 Custom Variant and Variant Library Synthesis for HEMK1

(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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1 disease for HEMK1:    
About MalaCards
acrocephalosyndactylia

2 diseases from the University of Copenhagen DISEASES database for HEMK1:
Brachydactyly     Acrocephalosyndactylia

Find genes that share disorders with HEMK1           About GenesLikeMe

Genetic Association Database (GAD): HEMK1
Human Genome Epidemiology (HuGE) Navigator: HEMK1 (1 document)

Export disorders for HEMK1 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 HEMK1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with HEMK1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Is the HemK family of putative S-adenosylmethionine-dependent methyltransferases a &quot;missing&quot; zeta subfamily of adenine methyltransferases? A hypothesis. (PubMed id 10690633)1, 3, 9 Bujnicki J.M. and Radlinska M. (IUBMB Life 1999)
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
  3. The human mitochondrial translation release factor HMRF1L is methylated in the GGQ motif by the methyltransferase HMPrmC. (PubMed id 18541145)1, 2 Ishizawa T.... Takeuchi N. (Biochem. Biophys. Res. Commun. 2008)
  4. 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)
  5. 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)
  6. (PubMed id )2 

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
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  Query String
PubMed
OMIM
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 51409 HGNC: 24923 AceView: HEMK1 Ensembl:ENSG00000114735 euGenes: HUgn51409
ECgene: HEMK1 Kegg: 51409 H-InvDB: HEMK1

(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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NameDescription
PharmGKB entry for HEMK1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HEMK1 gene:
Search GeneIP for patents involving HEMK1

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



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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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