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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

MKRN3 Gene

protein-coding   GIFtS: 52
GCID: GC15P023810

Makorin Ring Finger Protein 3


(Previous symbols: ZNF127, D15S9)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Makorin Ring Finger Protein 31 2     RING Finger Protein 632 3
ZNF1271 2 3 5     ZFP1272 5
D15S91 2 3     CPPB22
Zinc Finger Protein 1271 2 3     Probable E3 Ubiquitin-Protein Ligase Makorin-32
RNF632 3     EC 6.3.2.-3

External Ids:    HGNC: 71141   Entrez Gene: 76812   Ensembl: ENSG000001794557   OMIM: 6038565   UniProtKB: Q130643   

Export aliases for MKRN3 gene to outside databases

Previous GC identifers: GC15U990051 GC15P016700 GC15P021228 GC15P021358 GC15P021361 GC15P001945


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for MKRN3 Gene:
The protein encoded by this gene contains a RING (C3HC4) zinc finger motif and several C3H zinc finger motifs.
This gene is intronless and imprinted, with expression only from the paternal allele. Disruption of the
imprinting at this locus may contribute to Prader-Willi syndrome. An antisense RNA of unknown function has been
found overlapping this gene. (provided by RefSeq, Jul 2008)

GeneCards Summary for MKRN3 Gene: 
MKRN3 (makorin ring finger protein 3) is a protein-coding gene. Diseases associated with MKRN3 include canavan disease, and prader-willi syndrome. GO annotations related to this gene include ligase activity and nucleic acid binding. An important paralog of this gene is MKRN2.

UniProtKB/Swiss-Prot: MKRN3_HUMAN, Q13064
Function: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins (By
similarity)




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000015.9  NT_026446.14  NC_018926.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the MKRN3 gene promoter:
         AML1a   Pax-6   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   C/EBPalpha   HEN1   FOXO1a   NF-kappaB1   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidMKRN3 promoter sequence
   Search SABiosciences Chromatin IP Primers for MKRN3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat MKRN3


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

Entrez Gene cytogenetic band: 15q11-q13   Ensembl cytogenetic band:  15q11.2   HGNC cytogenetic band: 15q11-q13

MKRN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MKRN3 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P023810:  view genomic region     (about GC identifiers)

Start:
23,810,454 bp from pter      End:
23,873,064 bp from pter
Size:
62,611 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: MKRN3_HUMAN, Q13064 (See protein sequence)
Recommended Name: Probable E3 ubiquitin-protein ligase makorin-3  
Size: 507 amino acids; 55645 Da
Miscellaneous: Imprinted, expressed from the paternal chromosome only. A deficiency of MKRN3 is not sufficient to
cause Prader-Willi syndrome (PWS)

Explore the universe of human proteins at neXtProt for MKRN3: NX_Q13064

Explore proteomics data for MKRN3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q13064

  • MKRN3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    MKRN3 Protein Expression
    REFSEQ proteins: NP_005655.1  
    ENSEMBL proteins: 
     ENSP00000457884   ENSP00000456779   ENSP00000455368   ENSP00000313881  

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    Cloud-Clone Corp. Proteins for MKRN3 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030529ribonucleoprotein complex TAS10196367

    MKRN3 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    RNF: RING-type (C3HC4) zinc fingers

    5/6 InterPro protein domains (see all 6):
     IPR000571 Znf_CCCH
     IPR001841 Znf_RING
     IPR026294 Makorin_3
     IPR013083 Znf_RING/FYVE/PHD
     IPR017907 Znf_RING_CS

    Graphical View of Domain Structure for InterPro Entry Q13064

    ProtoNet protein and cluster: Q13064

    2 Blocks protein domains:
    IPB000571 Zn-finger
    IPB001841 Zn-finger


    UniProtKB/Swiss-Prot: MKRN3_HUMAN, Q13064
    Similarity: Contains 3 C3H1-type zinc fingers
    Similarity: Contains 1 RING-type zinc finger


    MKRN3 for domains           About GeneDecksing


    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: MKRN3_HUMAN, Q13064
    Function: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins (By
    similarity)

         Genatlas biochemistry entry for MKRN3:
    makorin,ring finger protein,3,associated with a nuclear matrix attachment sequence (MAR),ubiquitously expressed
    from the paternal allele (maternally imprinted),mediating ubiquitin-conjugating enzyme (E2)-dependent
    ubiquitination

         Enzyme Number (IUBMB): EC 6.3.2.-1

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0005515protein binding IPI--
    GO:0008270zinc ion binding IEA--
    GO:0016874ligase activity IEA--
    GO:0046872metal ion binding ----
         
    MKRN3 for ontologies           About GeneDecksing


    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidMKRN3 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    UniProtKB/Swiss-Prot: MKRN3_HUMAN, Q13064
    Pathway: Protein modification; protein ubiquitination

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for MKRN3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/36 Interacting proteins for MKRN3 (Q130641, 3 ENSP000003138814) via UniProtKB, MINT, STRING, and/or I2D (see all 36)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    TSG101Q998163, ENSP000002519684I2D: score=2 STRING: ENSP00000251968
    UBE2D2P628373, ENSP000003817174I2D: score=2 STRING: ENSP00000381717
    UBE2D3P610773, ENSP000003497224I2D: score=2 STRING: ENSP00000349722
    UBE2IP632793, ENSP000003248974I2D: score=2 STRING: ENSP00000324897
    UBE2NP610883, ENSP000003161764I2D: score=2 STRING: ENSP00000316176
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016567protein ubiquitination IEA--

    MKRN3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for MKRN3

    Search CenterWatch for drugs/clinical trials and news about MKRN3

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for MKRN3 gene: 
    NM_005664.3  

    Unigene Clusters for MKRN3:

    Makorin ring finger protein 3
    Hs.72964  [show with all ESTs], Hs.679587  [show with all ESTs]
    Unigene Representative Sequences: NM_005664, BC070293
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000570112 ENST00000568252(uc001ywi.3) ENST00000564592(uc010ayi.1)
    ENST00000568945 ENST00000314520(uc001ywh.4)
    miRNA
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    hsa-miR-30c hsa-miR-607 hsa-miR-30d hsa-miR-519a hsa-miR-1297 hsa-miR-570 hsa-miR-30a hsa-miR-4325
    SwitchGear 3'UTR luciferase reporter plasmidMKRN3 3' UTR sequence
    Inhib. RNA
    Products:
         
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat MKRN3
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat MKRN3

    Additional mRNA sequence: BC070293.1 

    4 DOTS entries:

    DT.206625  DT.121017966  DT.91935268  DT.121017976 

    17 AceView cDNA sequences:

    AI939624 BC070293 AI494223 BG056640 BC044639 NM_005664 BG481814 BG621437 
    AA310871 AI497659 BF307979 AI936618 BQ226594 BE728344 AW445166 BE903470 
    AW952653 

    GeneLoc Exon Structure


    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    MKRN3 expression in normal human tissues (normalized intensities)      MKRN3 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAATAATTTA
    MKRN3 Expression
    About this image


    MKRN3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/6 selected tissues (see all 6) fully expand
     
     Peripheral Nervous System (Nervous System)    fully expand to see all 4 entries
             autonomic/sympathetic/ganglion   
     
     Gut Tube (Gastrointestinal Tract)    fully expand to see all 2 entries
             Midgut
     
     Spinal Cord (Nervous System)
             spinal/ganglion/dorsal root ganglion   
     
     Nose (Sensory Organs)
             sensory organ/nose/nasal cavity   
     
     Eye (Sensory Organs)
             Retina

    See MKRN3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for MKRN3

    SOURCE GeneReport for Unigene clusters: Hs.72964 Hs.679587

    UniProtKB/Swiss-Prot: MKRN3_HUMAN, Q13064
    Tissue specificity: Ubiquitous

        SABiosciences Custom PCR Arrays for MKRN3
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MKRN3

    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for MKRN3 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Mkrn31 , 5 makorin, ring finger protein, 31, 5 77.91(n)1
    69.44(a)1
      7 (34.37 cM)5
    226521  NM_011746.21  NP_035876.21 
     624175935 
    zebrafish
    (Danio rerio)
    Actinopterygii mkrn16
    makorin, ring finger protein, 1
    44(a)
    1 → many
    4(11356798-11372358)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG124773   -- 50(a)
    (best of 4)
      75D7   --
    worm
    (Caenorhabditis elegans)
    Secernentea Y55F3AM.66
    Protein Y55F3AM.6, isoform a
    26(a)
    1 → many
    IV(992289-997652)


    ENSEMBL Gene Tree for MKRN3 (if available)
    TreeFam Gene Tree for MKRN3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for MKRN3 gene
    MKRN22  MKRN12  
    3 SIMAP similar genes for MKRN3 using alignment to 4 protein entries:     MKRN3_HUMAN (see all proteins):
    MKRN1    MKRN4P    MKRN2

    MKRN3 for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/143 SNPs in MKRN3 are shown (see all 143)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 15 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0359564
    A colorectal cancer sample4--see VAR_0359562 S T mis40--------
    VAR_0359554
    A colorectal cancer sample4--see VAR_0359552 T M mis40--------
    rs1450482771,2
    --3802959(+) TAATTG/TTATAT 1 -- us2k10--------
    rs1489609311,2
    C--3803483(+) TTGGAC/G/TTCCTG 1 -- us2k10--------
    rs1436381161,2
    --3803644(+) ATACAA/GATTTT 1 -- us2k10--------
    rs1480897731,2
    C--3803655(+) TTTTGC/TCTTTA 1 -- us2k10--------
    rs1866079811,2
    --3803741(+) CCATAC/TTCACA 1 -- us2k10--------
    rs1419734761,2
    --3803832(+) CCTAAC/TTTTGT 1 -- us2k10--------
    rs1917797141,2
    --3804178(+) AAAGAA/GACTTA 1 -- us2k10--------
    rs343898271,2
    C--3804187(+) TATAG-/AAAAAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for MKRN3 (23810454 - 23873064 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for MKRN3:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv832931CNV Gain17160897
    nsv903594CNV Gain21882294
    dgv699e1CNV Complex17122850

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 603856    OMIM disorders: --

    4 diseases for MKRN3:    About MalaCards
    canavan disease    prader-willi syndrome    intellectual disability    angelman syndrome

    2 diseases from the University of Copenhagen DISEASES database for MKRN3:
    Prader-Willi syndrome     Angelman syndrome

    MKRN3 for disorders           About GeneDecksing


    Export disorders for MKRN3 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)
    About This Section

    PubMed articles for MKRN3 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with MKRN3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel imprinted gene, encoding a RING zinc-finger protein, and overlapping antisense transcript in the Prader-Willi syndrome critical region. (PubMed id 10196367)1, 2, 3 Jong M.T.C....Nicholls R.D. (1999)
    2. A paternal deletion of MKRN3, MAGEL2 and NDN does not result in Prader-Willi syndrome. (PubMed id 19066619)1, 2 Kanber D.... Buiting K. (2009)
    3. 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. (2004)
    4. Central precocious puberty caused by mutations in the imprinted gene MKRN3. (PubMed id 23738509)1 Abreu A.P....Kaiser U.B. (2013)
    5. Systematic analysis of dimeric E3-RING interactions re veals increased combinatorial complexity in human ubiquitination networks. (PubMed id 22493164)1 Woodsmith J....Sanderson C.M. (2012)
    6. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)
    7. Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. (PubMed id 19549727)1 Markson G....Sanderson C.M. (2009)
    8. Genomic imprinting disorders in humans: a mini-review . (PubMed id 19844787)1 Butler M.G. (2009)
    9. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (2006)
    10. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 7681 HGNC: 7114 AceView: MKRN3 Ensembl:ENSG00000179455 euGenes: HUgn7681
    ECgene: MKRN3 H-InvDB: MKRN3

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for MKRN3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for MKRN3 gene:
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