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

MKRN3 Gene

protein-coding   GIFtS: 51
GCID: GC15P023810

makorin ring finger protein 3


(Previous symbols: ZNF127, D15S9)
 Explore 4 diseases affiliated with
MKRN3 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for MKRN3    

Aliases
for MKRN3 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Makorin Ring Finger Protein 31 2     Zinc Finger Protein 1272 3
ZNF1271 2 3 5     RING Finger Protein 632 3
D15S91 2 3     MGC882881
RNF631 2 3     Probable E3 Ubiquitin-Protein Ligase Makorin-32
ZFP1271 2 5     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


Summaries
for MKRN3 gene

(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:
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)

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




Genomic Views
for MKRN3 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000015.9  NC_018926.1  NT_026446.14  
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 plasmid: MKRN3 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

Proteins
for MKRN3 gene

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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q13064

    • MKRN3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_005655.1  
    ENSEMBL proteins: 
     ENSP00000457884   ENSP00000456779   ENSP00000455368   ENSP00000313881  

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    Uscn 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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    Protein Domains /
    Families
    for MKRN3 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    MKRN3 for domains           About GeneDecksing

    5/6 InterPro domains/families (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 families:
    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


    Function
    for MKRN3 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: 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

    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 plasmid: MKRN3 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Clone
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0005515protein binding IPI--
    GO:0008270zinc ion binding IEA--
    GO:0016874ligase activity IEA--


    MKRN3 for ontologies           About GeneDecksing



    Pathways & Interactions
    for MKRN3 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 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)

    5/35 Interacting proteins for MKRN3 (Q130641, 3 ENSP000003138814) via UniProtKB, MINT, STRING, and/or I2D (see all 35)

    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



    Drugs & Compounds
    for MKRN3 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 

    Transcripts
    for MKRN3 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, 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
    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)

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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 plasmid: MKRN3 3' UTR sequence
    Inhib. RNA
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    Clone
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    Primer
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    Additional cDNA sequence: BC070293.1 

    4 DOTS entries:

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

    17 AceView cDNA sequences:

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

    GeneLoc Exon Structure


    Expression
    for MKRN3 gene

    (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)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAATAATTTA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    MKRN3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    5 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Gut TubeMidgutMidgut Endoderm CellsEndoderm
    Neural TubeNeural TubeSpinal Neural Tube CellsNeural Ectoderm
    EyeRetinaEye
    Gut TubeMidgutGut Tube
    Spinal CordPresumptive Spinal CordSpinal Cord
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    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

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    In Situ
    Assay Products:     
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    Orthologs
    for MKRN3 gene

    (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 eukaryotes.

    Orthologs for MKRN3 gene from 8/22 species (see all 22)    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 
    chicken
    (Gallus gallus)    		 Aves --
    		 Uncharacterized protein
    		 35(a)
    		 possible ortholog
    		 26(3916010-3918143)
    lizard
    (Anolis carolinensis)    		 Reptilia --
    		 --
    		 50(a)
    		 possible ortholog
    		 4(120445977-120447953)
    zebrafish
    (Danio rerio)    		 Actinopterygii mkrn46
    		 makorin, ring finger protein, 4
    		 23(a)
    		 possible ortholog
    		 8(24578900-24584156)
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG124773   -- 50(a)
    (best of 4)    		   75D7   --
    worm
    (Caenorhabditis elegans)    		 Secernentea Y55F3AM.66
    		 Protein Y55F3AM.6, isoform a
    		 27(a)
    		 1 → many
    		 IV(992289-997652)
    thale cress
    (Arabidopsis thaliana)    		 eudicotyledons AT3G085056
    		 E3 ubiquitin-protein ligase makorin
    		 30(a)
    		 1 → many
    		 3(2580077-2582129)
    rice
    (Oryza sativa)    		 Liliopsida --
    		 Zinc finger C-x8-C-x5-C-x3-H type domain containin...
    		 28(a)
    		 1 → many
    		 6(12351311-12357105)


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

    Paralogs
    for MKRN3 gene

    (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



    Genomic Variants
    for MKRN3 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/100 NCBI SNPs in MKRN3 are shown (see all 100)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 15 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs740055771,2
    		C,--1945442(+) CAAAAC/TGCTCA 1 -- us2k12Minor allele frequency- T:0.05WA 120
    rs734361761,2
    		C,--1945517(+) TCCTGC/TCACAA 1 -- us2k11Minor allele frequency- T:0.50WA 2
    rs2018525941,2
    		C--1948696(+) GGCTGG/TTNNNN 1 -- ds50010--------
    rs2000801951,2
    		C--1948704(-) TCACAC/TCCACA 1 -- ds50010--------
    rs1450482771,2
    		--23808458(+) TAATTG/TTATAT 2 -- us2k10--------
    rs1489609311,2
    		--23808982(+) TTGGAC/TTCCTG 2 -- us2k10--------
    rs1436381161,2
    		--23809143(+) ATACAA/GATTTT 2 -- us2k10--------
    rs1480897731,2
    		--23809154(+) TTTTGC/TCTTTA 2 -- us2k10--------
    rs1866079811,2
    		--23809240(+) CCATAC/TTCACA 2 -- us2k10--------
    rs1419734761,2
    		--23809331(+) CCTAAC/TTTTGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for MKRN3 (23810454 - 23873064 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for MKRN3
         2 CNVs: 8784 3951

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    Disorders / Diseases
    for MKRN3 gene

    (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.)
    About This Section
    MKRN3 for disorders           About GeneDecksing

    OMIM gene information: 603856    OMIM disorders: --

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

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

    Export disorders for MKRN3 gene to outside databases

    Publications
    for MKRN3 gene

    (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:
    (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. 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)
    3. 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)
    4. Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. (PubMed id 19549727)1 Markson G....Sanderson C.M. (2009)
    5. A paternal deletion of MKRN3, MAGEL2 and NDN does not result in Prader-Willi syndrome. (PubMed id 19066619)2 Kanber D.... Buiting K. (2009)
    6. Genomic imprinting disorders in humans: a mini-review . (PubMed id 19844787)1 Butler M.G. (2009)
    7. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (2006)
    8. 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)
    9. 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. (2002)
    10. Prader-Willi Syndrome (PubMed id 20301505)1 Driscoll D.J....Cassidy S.B. (1993)

    External Searches for MKRN3 gene

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    Genome Databases showing MKRN3 gene

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

    Other Databases showing MKRN3 gene

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    Specialized Databases showing MKRN3 gene

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

    Intellectual Property
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