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

ZMYM1 Gene

protein-coding   GIFtS: 47
GCID: GC01P035526

Zinc Finger, MYM-Type 1

(Previous names: zinc finger, MYM domain containing 1)
  Search for ZMYM1
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

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Zinc Finger, MYM-Type 11 2
Zinc Finger, MYM Domain Containing 11 2
MYM2
RP11-181E22.42
Zinc Finger MYM-Type Protein 12

External Ids:    HGNC: 262531   Entrez Gene: 798302   Ensembl: ENSG000001970567   UniProtKB: Q5SVZ63   
ORGUL members:         
NONCODE14:n342253      

Export aliases for ZMYM1 gene to outside databases

Previous GC identifers: GC01P034972 GC01P035214 GC01P035317 GC01P033662


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

GeneCards Summary for ZMYM1 Gene: 
ZMYM1 (zinc finger, MYM-type 1) is a protein-coding gene, and is affiliated with the lncRNA class. GO annotations related to this gene include protein dimerization activity and nucleic acid binding. An important paralog of this gene is ZMYM4.


(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_000001.10  NT_032977.9  NC_018912.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZMYM1 gene promoter:
         CREB   AREB6   MZF-1   Sp1   deltaCREB   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZMYM1 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZMYM1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZMYM1


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

Entrez Gene cytogenetic band: 1p34.3   Ensembl cytogenetic band:  1p34.3   HGNC cytogenetic band: 1p34.3

ZMYM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZMYM1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P035526:  view genomic region     (about GC identifiers)

Start:
35,525,387 bp from pter      End:
35,581,460 bp from pter
Size:
56,074 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: ZMYM1_HUMAN, Q5SVZ6 (See protein sequence)
Recommended Name: Zinc finger MYM-type protein 1  
Size: 1142 amino acids; 128717 Da
Subcellular location: Nucleus (Potential)
Secondary accessions: D3DPR7 Q7Z3Q4

Explore the universe of human proteins at neXtProt for ZMYM1: NX_Q5SVZ6

Explore proteomics data for ZMYM1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q5SVZ6

  • ZMYM1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    ZMYM1 Protein Expression
    REFSEQ proteins: NP_079048.3  
    ENSEMBL proteins: 
     ENSP00000394233   ENSP00000352920   ENSP00000362427  

    Human Recombinant Protein Products for ZMYM1: 
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    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for ZMYM1 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    ZMYM1 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: 
    ZMYM: Zinc fingers, MYM type

    5/6 InterPro protein domains (see all 6):
     IPR006580 Znf_TTF
     IPR025398 DUF4371
     IPR008906 HATC
     IPR010507 Znf_MYM
     IPR012337 RNaseH-like_dom

    Graphical View of Domain Structure for InterPro Entry Q5SVZ6

    ProtoNet protein and cluster: Q5SVZ6

    2 Blocks protein domains:
    IPB008906 HAT dimerisation
    IPB011017 TRASH


    UniProtKB/Swiss-Prot: ZMYM1_HUMAN, Q5SVZ6
    Similarity: Contains 4 MYM-type zinc fingers
    Similarity: Contains 1 TTF-type zinc finger


    ZMYM1 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

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0008270zinc ion binding IEA--
    GO:0046983protein dimerization activity IEA--
         
    ZMYM1 for ontologies           About GeneDecksing


    Animal Models:
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for ZMYM1 
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    SwitchGear 3'UTR luciferase reporter plasmidZMYM1 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZMYM1


    (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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZMYM1

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for ZMYM1 (ENSP000003529204) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MFSD2AENSP000003618954STRING: ENSP00000361895
    TMEM59ENSP000002348314STRING: ENSP00000234831
    SUMO2ENSP000004059654STRING: ENSP00000405965
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    (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 ZMYM1

    Search CenterWatch for drugs/clinical trials and news about ZMYM1

    (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 ZMYM1 gene: 
    NM_024772.3  

    Unigene Cluster for ZMYM1:

    Zinc finger, MYM-type 1
    Hs.471243  [show with all ESTs]
    Unigene Representative Sequence: CR936813
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000417119 ENST00000359858(uc001byl.1 uc001bym.3 uc010ohu.2 uc009vut.3)
    ENST00000466390 ENST00000488455(uc009vus.1) ENST00000475654 ENST00000373329
    ENST00000373330(uc001byn.3 uc001byo.3) ENST00000476269 ENST00000463393

    miRNA
    Products:
         
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    6 QIAGEN miScript miRNA Assays for microRNAs that regulate ZMYM1:
    hsa-miR-3671 hsa-miR-548p hsa-miR-374b hsa-miR-374a hsa-miR-616* hsa-miR-373*
    SwitchGear 3'UTR luciferase reporter plasmidZMYM1 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ZMYM1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat ZMYM1

    Additional mRNA sequence: 

    AK026804.1 AK096206.1 AK125741.1 AK299779.1 AK308655.1 BC037313.1 BX537537.1 BX648307.1 
    CR936813.1 

    9 DOTS entries:

    DT.443319  DT.121356682  DT.100024634  DT.101980075  DT.101970072  DT.121356657  DT.121356683  DT.405279 
    DT.100725907 

    24/69 AceView cDNA sequences (see all 69):

    BM552225 AA453867 AK125741 CA455078 AK096206 BC037313 CB131944 BP338027 
    CB132609 BX537537 BU852345 AW197345 W48560 BU568057 BU854440 AA905104 
    BU568340 BX473043 CD683862 BU561365 AW593217 BU569739 AW590498 AA347587 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for ZMYM1 (see all 6)    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b
    SP1:                                                  -     -                                             
    SP2:              -                                   -     -                                             
    SP3:        -     -     -                             -     -                                             
    SP4:              -     -                             -     -                                             
    SP5:              -     -           -                                                                     


    ECgene alternative splicing isoforms for ZMYM1

    (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

    ZMYM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGAGTGCCTA
    ZMYM1 Expression
    About this image


    See ZMYM1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZMYM1

    SOURCE GeneReport for Unigene cluster: Hs.471243
        SABiosciences Custom PCR Arrays for ZMYM1
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    In Situ
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    (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 ZMYM1 gene from 6/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zmym11 , 5 zinc finger, MYM domain containing 11, 5 73.26(n)1
    63.4(a)1
      4 (61.22 cM)5
    683101  NM_026670.41  NP_080946.31 
     1270470945 
    lizard
    (Anolis carolinensis)
    Reptilia ZMYM16
    zinc finger, MYM-type 1
    38(a)
    1 ↔ 1
    GL343558.1(321265-328034)
    zebrafish
    (Danio rerio)
    Actinopterygii zmym46
    CR774184.16
    (see all 3)
    Uncharacterized protein
    (see all 3)
    12(a)
    12(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    19(41029866-41074277)
    17(14572557-14615356)
    fruit fly
    (Drosophila melanogaster)
    Insecta woc6
    without children
    7(a)
    1 → many
    3R(23082315-23089758)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G065411 TTF-type zinc finger protein with HAT dimerisation more 46.41(n)
    31.14(a)
      6240332  NM_001161028.1  NP_001154500.1 
    rice
    (Oryza sativa)
    Liliopsida Os01g02936001 hypothetical protein 44.58(n)
    28.79(a)
      4326714  NM_001049333.2  NP_001042798.2 


    ENSEMBL Gene Tree for ZMYM1 (if available)
    TreeFam Gene Tree for ZMYM1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZMYM1 gene
    ZMYM42  ENSG000002717412  ZMYM52  ZMYM32  ZMYM62  ZMYM22  QRICH12  
    2 SIMAP similar genes for ZMYM1 using alignment to 3 protein entries:     ZMYM1_HUMAN (see all proteins):
    ZMYM4    ZMYM6

    ZMYM1 for paralogs           About GeneDecksing


    3 Pseudogenes.org Pseudogenes for ZMYM1
    PGOHUM00000247658 PGOHUM00000240093 PGOHUM00000242054


    (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

    10/859 SNPs in ZMYM1 are shown (see all 859)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1999284881,2
    C--35556688(-) ATTCCC/TTNNNN 1 -- int10--------
    rs1876173751,2
    --35624729(+) CTTTAC/TAAGAT 1 -- us2k10--------
    rs729050611,2
    C,F--35625147(+) TTCCCC/TGTCTT 1 -- us2k12Minor allele frequency- T:0.03WA 120
    rs743717601,2
    F--35625417(+) TATGAA/CTATTA 1 -- us2k11Minor allele frequency- C:0.02WA 118
    rs1928163121,2
    --35625438(+) ATAAAC/TGTTGG 1 -- us2k10--------
    rs1463441611,2
    --35625637(+) TCAAAC/TATGAT 1 -- us2k10--------
    rs2010616921,2
    --35625752(+) ATTGT-/CCAAAA 1 -- us2k10--------
    rs1420356661,2
    C--35625753(+) TTGTC-/AAAAAA 1 -- us2k10--------
    rs1165307011,2
    C,F--35625770(+) AAAATA/CTGCCA 1 -- us2k11Minor allele frequency- C:0.04WA 118
    rs1840620371,2
    --35625845(+) GACGCA/CGTCTC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ZMYM1 (35525387 - 35581460 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for ZMYM1:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv422CNV Insertion18451855
    nsv870757CNV Gain21882294

    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

    ZMYM1 for disorders           About MalaCards

    ZMYM1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): ZMYM1

    Export disorders for ZMYM1 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 ZMYM1 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with ZMYM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    3. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    4. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    5. Comparative proteomic analysis identifies a role for S UMO in protein quality control. (PubMed id 21693764)1 Tatham M.H....Hay R.T. (2011)
    6. Global identification of modular cullin-RING ligase su bstrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (2011)
    7. Systematic analysis of human protein complexes identi fies chromosome segregation proteins. (PubMed id 20360068)1 Hutchins J.R....Peters J.M. (2010)
    8. System-wide changes to SUMO modifications in response to heat shock. (PubMed id 19471022)1 Golebiowski F....Hay R.T. (2009)
    9. Genome-wide association with diabetes-related traits in the Framingham Heart Study. (PubMed id 17903298)4 Meigs J.B....Dupuis J. (2007)
    10. Genome-wide association with select biomarker traits in the Framingham Heart Study. (PubMed id 17903293)4 Benjamin E.J....Vasan R.S. (2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 79830 HGNC: 26253 AceView: ZMYM1 Ensembl:ENSG00000197056 euGenes: HUgn79830
    ECgene: ZMYM1 H-InvDB: ZMYM1

    (According to HUGE)
    About This Section
      --

    (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 ZMYM1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for ZMYM1 gene:
    Search GeneIP for patents involving ZMYM1

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



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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