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SMCO2 Gene

protein-coding   GIFtS: 27
GCID: GC12P027620

Single-Pass Membrane Protein With Coiled-Coil Domains 2

(Previous name: chromosome 12 open reading frame 70)
(Previous symbol: C12orf70)
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(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
Single-Pass Membrane Protein With Coiled-Coil Domains 21 2
C12orf701 2 3
Chromosome 12 Open Reading Frame 701
Single-Pass Membrane And Coiled-Coil Domain-Containing Protein 22

External Ids:    HGNC: 344481   Entrez Gene: 3413462   Ensembl: ENSG000001659357   UniProtKB: A6NFE23   

Export aliases for SMCO2 gene to outside databases


(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 SMCO2 Gene:
SMCO2 (single-pass membrane protein with coiled-coil domains 2) is a protein-coding 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000012.11  NC_018923.2  NT_009714.18  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SMCO2
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMCO2


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

Entrez Gene cytogenetic band: 12p11.23   Ensembl cytogenetic band:  12p11.23   HGNC cytogenetic band: 12p11.23

SMCO2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMCO2 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P027620:  view genomic region     (about GC identifiers)

Start:
27,619,743 bp from pter      End:
27,655,118 bp from pter
Size:
35,376 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SMCO2_HUMAN, A6NFE2 (See protein sequence)
Recommended Name: Single-pass membrane and coiled-coil domain-containing protein 2  
Size: 343 amino acids; 39487 Da

Explore the universe of human proteins at neXtProt for SMCO2: NX_A6NFE2

Explore proteomics data for SMCO2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SMCO2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001138482.1  
    ENSEMBL proteins: 
     ENSP00000298876   ENSP00000441688   ENSP00000387617  

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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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    1 InterPro protein domain:
     IPR026617 SMCO2/5

    Graphical View of Domain Structure for InterPro Entry A6NFE2

    ProtoNet protein and cluster: A6NFE2


    Find genes that share domains with SMCO2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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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    Phenotypes:
         1 MGI phenotypic allele for 1700023A16Rik (no phenotypes)

    Find genes that share phenotypes with SMCO2           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SMCO2

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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
    SMCO2_HUMAN, A6NFE2: Membrane; Single-pass membrane protein (Potential)

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with SMCO2           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SMCO2
    Interactions:

        Search GeneGlobe Interaction Network for SMCO2

    (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 SMCO2



    (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 SMCO2 gene: 
    NM_001145010.1  

    Unigene Cluster for SMCO2:

    Single-pass membrane protein with coiled-coil domains 2
    Hs.282121  [show with all ESTs]
    Unigene Representative Sequence: NM_001145010
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000298876 ENST00000543991 ENST00000535986 ENST00000538647 ENST00000541168
    ENST00000416383(uc010sjq.2)
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    2 DOTS entries:

    DT.99987291  DT.91939565 

    5 AceView cDNA sequences:

    AI634578 BX369976 BU854173 AL572713 BF807165 

    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™, 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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    SMCO2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SMCO2 Expression
    About this image

    SMCO2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMCO2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.282121
        Custom PCR Arrays for SMCO2
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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)
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    This gene was present in the common ancestor of human and mouse.

    Orthologs for SMCO2 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 1700023A16Rik5
    Smco21
    RIKEN cDNA 1700023A16 gene5
    single-pass membrane protein with coiled-coil domains more1
    66.05(n)1
    50.62(a)1
      6 (77.70 cM)5
    693711  NM_027059.11  NP_081335.11 
     1468501045 


    ENSEMBL Gene Tree for SMCO2 (if available)
    TreeFam Gene Tree for SMCO2 (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 SMCO2 (see all 893)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1877551741,2
    --27617818(+) TTAGCC/TGGGCA 1 -- us2k10--------
    rs3066321,2
    C,F,A--27617823(+) cgggcG/Atggtg 1 -- us2k14Minor allele frequency- A:0.30NA CSA 10
    rs1139044291,2
    C,F--27617913(+) GCCGAG/AATCGT 1 -- us2k11Minor allele frequency- A:0.50NA 2
    rs1923139771,2
    --27617934(+) TCCAGC/TCTGAG 1 -- us2k10--------
    rs1422618791,2
    C--27618029(+) ATTTGG/TCCGAG 1 -- us2k10--------
    rs1463596391,2
    --27618057(+) TACGCA/GAAGTG 1 -- us2k10--------
    rs1822334141,2
    --27618076(+) ACAGTA/GCTGCT 1 -- us2k10--------
    rs1865446031,2
    --27618180(+) ATATAC/TGTAAA 1 -- us2k10--------
    rs1929671351,2
    --27618207(+) CTAGCA/GCATTA 1 -- us2k10--------
    rs1163182911,2
    C,F--27618334(+) TAGGAG/ACATAG 1 -- us2k11Minor allele frequency- A:0.02WA 118

    HapMap Linkage Disequilibrium report for SMCO2 (27619743 - 27655118 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SMCO2: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SMCO2
    DNA2.0 Custom Variant and Variant Library Synthesis for SMCO2

    (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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      --

    (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 article for SMCO2 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SMCO2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)1, 2 Scherer S.E.... Gibbs R.A. (Nature 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 341346 HGNC: 34448 AceView: LOC341346 Ensembl:ENSG00000165935 euGenes: HUgn341346
    ECgene: SMCO2 H-InvDB: SMCO2

    (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 SMCO2 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 SMCO2 gene:
    Search GeneIP for patents involving SMCO2

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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