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SMCO1 Gene

protein-coding   GIFtS: 25
GCID: GC03M196234

Single-Pass Membrane Protein With Coiled-Coil Domains 1

(Previous name: chromosome 3 open reading frame 43)
(Previous symbol: C3orf43)
  Search for SMCO1
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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 11 2 3
C3orf431 2 3
Chromosome 3 Open Reading Frame 431 2
Single-Pass Membrane And Coiled-Coil Domain-Containing Protein 12

External Ids:    HGNC: 274071   Entrez Gene: 2557982   Ensembl: ENSG000002140977   UniProtKB: Q147U73   

Export aliases for SMCO1 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 SMCO1 Gene:
SMCO1 (single-pass membrane protein with coiled-coil domains 1) 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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Regulatory elements:
   Search for regulatory transcription factor binding sites for SMCO1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SMCO1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMCO1


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

Entrez Gene cytogenetic band: 3q29   Ensembl cytogenetic band:  3q29   HGNC cytogenetic band: 3q29

SMCO1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMCO1 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M196234:  view genomic region     (about GC identifiers)

Start:
196,233,748 bp from pter      End:
196,242,237 bp from pter
Size:
8,490 bases      Orientation:
minus 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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SMCO1_HUMAN, Q147U7 (See protein sequence)
Recommended Name: Single-pass membrane and coiled-coil domain-containing protein 1  
Size: 214 amino acids; 24598 Da
Secondary accessions: B3KW20

Explore the universe of human proteins at neXtProt for SMCO1: NX_Q147U7

Explore proteomics data for SMCO1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SMCO1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001071125.1  
    ENSEMBL proteins: 
     ENSP00000380671   ENSP00000413102  

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    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.


    (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:
     IPR027875 DUF4547

    Graphical View of Domain Structure for InterPro Entry Q147U7

    ProtoNet protein and cluster: Q147U7


    SMCO1 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,
    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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
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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
    SMCO1_HUMAN, Q147U7: 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--

    SMCO1 for ontologies           About GeneDecksing


    (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 SMCO1
    Interactions:

        Search GeneGlobe Interaction Network for SMCO1

    (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 SMCO1



    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SMCO1 gene: 
    NM_001077657.1  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000397537(uc003fws.3) ENST00000452776(uc003fwr.3)
    miRNA
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    20 AceView cDNA sequences:

    AK123917 F25023 AL833443 F32261 BG213231 AL833140 AL601444 F35788 
    F32891 F24541 F23204 F35878 F16592 F27879 F25688 F26141 
    F29050 AA192210 BF671349 BF576863 

    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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    SMCO1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SMCO1 Expression
    About this image

    SMCO1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMCO1 Protein Expression
        Custom PCR Arrays for SMCO1
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    In Situ
    Assay Products:
     

     
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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 chordates.

    Orthologs for SMCO1 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia 2310010M20Rik5
    Smco11
    RIKEN cDNA 2310010M20 gene5
    single-pass membrane protein with coiled-coil domains more1
    80.37(n)1
    75.7(a)1
      16 (22.50 cM)5
    695761  NM_183283.21  NP_899106.21 
     322714685 
    lizard
    (Anolis carolinensis)
    Reptilia SMCO16
    single-pass membrane protein with coiled-coil doma...
    50(a)
    1 ↔ 1
    AAWZ02041730(2343-5297)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia c3orf431 chromosome 3 open reading frame 43 46.77(n)
    27.86(a)
      100127809  XM_002935724.2  XP_002935770.2 


    ENSEMBL Gene Tree for SMCO1 (if available)
    TreeFam Gene Tree for SMCO1 (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 SMCO1 (see all 350)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs98229911,2
    C,F--196099989(+) ccaacC/Ttctag 1 -- us2k12Minor allele frequency- T:0.15WA 120
    rs1875470651,2
    --196233262(+) AGCTGA/CTGTGT 1 -- ds50010--------
    rs1482556071,2
    C--196233405(+) AGCATC/TGGCAC 1 -- ds50010--------
    rs738912721,2
    C,F--196233761(+) AGGCAA/GAGTAG 1 -- ut315Minor allele frequency- G:0.16WA CSA NA 243
    rs67788891,2
    C,F,A,H--196233795(+) tcttgA/Gcagtg 1 -- ut3123Minor allele frequency- G:0.47EA NS NA WA CSA 2122
    rs1906028061,2
    --196233811(+) GGACCC/TGAAGG 1 -- ut310--------
    rs732196501,2
    C,F--196233847(+) CTATGG/AGTTTT 1 -- ut311Minor allele frequency- A:0.02NA 120
    rs1835579861,2
    --196233951(+) AATCGC/TGGAAG 1 -- ut310--------
    rs1503290171,2
    --196234234(+) AGGTGC/GTTGGA 1 -- ut310--------
    rs1139304821,2
    C,F--196234264(+) TGTCCG/AGCCTT 1 -- ut311Minor allele frequency- A:0.50CSA 2

    HapMap Linkage Disequilibrium report for SMCO1 (196233748 - 196242237 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SMCO1: --
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing SMCO1
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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.)
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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 articles for SMCO1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SMCO1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. 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)

    (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: 255798 HGNC: 27407 AceView: LOC255798 Ensembl:ENSG00000214097 euGenes: HUgn255798
    ECgene: SMCO1 H-InvDB: SMCO1

    (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 SMCO1 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 SMCO1 gene:
    Search GeneIP for patents involving SMCO1

    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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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