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

SMIM4 Gene

protein-coding   GIFtS: 31
GCID: GC03P052570

Small Integral Membrane Protein 4

(Previous name: chromosome 3 open reading frame 78)
(Previous symbol: C3orf78)
  Search for SMIM4
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
Small Integral Membrane Protein 41 2
C3orf781 2 3
Chromosome 3 Open Reading Frame 781
UPF0640 Protein C3orf782

External Ids:    HGNC: 372571   Entrez Gene: 4409572   Ensembl: ENSG000001682737   UniProtKB: Q8WVI03   

Export aliases for SMIM4 gene to outside databases


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

GeneCards Summary for SMIM4 Gene: 
SMIM4 (small integral membrane protein 4) 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NT_022517.18  NC_018914.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SMIM4
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SMIM4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMIM4


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

Entrez Gene cytogenetic band: 3p21.1   Ensembl cytogenetic band:  3p21.1   HGNC cytogenetic band: 3p21.1

SMIM4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMIM4 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P052570:  view genomic region     (about GC identifiers)

Start:
52,568,029 bp from pter      End:
52,613,253 bp from pter
Size:
45,225 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: SMIM4_HUMAN, Q8WVI0 (See protein sequence)
Recommended Name: Small integral membrane protein 4  
Size: 70 amino acids; 8696 Da
Subcellular location: Membrane; Single-pass membrane protein (Potential)
Sequence caution: Sequence=AAH17996.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

Explore the universe of human proteins at neXtProt for SMIM4: NX_Q8WVI0

Explore proteomics data for SMIM4 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8WVI0

  • SMIM4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SMIM4 Protein Expression
    REFSEQ proteins: NP_001118239.1  
    ENSEMBL proteins: 
     ENSP00000305661   ENSP00000417806   ENSP00000418000  

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    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IEA--
    GO:0016021integral to membrane IEA--

    SMIM4 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

    ProtoNet protein and cluster: Q8WVI0

    UniProtKB/Swiss-Prot: SMIM4_HUMAN, Q8WVI0
    Similarity: Belongs to the SMIM4 family


    (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

    Animal Models:
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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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SMIM4

    (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 SMIM4

    Search CenterWatch for drugs/clinical trials and news about SMIM4

    (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,
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    About This Section

    REFSEQ mRNAs for SMIM4 gene: 
    NM_001124767.1  

    Unigene Cluster for SMIM4:

    Small integral membrane protein 4
    Hs.660577  [show with all ESTs]
    Unigene Representative Sequence: AK095910
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000491607 ENST00000482728 ENST00000307106 ENST00000477703(uc003dep.2)
    ENST00000476842
    miRNA
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    Additional mRNA sequence: 

    AK095910.1 BC017996.1 

    9 DOTS entries:

    DT.108232  DT.100023604  DT.70104594  DT.40211457  DT.97794681  DT.100716371  DT.120869733  DT.70103841 
    DT.100777736 

    24/55 AceView cDNA sequences (see all 55):

    BQ652434 AI654826 AK091962 BF062091 AI245887 AA314869 AI867707 BM023268 
    BM674004 BM715543 BF002771 BQ268714 AI681702 AA926752 AW003138 BG031013 
    AA780136 BE220694 BE217998 AW183261 BC017996 AI376841 AI220401 AA569376 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for SMIM4    About this scheme

    ExUns: 1a · 1b ^ 2
    SP1:        -         
    SP2:                  


    ECgene alternative splicing isoforms for SMIM4

    (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
    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --


    See SMIM4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SMIM4

    SOURCE GeneReport for Unigene cluster: Hs.660577
        SABiosciences Custom PCR Arrays for SMIM4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMIM4

    (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 SMIM4 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 Smim45 RIKEN cDNA 2010107H07 gene   --   14 (19.09 cM) 31124505 
    lizard
    (Anolis carolinensis)
    Reptilia C3ORF786
    Uncharacterized protein
    70(a)
    1 ↔ 1
    2(154791602-154792886)
    zebrafish
    (Danio rerio)
    Actinopterygii SMIM46
    small integral membrane protein 4
    52(a)
    1 ↔ 1
    23(19964499-19966056)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG327366
    --
    37(a)
    1 ↔ 1
    X(6905390-6906170)


    ENSEMBL Gene Tree for SMIM4 (if available)
    TreeFam Gene Tree for SMIM4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/63 SNPs in SMIM4 are shown (see all 63)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1501537891,2
    --52571106(+) TTGGCA/GTCCAG 1 -- int10--------
    rs1387486081,2
    --52571177(+) CTGCCC/TTTCAC 1 -- int10--------
    rs1891419331,2
    --52571489(+) GACTTA/CCCCAA 1 -- int10--------
    rs1819021951,2
    --52571742(+) TCAGTG/TCTGTG 1 -- int10--------
    rs1120139611,2
    F--52571822(+) CTTCCG/TGAAGC 1 -- int11Minor allele frequency- T:0.50CSA 2
    rs98760741,2
    C,F--52571843(+) taaagT/Gaggac 1 -- int11Minor allele frequency- G:0.03WA 118
    rs1177364621,2
    C,F--52571869(+) GTGTCA/TGTCAG 1 -- int11Minor allele frequency- T:0.01EA 120
    rs1418126991,2
    C--52571926(+) AGGAGC/TACTTG 1 -- int10--------
    rs76388081,2
    C,F,A,H--52572056(+) GAGTCA/GTTTTA 1 -- int129Minor allele frequency- G:0.49NA EA NS WA CSA 2716
    rs1908604891,2
    --52572157(+) GCCTGA/GTCTAG 1 -- int10--------

    HapMap Linkage Disequilibrium report for SMIM4 (52568029 - 52613253 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SMIM4: --
    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
      --

    (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 SMIM4 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SMIM4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    2. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (2006)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
    5. 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)
    6. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 440957 HGNC: 37257 AceView: LOC440957 Ensembl:ENSG00000168273 euGenes: HUgn440957
    ECgene: SMIM4 H-InvDB: SMIM4

    (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 SMIM4 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 SMIM4 gene:
    Search GeneIP for patents involving SMIM4

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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     Browse SwitchGear 3'UTR luciferase reporter plasmids for SMIM4
     Browse SwitchGear Promoter luciferase reporter plasmids for SMIM4
     Search ThermoFisher Antibodies for SMIM4
     Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SMIM4
     inGenious Targeting Laboratory - Custom generated mouse model solutions for SMIM4
     inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for SMIM4
    Customized:
     lentivirus for stable overexpression of SMIM4
     lentivirus expression plasmids for stable overexpression of SMIM4
     adenovirus for overexpression of SMIM4
     Search LSBio for Antibodies for SMIM4
    Customized transgenic rodents for:
     Humanization
     Biomarker expression
     Off-target effect monitoring
     Translational medicine
     Tissue-specific gene expresssion
     Time-controlled gene expresssion
           
    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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