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Aliases for SMCO2 Gene

Aliases for SMCO2 Gene

  • Single-Pass Membrane Protein With Coiled-Coil Domains 2 2 3 5
  • C12orf70 3 4
  • Single-Pass Membrane And Coiled-Coil Domain-Containing Protein 2 3
  • Chromosome 12 Open Reading Frame 70 2

External Ids for SMCO2 Gene

Previous HGNC Symbols for SMCO2 Gene

  • C12orf70

Previous GeneCards Identifiers for SMCO2 Gene

  • GC12P027620
  • GC12P027466

Summaries for SMCO2 Gene

GeneCards Summary for SMCO2 Gene

SMCO2 (Single-Pass Membrane Protein With Coiled-Coil Domains 2) is a Protein Coding gene.

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMCO2 Gene

Genomics for SMCO2 Gene

Regulatory Elements for SMCO2 Gene

Enhancers for SMCO2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12G027547 2 FANTOM5 Ensembl ENCODE dbSUPER 11 +106.4 106359 11.9 MLX CREB3L1 ZFP64 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 PPFIBP1 SMCO2 ENSG00000248100 LOC100506578
GH12G027570 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.8 +127.0 127000 6.8 JUN MAX RAD21 YY1 FOSL1 GATA2 ZNF366 HNF4G FOS PRDM10 PPFIBP1 SMCO2 ARNTL2-AS1 STK38L LOC100506578 ENSG00000248100
GH12G027588 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.3 +145.6 145559 8.4 CTCF ZNF146 FOXA2 TAF1 MAX BMI1 RAD21 YY1 GATA3 POLR2A PPFIBP1 ARNTL2-AS1 SMCO2 LOC100506578 ENSG00000248100
GH12G027613 1.4 Ensembl ENCODE dbSUPER 11.3 +170.6 170603 6.9 PKNOX1 KLF17 SIN3A FEZF1 GATA2 ZNF366 ZSCAN5C SCRT2 RCOR1 FOS SMCO2 ARNTL2-AS1 REP15 PPFIBP1 ENSG00000256377 ENSG00000256557 GC12P027690
GH12G027537 1.3 Ensembl ENCODE dbSUPER 11.3 +91.9 91884 2.5 ARNT FEZF1 ZIC2 ZNF664 ZFHX2 SMC3 ZNF600 TCF7L2 BHLHE40 NR3C1 SMCO2 ENSG00000248100 PPFIBP1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SMCO2 on UCSC Golden Path with GeneCards custom track

Genomic Location for SMCO2 Gene

Chromosome:
12
Start:
27,446,744 bp from pter
End:
27,502,322 bp from pter
Size:
55,579 bases
Orientation:
Plus strand

Genomic View for SMCO2 Gene

Genes around SMCO2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMCO2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMCO2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMCO2 Gene

Proteins for SMCO2 Gene

  • Protein details for SMCO2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NFE2-SMCO2_HUMAN
    Recommended name:
    Single-pass membrane and coiled-coil domain-containing protein 2
    Protein Accession:
    A6NFE2

    Protein attributes for SMCO2 Gene

    Size:
    343 amino acids
    Molecular mass:
    39487 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SMCO2 Gene

Post-translational modifications for SMCO2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SMCO2 Gene

Domains & Families for SMCO2 Gene

Protein Domains for SMCO2 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SMCO2: view

No data available for Gene Families , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SMCO2 Gene

Function for SMCO2 Gene

Phenotypes for SMCO2 Gene

genes like me logo Genes that share phenotypes with SMCO2: view

Animal Models for SMCO2 Gene

MGI Knock Outs for SMCO2:

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for SMCO2 Gene

Localization for SMCO2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMCO2 Gene

Membrane; Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMCO2 gene
Compartment Confidence
peroxisome 2
cytosol 2
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SMCO2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SMCO2: view

Pathways & Interactions for SMCO2 Gene

SuperPathways for SMCO2 Gene

No Data Available

Interacting Proteins for SMCO2 Gene

Gene Ontology (GO) - Biological Process for SMCO2 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SMCO2 Gene

Drugs & Compounds for SMCO2 Gene

No Compound Related Data Available

Transcripts for SMCO2 Gene

mRNA/cDNA for SMCO2 Gene

(6) REFSEQ mRNAs :
(0) Additional mRNA sequences :
-
(5) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SMCO2 Gene

Single-pass membrane protein with coiled-coil domains 2:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMCO2 Gene

No ASD Table

Relevant External Links for SMCO2 Gene

GeneLoc Exon Structure for
SMCO2
ECgene alternative splicing isoforms for
SMCO2

Expression for SMCO2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SMCO2 Gene

mRNA differential expression in normal tissues according to GTEx for SMCO2 Gene

This gene is overexpressed in Esophagus - Mucosa (x4.8) and Testis (x4.5).

Protein differential expression in normal tissues from HIPED for SMCO2 Gene

This gene is overexpressed in Plasma (64.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SMCO2 Gene



Protein tissue co-expression partners for SMCO2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SMCO2 Gene:

SMCO2

SOURCE GeneReport for Unigene cluster for SMCO2 Gene:

Hs.282121
genes like me logo Genes that share expression patterns with SMCO2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMCO2 Gene

Orthologs for SMCO2 Gene

This gene was present in the common ancestor of mammals.

Orthologs for SMCO2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMCO2 34 35
  • 98.74 (n)
cow
(Bos Taurus)
Mammalia C5H12orf70 34
  • 78.2 (n)
SMCO2 35
  • 54 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMCO2 34 35
  • 77.61 (n)
mouse
(Mus musculus)
Mammalia Smco2 34 16 35
  • 66.05 (n)
rat
(Rattus norvegicus)
Mammalia LOC100361371 34
  • 64.12 (n)
Species where no ortholog for SMCO2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for SMCO2 Gene

ENSEMBL:
Gene Tree for SMCO2 (if available)
TreeFam:
Gene Tree for SMCO2 (if available)

Paralogs for SMCO2 Gene

No data available for Paralogs for SMCO2 Gene

Variants for SMCO2 Gene

Sequence variations from dbSNP and Humsavar for SMCO2 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1000030754 -- 27,506,837(+) GAACA(A/C)ATCAG utr-variant-3-prime
rs1000041098 -- 27,488,704(+) GTAAC(A/G)CTGCT intron-variant
rs1000107868 -- 27,490,014(+) CACAC(A/G)TATAC intron-variant
rs1000113439 -- 27,482,507(+) CGTTG(A/G)CCAGG intron-variant
rs1000142942 -- 27,487,722(+) CTAGC(A/G)TTTGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMCO2 Gene

Variant ID Type Subtype PubMed ID
dgv1406n100 CNV gain 25217958
dgv1407n100 CNV loss 25217958
dgv16n64 CNV loss 17921354
dgv2417n54 CNV gain 21841781
dgv2418n54 CNV loss 21841781
dgv2419n54 CNV loss 21841781
dgv24e203 CNV loss 21179565
dgv271e199 CNV deletion 23128226
dgv36n17 CNV loss 16327808
dgv469e212 CNV loss 25503493
dgv470e212 CNV loss 25503493
esv2421622 CNV deletion 20811451
esv2672053 CNV deletion 23128226
esv2745664 CNV deletion 23290073
esv2745668 CNV deletion 23290073
esv2759887 CNV loss 17122850
esv28340 CNV loss 19812545
esv3548928 CNV deletion 23714750
esv3580202 CNV loss 25503493
esv3584649 CNV loss 24956385
esv3628940 CNV gain 21293372
esv3628941 CNV loss 21293372
esv3628942 CNV gain 21293372
esv3628943 CNV gain 21293372
esv3892166 CNV loss 25118596
nsv1052330 CNV gain 25217958
nsv436825 CNV insertion 17901297
nsv437732 CNV loss 16327808
nsv438198 CNV loss 16468122
nsv438199 CNV loss 16468122
nsv442638 CNV loss 18776908
nsv498784 CNV loss 21111241
nsv514659 CNV loss 21397061
nsv517383 CNV loss 19592680
nsv519752 CNV gain+loss 19592680
nsv521872 CNV gain 19592680
nsv523517 CNV gain 19592680
nsv651 CNV deletion 18451855
nsv8931 CNV loss 18304495
nsv951344 CNV deletion 24416366
nsv983483 CNV deletion 23825009

Variation tolerance for SMCO2 Gene

Gene Damage Index Score: 4.19; 61.91% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMCO2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMCO2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMCO2 Gene

Disorders for SMCO2 Gene

Relevant External Links for SMCO2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMCO2

No disorders were found for SMCO2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMCO2 Gene

Publications for SMCO2 Gene

  1. The finished DNA sequence of human chromosome 12. (PMID: 16541075) Scherer S.E. … Gibbs R.A. (Nature 2006) 3 4 64

Products for SMCO2 Gene

Sources for SMCO2 Gene

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