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Aliases for SMC5 Gene

Aliases for SMC5 Gene

  • Structural Maintenance Of Chromosomes 5 2 3 5
  • SMC Protein 5 3 4
  • SMC5L1 3 4
  • SMC-5 3 4
  • HSMC5 3 4
  • SMC5 Structural Maintenance Of Chromosomes 5-Like 1 (Yeast) 2
  • SMC5 Structural Maintenance Of Chromosomes 5-Like 1 3
  • Structural Maintenance Of Chromosomes Protein 5 3
  • KIAA0594 4

External Ids for SMC5 Gene

Previous HGNC Symbols for SMC5 Gene

  • SMC5L1

Previous GeneCards Identifiers for SMC5 Gene

  • GC09P072063
  • GC09P072873
  • GC09P042713

Summaries for SMC5 Gene

GeneCards Summary for SMC5 Gene

SMC5 (Structural Maintenance Of Chromosomes 5) is a Protein Coding gene. Among its related pathways are SUMOylation and Metabolism of proteins.

UniProtKB/Swiss-Prot for SMC5 Gene

  • Core component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs). Required for recruitment of telomeres to PML nuclear bodies. Required for sister chromatid cohesion during prometaphase and mitotic progression; the function seems to be independent of SMC6. SMC5-SMC6 complex may prevent transcription of episomal DNA, such as circular viral DNA genome (PubMed:26983541).

Gene Wiki entry for SMC5 Gene

Additional gene information for SMC5 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMC5 Gene

Genomics for SMC5 Gene

GeneHancer (GH) Regulatory Elements for SMC5 Gene

Promoters and enhancers for SMC5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09I070255 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 583.5 -0.7 -742 5.8 HDGF PKNOX1 CLOCK ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B ZNF766 SMC5 SMC5-AS1 PTAR1 MAMDC2-AS1 MAMDC2 RPL24P8 GC09M070097
GH09I070417 Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 22.6 +161.2 161175 5.6 CLOCK ZFP64 FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC MEF2D LOC101927086 SMC5 SMC5-AS1 PTAR1 MAMDC2-AS1 KLF9 LOC105376079
GH09I070409 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.2 +153.5 153541 6.6 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 KLF9 SMC5 SMC5-AS1 GC09P070383
GH09I070599 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 13.4 +342.5 342472 3.2 ATF1 FEZF1 IRF4 YY1 GLIS2 ARID2 ZNF143 FOS RUNX3 RXRA SMC5 PTAR1 KLF9 TRPM3 GC09P070607 RN7SL726P LOC101927086
GH09I069758 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 11.5 -499.4 -499415 2.9 FOXA2 ARID4B SIN3A DMAP1 ZNF48 YY1 POLR2B ZNF766 GLIS2 ZNF213 PTAR1 LOC105376076 SMC5 FAM122A APBA1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SMC5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SMC5 gene promoter:

Genomic Locations for SMC5 Gene

Genomic Locations for SMC5 Gene
chr9:70,258,962-70,354,888
(GRCh38/hg38)
Size:
95,927 bases
Orientation:
Plus strand
chr9:72,873,878-72,969,804
(GRCh37/hg19)

Genomic View for SMC5 Gene

Genes around SMC5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMC5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMC5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMC5 Gene

Proteins for SMC5 Gene

  • Protein details for SMC5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IY18-SMC5_HUMAN
    Recommended name:
    Structural maintenance of chromosomes protein 5
    Protein Accession:
    Q8IY18
    Secondary Accessions:
    • A6NM81
    • O60335
    • Q05D92
    • Q5VZ60
    • Q96SB9

    Protein attributes for SMC5 Gene

    Size:
    1101 amino acids
    Molecular mass:
    128806 Da
    Quaternary structure:
    • Forms a heterodimer with SMC6 (PubMed:11408570). Component of the SMC5-SMC6 complex which consists at least of SMC5, SMC6, NSMCE2, NSMCE1, NSMCE4A or EID3 and NSMCE3 (PubMed:18086888). Interacts with NSMCE2 (PubMed:16055714). Interacts with SLF2; this interaction induces an association of the SLF1-SLF2 complex with the SMC5-SMC6 complex (PubMed:25931565). Interacts with RAD18; this interaction is increased in a SLF1 or SLF2-dependent manner (PubMed:25931565).
    • (Microbial infection) SMC5-SMC6 complex interacts with Hepatitis B X protein.
    SequenceCaution:
    • Sequence=AAH17666.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

neXtProt entry for SMC5 Gene

Post-translational modifications for SMC5 Gene

Other Protein References for SMC5 Gene

No data available for DME Specific Peptides for SMC5 Gene

Domains & Families for SMC5 Gene

Gene Families for SMC5 Gene

Protein Domains for SMC5 Gene

Suggested Antigen Peptide Sequences for SMC5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8IY18

UniProtKB/Swiss-Prot:

SMC5_HUMAN :
  • The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of SMC6, forming a V-shaped heterodimer.
  • Belongs to the SMC family. SMC5 subfamily.
Domain:
  • The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of SMC6, forming a V-shaped heterodimer.
Family:
  • Belongs to the SMC family. SMC5 subfamily.
genes like me logo Genes that share domains with SMC5: view

Function for SMC5 Gene

Molecular function for SMC5 Gene

UniProtKB/Swiss-Prot Function:
Core component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs). Required for recruitment of telomeres to PML nuclear bodies. Required for sister chromatid cohesion during prometaphase and mitotic progression; the function seems to be independent of SMC6. SMC5-SMC6 complex may prevent transcription of episomal DNA, such as circular viral DNA genome (PubMed:26983541).

Phenotypes From GWAS Catalog for SMC5 Gene

Gene Ontology (GO) - Molecular Function for SMC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11408570
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with SMC5: view
genes like me logo Genes that share phenotypes with SMC5: view

Animal Models for SMC5 Gene

MGI Knock Outs for SMC5:
  • Smc5 tm1b(KOMP)Wtsi
  • Smc5 tm1d(KOMP)Wtsi

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SMC5 Gene

Localization for SMC5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMC5 Gene

Nucleus. Chromosome. Nucleus, PML body. Chromosome, telomere. Note=Associates with chromatin (PubMed:25931565). Colocalizes with SMC6 on the X-Y chromosome pair within the sex vesicle during late pachytene/diplotene (By similarity). Localizes to PML nuclear bodies in ALT cell lines (PubMed:17589526). Accumulates with RAD18 and the SLF1-SLF2 complex at replication-coupled DNA interstrand repair and DNA double-strand breaks (DSBs) sites on chromatin in a ubiquitin-dependent manner (PubMed:25931565). {ECO:0000250 UniProtKB:Q8CG46, ECO:0000269 PubMed:25931565}.

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 SMC5 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000781 chromosome, telomeric region IDA,IEA 17589526
GO:0000803 sex chromosome ISS --
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with SMC5: view

Pathways & Interactions for SMC5 Gene

genes like me logo Genes that share pathways with SMC5: view

Gene Ontology (GO) - Biological Process for SMC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000722 telomere maintenance via recombination IMP 17589526
GO:0000724 double-strand break repair via homologous recombination IMP 16810316
GO:0006281 DNA repair IEA --
GO:0006303 NOT double-strand break repair via nonhomologous end joining IMP 16810316
GO:0006310 DNA recombination IEA --
genes like me logo Genes that share ontologies with SMC5: view

No data available for SIGNOR curated interactions for SMC5 Gene

Drugs & Compounds for SMC5 Gene

(4) Drugs for SMC5 Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
KPT-185 Pharma CRM1 inhibitor,selective and irrversible 0
KPT-276 Pharma 0
KPT-330 Pharma 0
Verdinexor (KPT-335) Pharma 0

(4) ApexBio Compounds for SMC5 Gene

Compound Action Cas Number
KPT-185 CRM1 inhibitor,selective and irrversible 1333151-73-7
KPT-276 1421919-75-6
KPT-330 1393477-72-9
Verdinexor (KPT-335) 1392136-43-4
genes like me logo Genes that share compounds with SMC5: view

Drug Products

Transcripts for SMC5 Gene

Unigene Clusters for SMC5 Gene

Structural maintenance of chromosomes 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMC5 Gene

No ASD Table

Relevant External Links for SMC5 Gene

GeneLoc Exon Structure for
SMC5
ECgene alternative splicing isoforms for
SMC5

Expression for SMC5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SMC5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMC5 Gene

This gene is overexpressed in Blymphocyte (25.1), Lymph node (15.7), Testis (7.4), and Peripheral blood mononuclear cells (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SMC5 Gene



Protein tissue co-expression partners for SMC5 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMC5 Gene:

SMC5

SOURCE GeneReport for Unigene cluster for SMC5 Gene:

Hs.534189

mRNA Expression by UniProt/SwissProt for SMC5 Gene:

Q8IY18-SMC5_HUMAN
Tissue specificity: Widely expressed (PubMed:11408570). Strongly expressed in testis (PubMed:11408570).

Evidence on tissue expression from TISSUES for SMC5 Gene

  • Liver(4.3)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with SMC5: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMC5 Gene

Orthologs for SMC5 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SMC5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMC5 34 33
  • 99.67 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMC5 34 33
  • 92.19 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SMC5 34 33
  • 90.86 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smc5 33
  • 87.21 (n)
mouse
(Mus musculus)
Mammalia Smc5 33 16 34
  • 87.06 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMC5 34
  • 67 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMC5 34
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMC5 34 33
  • 70.12 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMC5 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smc5 33
  • 68.85 (n)
African clawed frog
(Xenopus laevis)
Amphibia smc5 33
zebrafish
(Danio rerio)
Actinopterygii smc5 34 33
  • 60.65 (n)
OneToOne
-- 33
fruit fly
(Drosophila melanogaster)
Insecta Smc5 33 34
  • 43.55 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011623 33
  • 42.3 (n)
worm
(Caenorhabditis elegans)
Secernentea smc-5 34
  • 27 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMC5 33 34
  • 59.01 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL337C 33
  • 55.56 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F07997g 33
  • 44.78 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons SMC5 33
  • 46.1 (n)
rice
(Oryza sativa)
Liliopsida Os05g0596600 33
  • 46.39 (n)
corn
(Zea mays)
Liliopsida Zm.1043 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes smc5 33
  • 44.64 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU09065 33
  • 43.49 (n)
Species where no ortholog for SMC5 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMC5 Gene

ENSEMBL:
Gene Tree for SMC5 (if available)
TreeFam:
Gene Tree for SMC5 (if available)

Paralogs for SMC5 Gene

Pseudogenes.org Pseudogenes for SMC5 Gene

genes like me logo Genes that share paralogs with SMC5: view

No data available for Paralogs for SMC5 Gene

Variants for SMC5 Gene

Sequence variations from dbSNP and Humsavar for SMC5 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000020022 -- 70,284,705(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000032247 -- 70,288,119(+) G/A intron_variant
rs1000098889 -- 70,306,562(+) G/A intron_variant
rs1000112580 -- 70,300,210(+) T/G intron_variant
rs1000151352 -- 70,299,686(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SMC5 Gene

Variant ID Type Subtype PubMed ID
nsv831615 CNV gain 17160897
nsv6555 CNV insertion 18451855
nsv507515 OTHER sequence alteration 20534489
nsv1049132 CNV gain 25217958
nsv1047862 CNV gain 25217958
esv2484591 CNV deletion 19546169
dgv2159e212 CNV loss 25503493

Variation tolerance for SMC5 Gene

Residual Variation Intolerance Score: 16.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.82; 73.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMC5 Gene

Human Gene Mutation Database (HGMD)
SMC5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMC5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMC5 Gene

Disorders for SMC5 Gene

Additional Disease Information for SMC5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SMC5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMC5 Gene

Publications for SMC5 Gene

  1. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9628581) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  2. Hepatitis B virus X protein identifies the Smc5/6 complex as a host restriction factor. (PMID: 26983541) Decorsière A … Strubin M (Nature 2016) 3 4 58
  3. DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. (PMID: 25931565) Räschle M … Mann M (Science (New York, N.Y.) 2015) 3 4 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Predisposition for TMPRSS2-ERG fusion in prostate cancer by variants in DNA repair genes. (PMID: 19861517) Luedeke M … Maier C (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2009) 3 44 58

Products for SMC5 Gene

Sources for SMC5 Gene

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