Aliases for SMC5 Gene

Aliases for SMC5 Gene

  • Structural Maintenance Of Chromosomes 5 2 3 5
  • Structural Maintenance Of Chromosomes Protein 5 3 4
  • SMC Protein 5 3 4
  • KIAA0594 2 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
  • SMC5 5

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. Diseases associated with SMC5 include Chromosome 5P13 Duplication Syndrome and Cornelia De Lange Syndrome. Among its related pathways are SUMOylation and Metabolism of proteins. An important paralog of this gene is SMC6.

UniProtKB/Swiss-Prot Summary 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

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMC5 Gene

Genomics for SMC5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SMC5 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMC5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMC5

Top Transcription factor binding sites by QIAGEN in the SMC5 gene promoter:
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alpha isoform 3
  • AP-2alpha isoform 4
  • AP-2alphaA
  • c-Myb
  • FOXO1
  • FOXO1a
  • HSF2
  • RREB-1

Genomic Locations for SMC5 Gene

Latest Assembly
chr9:70,258,962-70,354,873
(GRCh38/hg38)
Size:
95,912 bases
Orientation:
Plus strand

Previous Assembly
chr9:72,873,894-72,969,789
(GRCh37/hg19 by Entrez Gene)
Size:
95,896 bases
Orientation:
Plus strand

chr9:72,873,937-72,969,804
(GRCh37/hg19 by Ensembl)
Size:
95,868 bases
Orientation:
Plus strand

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

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:
  • Structural maintenance of chromosomes protein 5 (SMC5_HUMAN)

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:0000166 nucleotide binding IEA --
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 Smc5<tm1b(KOMP)Wtsi>
  • Smc5 Smc5<tm1d(KOMP)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMC5

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
cytoskeleton 2
cytosol 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 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:0000775 chromosome, centromeric region IEA --
GO:0000781 chromosome, telomeric region IEA,IDA 17589526
GO:0000803 sex chromosome IEA,ISS --
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm TAS --
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 for research

Transcripts for SMC5 Gene

mRNA/cDNA for SMC5 Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMC5

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

No ASD Table

Relevant External Links for SMC5 Gene

GeneLoc Exon Structure for
SMC5

Expression for SMC5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for SMC5 Gene



Protein tissue co-expression partners for SMC5 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.5)
  • Nervous system(4.4)
  • Blood(2.3)
  • Heart(2.2)
  • Skin(2.2)
  • Kidney(2)
genes like me logo Genes that share expression patterns with SMC5: view

Primer products for research

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 29 30
  • 99.67 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SMC5 29 30
  • 92.19 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SMC5 29 30
  • 90.86 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Smc5 29
  • 87.21 (n)
Mouse
(Mus musculus)
Mammalia Smc5 29 16 30
  • 87.06 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SMC5 30
  • 67 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SMC5 30
  • 66 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SMC5 29 30
  • 70.12 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SMC5 30
  • 62 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia smc5 29
  • 68.85 (n)
African clawed frog
(Xenopus laevis)
Amphibia smc5 29
Zebrafish
(Danio rerio)
Actinopterygii smc5 29 30
  • 60.65 (n)
OneToOne
-- 29
Fruit Fly
(Drosophila melanogaster)
Insecta Smc5 29 30
  • 43.55 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011623 29
  • 42.3 (n)
Worm
(Caenorhabditis elegans)
Secernentea smc-5 30
  • 27 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMC5 29 30
  • 59.01 (n)
OneToOne
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AEL337C 29
  • 55.56 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F07997g 29
  • 44.78 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons SMC5 29
  • 46.1 (n)
Rice
(Oryza sativa)
Liliopsida Os05g0596600 29
  • 46.39 (n)
Corn
(Zea mays)
Liliopsida Zm.1043 29
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes smc5 29
  • 44.64 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU09065 29
  • 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for SMC5: view image
Alliance of Genome Resources:
Additional Orthologs for SMC5

Paralogs for SMC5 Gene

Paralogs for SMC5 Gene

Pseudogenes.org Pseudogenes for SMC5 Gene

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

Variants for SMC5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMC5 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs12005618 Benign: not provided 70,264,388(+) G/A
NM_015110.4(SMC5):c.270G>A (p.Val90=)
SYNONYMOUS
rs59648118 Benign: not provided 70,323,530(+) G/A
NM_015110.4(SMC5):c.2198G>A (p.Arg733Gln)
MISSENSE
rs73456610 Benign: not provided 70,318,682(+) C/T
NM_015110.4(SMC5):c.1975C>T (p.Leu659=)
SYNONYMOUS
rs73647461 Benign: not provided 70,318,889(+) A/G
NM_015110.4(SMC5):c.2076A>G (p.Gln692=)
SYNONYMOUS
rs73647462 Benign: not provided 70,323,612(+) G/A
NM_015110.4(SMC5):c.2274+6G>A
INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SMC5 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

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
Leiden Open Variation Database (LOVD)
SMC5

SNP Genotyping and Copy Number Assays for research

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

Disorders for SMC5 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SMC5 Gene - From: COP

Disorder Aliases PubMed IDs
chromosome 5p13 duplication syndrome
  • 5p13 microduplication syndrome
cornelia de lange syndrome
  • brachmann de lange syndrome
isolated growth hormone deficiency, type ia
  • ighd1a
- elite association - COSMIC cancer census association via MalaCards
Search SMC5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SMC5

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SMC5: view

No data available for 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
  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
  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
  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 40
  5. SMC5 and MMS21 are required for chromosome cohesion and mitotic progression. (PMID: 19502785) Behlke-Steinert S … Margolis RL (Cell cycle (Georgetown, Tex.) 2009) 3 4

Products for SMC5 Gene

Sources for SMC5 Gene