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SMC6 structural maintenance of chromosomes 6 [ Homo sapiens (human) ]

Gene ID: 79677, updated on 7-Apr-2024

Summary

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Official Symbol
SMC6provided by HGNC
Official Full Name
structural maintenance of chromosomes 6provided by HGNC
Primary source
HGNC:HGNC:20466
See related
Ensembl:ENSG00000163029 MIM:609387; AllianceGenome:HGNC:20466
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SMC-6; hSMC6; SMC6L1
Summary
Enables ubiquitin protein ligase binding activity. Involved in several processes, including cellular senescence; positive regulation of chromosome segregation; and telomere maintenance via recombination. Located in chromosome and nuclear body. Part of Smc5-Smc6 complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 13.9), lymph node (RPKM 7.0) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
2p24.2
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (17663812..17753810, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (17695556..17785539, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (17845079..17935077, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene nascent polypeptide associated complex subunit alpha pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:17699235-17700434 Neighboring gene RAD51 associated protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15351 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:17724689-17725200 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:17725201-17725712 Neighboring gene visinin like 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:17760843-17761612 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:17771124-17772061 Neighboring gene uncharacterized LOC124908054 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:17825464-17826251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15352 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:17929152-17929835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11190 Neighboring gene uncharacterized LOC105373449 Neighboring gene GEN1 Holliday junction 5' flap endonuclease Neighboring gene Sharpr-MPRA regulatory region 14936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15353 Neighboring gene mesogenin 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency. Irwan ID, et al. Nat Microbiol, 2022 Dec. PMID 36376394, Free PMC Article
  2. The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. Serrano D, et al. Mol Cell, 2020 Dec 17. PMID 33301731, Free PMC Article
  3. Inducible Degradation of the Human SMC5/6 Complex Reveals an Essential Role Only during Interphase. Venegas AB, et al. Cell Rep, 2020 Apr 21. PMID 32320646
  4. SMC5/6 acts jointly with Fanconi anemia factors to support DNA repair and genome stability. Rossi F, et al. EMBO Rep, 2020 Feb 5. PMID 31867888, Free PMC Article
  5. The SMC5/6 Complex Interacts with the Papillomavirus E2 Protein and Influences Maintenance of Viral Episomal DNA. Bentley P, et al. J Virol, 2018 Aug 1. PMID 29848583, Free PMC Article

See all (72) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break.
    Title: The SMC5/6 complex: folding chromosomes back into shape when genomes take a break.
  2. Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency.
    Title: Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency.
  3. The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr.
    Title: The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr.
  4. Inducible Degradation of the Human SMC5/6 Complex Reveals an Essential Role Only during Interphase.
    Title: Inducible Degradation of the Human SMC5/6 Complex Reveals an Essential Role Only during Interphase.
  5. SMC5/6 acts jointly with Fanconi anemia factors to support DNA repair and genome stability.
    Title: SMC5/6 acts jointly with Fanconi anemia factors to support DNA repair and genome stability.
  6. The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine.
    Title: The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine.
  7. Molecular Insights into the Architecture of the Human SMC5/6 Complex.
    Title: Molecular Insights into the Architecture of the Human SMC5/6 Complex.
  8. Data suggest that SMC6 is not required for papillomavirus E2-mediated transcriptional activation, E1/E2-mediated transient replication, or differentiation-dependent amplification of viral DNA. However, a role for SMC5/6 complex was found in the papillomavirus genome maintenance.
    Title: The SMC5/6 Complex Interacts with the Papillomavirus E2 Protein and Influences Maintenance of Viral Episomal DNA.
  9. Study shows that the SMC5/6-hinge complex binds preferentially to ssDNA and that this interaction is affected by both 'latch' and 'hub' mutations, suggesting a key role for these unique features in controlling DNA association by the SMC5/6 complex.
    Title: Specialized interfaces of Smc5/6 control hinge stability and DNA association.
  10. SMC5/6 knockdown rescued HBx-deficient hepatitis b virus replication in human hepatocytes.
    Title: Hepatitis B Virus X Protein Promotes Degradation of SMC5/6 to Enhance HBV Replication.
Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ22116, FLJ35534

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA secondary structure binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular senescence IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromatin looping NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair via homologous recombination NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation by host of viral genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of chromosome segregation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein sumoylation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of telomere maintenance NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in telomere maintenance via recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in PML body IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Smc5-Smc6 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Smc5-Smc6 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Smc5-Smc6 complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
  
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome, telomeric region NAS
Non-traceable Author Statement
more info
 PubMed 
located_in interchromatin granule IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitotic spindle pole IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in sex chromosome ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in site of double-strand break IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
structural maintenance of chromosomes protein 6
Names
SMC protein 6
SMC6 structural maintenance of chromosomes 6-like 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001142286.2 → NP_001135758.1  structural maintenance of chromosomes protein 6

    See identical proteins and their annotated locations for NP_001135758.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL136544, AL832979, BC039828, CD369665, DB451629
    Consensus CDS
    CCDS1690.1
    UniProtKB/Swiss-Prot
    A8K8Q6, D6W518, Q05BV4, Q96SB8, Q9H0X3, Q9H6M0
    UniProtKB/TrEMBL
    A0A2S1ZR79, A0A2S1ZR87
    Related
    ENSP00000404092.2, ENST00000448223.7
    Conserved Domains (1) summary
    cl25732
    Location:48 → 1069
    SMC_N; RecF/RecN/SMC N terminal domain

  2. NM_024624.6 → NP_078900.1  structural maintenance of chromosomes protein 6

    See identical proteins and their annotated locations for NP_078900.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL832979, BC039828, CD369665
    Consensus CDS
    CCDS1690.1
    UniProtKB/Swiss-Prot
    A8K8Q6, D6W518, Q05BV4, Q96SB8, Q9H0X3, Q9H6M0
    UniProtKB/TrEMBL
    A0A2S1ZR79, A0A2S1ZR87
    Related
    ENSP00000323439.4, ENST00000351948.8
    Conserved Domains (1) summary
    cl25732
    Location:48 → 1069
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    17663812..17753810 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004916.3 → XP_016860405.1  structural maintenance of chromosomes protein 6 isoform X3

    UniProtKB/TrEMBL
    A0A2S1ZR79

  2. XM_011533108.4 → XP_011531410.1  structural maintenance of chromosomes protein 6 isoform X2

    UniProtKB/TrEMBL
    A0A2S1ZR79
    Conserved Domains (4) summary
    cd03276
    Location:969 → 1067
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    COG1196
    Location:48 → 1061
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam08702
    Location:635 → 715
    Fib_alpha; Fibrinogen alpha/beta chain family
    pfam17023
    Location:674 → 808
    DUF5098; Domain of unknown function (DUF5098)

  3. XM_017004913.3 → XP_016860402.1  structural maintenance of chromosomes protein 6 isoform X1

    UniProtKB/TrEMBL
    A0A2S1ZR79
    Conserved Domains (4) summary
    cd03276
    Location:996 → 1094
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    COG1196
    Location:48 → 1088
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam08702
    Location:662 → 742
    Fib_alpha; Fibrinogen alpha/beta chain family
    pfam17023
    Location:701 → 835
    DUF5098; Domain of unknown function (DUF5098)

  4. XM_047445837.1 → XP_047301793.1  structural maintenance of chromosomes protein 6 isoform X3

  5. XM_047445834.1 → XP_047301790.1  structural maintenance of chromosomes protein 6 isoform X2

  6. XM_017004914.2 → XP_016860403.1  structural maintenance of chromosomes protein 6 isoform X1

    UniProtKB/TrEMBL
    A0A2S1ZR79
    Conserved Domains (4) summary
    cd03276
    Location:996 → 1094
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    COG1196
    Location:48 → 1088
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam08702
    Location:662 → 742
    Fib_alpha; Fibrinogen alpha/beta chain family
    pfam17023
    Location:701 → 835
    DUF5098; Domain of unknown function (DUF5098)

  7. XM_047445835.1 → XP_047301791.1  structural maintenance of chromosomes protein 6 isoform X2

  8. XM_047445833.1 → XP_047301789.1  structural maintenance of chromosomes protein 6 isoform X1

  9. XM_047445838.1 → XP_047301794.1  structural maintenance of chromosomes protein 6 isoform X3

  10. XM_047445836.1 → XP_047301792.1  structural maintenance of chromosomes protein 6 isoform X2

  11. XM_017004915.3 → XP_016860404.1  structural maintenance of chromosomes protein 6 isoform X6

    UniProtKB/Swiss-Prot
    A8K8Q6, D6W518, Q05BV4, Q96SB8, Q9H0X3, Q9H6M0
    UniProtKB/TrEMBL
    A0A2S1ZR79, A0A2S1ZR87
    Conserved Domains (1) summary
    cl25732
    Location:48 → 1069
    SMC_N; RecF/RecN/SMC N terminal domain

  12. XM_011533107.4 → XP_011531409.1  structural maintenance of chromosomes protein 6 isoform X1

    UniProtKB/TrEMBL
    A0A2S1ZR79
    Conserved Domains (4) summary
    cd03276
    Location:996 → 1094
    ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
    COG1196
    Location:48 → 1088
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam08702
    Location:662 → 742
    Fib_alpha; Fibrinogen alpha/beta chain family
    pfam17023
    Location:701 → 835
    DUF5098; Domain of unknown function (DUF5098)

  13. XM_047445839.1 → XP_047301795.1  structural maintenance of chromosomes protein 6 isoform X4

    Related
    ENSP00000408644.1, ENST00000446852.5

  14. XM_047445840.1 → XP_047301796.1  structural maintenance of chromosomes protein 6 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    17695556..17785539 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343920.1 → XP_054199895.1  structural maintenance of chromosomes protein 6 isoform X3

  2. XM_054343918.1 → XP_054199893.1  structural maintenance of chromosomes protein 6 isoform X2

  3. XM_054343916.1 → XP_054199891.1  structural maintenance of chromosomes protein 6 isoform X1

  4. XM_054343921.1 → XP_054199896.1  structural maintenance of chromosomes protein 6 isoform X3

  5. XM_054343919.1 → XP_054199894.1  structural maintenance of chromosomes protein 6 isoform X2

  6. XM_054343917.1 → XP_054199892.1  structural maintenance of chromosomes protein 6 isoform X1

  7. XM_054343922.1 → XP_054199897.1  structural maintenance of chromosomes protein 6 isoform X4

  8. XM_054343923.1 → XP_054199898.1  structural maintenance of chromosomes protein 6 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96SB8.2 GenPept UniProtKB/Swiss-Prot:Q96SB8

Gene LinkOut

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