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

    Gene ID: 79677, updated on 2-Nov-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 DNA secondary structure binding activity and ubiquitin protein ligase binding activity. Involved in several processes, including cellular senescence; negative regulation by host of viral genome replication; and telomere maintenance via recombination. Located in chromosome and nuclear body. Part of Smc5-Smc6 complex. Is active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 13.9), lymph node (RPKM 7.0) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMC6 in Genome Data Viewer
    Location:
    2p24.2
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (17663812..17753810, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (17695556..17785539, complement)
    RS_2024_09 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 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. 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
    2. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Roy S, et al. Nucleic Acids Res, 2024 Mar 21. PMID 38375830, Free PMC Article
    3. Human Smc5/6 recognises transcription-generated positive DNA supercoils. Diman A, et al. Nat Commun, 2024 Sep 6. PMID 39242537, Free PMC Article
    4. 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
    5. Smc5/6-mediated regulation of replication progression contributes to chromosome assembly during mitosis in human cells. Gallego-Paez LM, et al. Mol Biol Cell, 2014 Jan. PMID 24258023, Free PMC Article

    See all (81) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Human Smc5/6 recognises transcription-generated positive DNA supercoils.
      Title: Human Smc5/6 recognises transcription-generated positive DNA supercoils.
    2. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress.
      Title: The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress.
    3. 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.
    4. Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency.
      Title: Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. Molecular Insights into the Architecture of the Human SMC5/6 Complex.
      Title: Molecular Insights into the Architecture of the Human SMC5/6 Complex.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    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_2024_08

    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

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