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

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

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 
    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001142286.2NP_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:481069
      SMC_N; RecF/RecN/SMC N terminal domain
    2. NM_024624.6NP_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:481069
      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_017004916.3XP_016860405.1  structural maintenance of chromosomes protein 6 isoform X3

      UniProtKB/TrEMBL
      A0A2S1ZR79
    2. XM_011533108.4XP_011531410.1  structural maintenance of chromosomes protein 6 isoform X2

      UniProtKB/TrEMBL
      A0A2S1ZR79
      Conserved Domains (4) summary
      cd03276
      Location:9691067
      ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
      COG1196
      Location:481061
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam08702
      Location:635715
      Fib_alpha; Fibrinogen alpha/beta chain family
      pfam17023
      Location:674808
      DUF5098; Domain of unknown function (DUF5098)
    3. XM_017004913.3XP_016860402.1  structural maintenance of chromosomes protein 6 isoform X1

      UniProtKB/TrEMBL
      A0A2S1ZR79
      Conserved Domains (4) summary
      cd03276
      Location:9961094
      ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
      COG1196
      Location:481088
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam08702
      Location:662742
      Fib_alpha; Fibrinogen alpha/beta chain family
      pfam17023
      Location:701835
      DUF5098; Domain of unknown function (DUF5098)
    4. XM_047445837.1XP_047301793.1  structural maintenance of chromosomes protein 6 isoform X3

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

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

      UniProtKB/TrEMBL
      A0A2S1ZR79
      Conserved Domains (4) summary
      cd03276
      Location:9961094
      ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
      COG1196
      Location:481088
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam08702
      Location:662742
      Fib_alpha; Fibrinogen alpha/beta chain family
      pfam17023
      Location:701835
      DUF5098; Domain of unknown function (DUF5098)
    7. XM_047445835.1XP_047301791.1  structural maintenance of chromosomes protein 6 isoform X2

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

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

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

    11. XM_017004915.3XP_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:481069
      SMC_N; RecF/RecN/SMC N terminal domain
    12. XM_011533107.4XP_011531409.1  structural maintenance of chromosomes protein 6 isoform X1

      UniProtKB/TrEMBL
      A0A2S1ZR79
      Conserved Domains (4) summary
      cd03276
      Location:9961094
      ABC_SMC6_euk; ATP-binding cassette domain of eukaryotic SM6 proteins
      COG1196
      Location:481088
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam08702
      Location:662742
      Fib_alpha; Fibrinogen alpha/beta chain family
      pfam17023
      Location:701835
      DUF5098; Domain of unknown function (DUF5098)
    13. XM_047445839.1XP_047301795.1  structural maintenance of chromosomes protein 6 isoform X4

      Related
      ENSP00000408644.1, ENST00000446852.5
    14. XM_047445840.1XP_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_054343920.1XP_054199895.1  structural maintenance of chromosomes protein 6 isoform X3

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

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

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

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

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

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

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