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

Gene ID: 79677, updated on 25-Nov-2021

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
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
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

See SMC6 in Genome Data Viewer
Location:
2p24.2
Exon count:
30
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (17663812..17753833, complement)
105.20201022 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 RAD51 associated protein 2 Neighboring gene visinin like 1 Neighboring gene uncharacterized LOC105373449 Neighboring gene GEN1 Holliday junction 5' flap endonuclease Neighboring gene Sharpr-MPRA regulatory region 14936 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

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 damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
part_of Smc5-Smc6 complex IDA
Inferred from Direct Assay
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 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
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
PubMed 
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)

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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_001142286.2NP_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
    Q96SB8
    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
    Q96SB8
    Related
    ENSP00000323439.4, ENST00000351948.8
    Conserved Domains (1) summary
    cl25732
    Location:481069
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    17663812..17753833 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004916.2XP_016860405.1  structural maintenance of chromosomes protein 6 isoform X4

  2. XM_011533108.3XP_011531410.1  structural maintenance of chromosomes protein 6 isoform X3

    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_017004913.2XP_016860402.1  structural maintenance of chromosomes protein 6 isoform X1

    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_017004914.1XP_016860403.1  structural maintenance of chromosomes protein 6 isoform X1

    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)
  5. XM_017004915.2XP_016860404.1  structural maintenance of chromosomes protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q96SB8
    Related
    ENSP00000384539.1, ENST00000402989.5
    Conserved Domains (1) summary
    cl25732
    Location:481069
    SMC_N; RecF/RecN/SMC N terminal domain
  6. XM_011533107.3XP_011531409.1  structural maintenance of chromosomes protein 6 isoform X1

    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)

RNA

  1. XR_939716.3 RNA Sequence

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