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    SMC5 structural maintenance of chromosomes 5 [ Homo sapiens (human) ]

    Gene ID: 23137, updated on 10-Dec-2024

    Summary

    Official Symbol
    SMC5provided by HGNC
    Official Full Name
    structural maintenance of chromosomes 5provided by HGNC
    Primary source
    HGNC:HGNC:20465
    See related
    Ensembl:ENSG00000198887 MIM:609386; AllianceGenome:HGNC:20465
    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
    ATELS2; SMC5L1
    Summary
    Enables DNA secondary structure binding activity. Involved in several processes, including DNA recombination; negative regulation by host of viral genome replication; and positive regulation of cell cycle process. Located in cell junction; chromosome; and nuclear body. Part of Smc5-Smc6 complex. Is active in nucleus. Implicated in mosaic variegated aneuploidy syndrome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 12.4), lymph node (RPKM 10.1) and 25 other tissues See more
    Orthologs
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    Genomic context

    See SMC5 in Genome Data Viewer
    Location:
    9q21.12
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (70258978..70354873)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (82425826..82521669)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (72873894..72969789)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MAM domain containing 2 Neighboring gene RNA, U2 small nuclear 5, pseudogene Neighboring gene SMC5 divergent transcript Neighboring gene RPL24 pseudogene 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:72889083-72889583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:72888582-72889082 Neighboring gene uncharacterized LOC124900273 Neighboring gene KLF9-II enhancer Neighboring gene ReSE screen-validated silencer GRCh37_chr9:73027338-73027530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:73028054-73028907 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:73033721-73034442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19943 Neighboring gene Sharpr-MPRA regulatory region 12362 Neighboring gene KLF transcription factor 9 Neighboring gene KLF9 divergent transcript Neighboring gene uncharacterized LOC105376079

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (613 hits/1282 screens)

    Associated conditions

    Description Tests
    Atelis syndrome 2
    MedGen: C5774282 OMIM: 620185 GeneReviews: Not available
    not available

    Pathways from PubChem

    Interactions

    General gene information

    Clone Names

    • KIAA0594

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding  
    enables ATP hydrolysis activity  
    enables DNA secondary structure binding PubMed 
    enables protein binding PubMed 
    enables single-stranded DNA binding  
    Process Evidence Code Pubs
    involved_in DNA damage response PubMed 
    involved_in cell division  
    involved_in cellular senescence PubMed 
    involved_in chromatin looping PubMed 
    involved_in chromosome condensation  
    involved_in chromosome segregation  
    involved_in double-strand break repair via homologous recombination  
    involved_in double-strand break repair via homologous recombination PubMed 
    involved_in double-strand break repair via homologous recombination PubMed 
    NOT involved_in double-strand break repair via nonhomologous end joining PubMed 
    involved_in mitotic cell cycle phase transition  
    involved_in negative regulation by host of viral genome replication PubMed 
    involved_in positive regulation of chromosome segregation PubMed 
    involved_in positive regulation of maintenance of mitotic sister chromatid cohesion PubMed 
    involved_in protein localization to chromosome, centromeric region  
    involved_in protein sumoylation PubMed 
    involved_in regulation of telomere maintenance PubMed 
    involved_in stem cell population maintenance  
    involved_in telomere maintenance via recombination PubMed 
    Component Evidence Code Pubs
    located_in PML body PubMed 
    part_of Smc5-Smc6 complex  
    part_of Smc5-Smc6 complex PubMed 
    part_of Smc5-Smc6 complex PubMed 
    located_in cell junction  
    located_in chromosome, centromeric region  
    located_in chromosome, telomeric region PubMed 
    located_in chromosome, telomeric region PubMed 
    located_in cytoplasm  
    located_in interchromatin granule PubMed 
    located_in nuclear speck  
    located_in nucleoplasm  
    is_active_in nucleus  
    is_active_in nucleus PubMed 
    located_in nucleus PubMed 
    located_in nucleus  
    located_in sex chromosome  
    located_in site of double-strand break PubMed 

    General protein information

    Preferred Names
    structural maintenance of chromosomes protein 5
    Names
    SMC protein 5
    SMC-5
    SMC5 structural maintenance of chromosomes 5-like 1
    hSMC5

    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_015110.4 → NP_055925.2  structural maintenance of chromosomes protein 5

      See identical proteins and their annotated locations for NP_055925.2

      Status: VALIDATED

      Source sequence(s)
      AA709087, AB011166, BC038225, DB220819, DB318469
      Consensus CDS
      CCDS6632.1
      UniProtKB/Swiss-Prot
      A6NM81, O60335, Q05D92, Q5VZ60, Q8IY18, Q96SB9
      Related
      ENSP00000354957.5, ENST00000361138.7
      Conserved Domains (2) summary
      cd03277
      Location:975 → 1077
      ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
      COG1196
      Location:53 → 1055
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      70258978..70354873
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005251837.3 → XP_005251894.1  structural maintenance of chromosomes protein 5 isoform X1

      Conserved Domains (2) summary
      cd03277
      Location:960 → 1062
      ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
      COG1196
      Location:53 → 1040
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    2. XM_005251839.3 → XP_005251896.1  structural maintenance of chromosomes protein 5 isoform X4

      Conserved Domains (2) summary
      cd03277
      Location:937 → 1039
      ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
      COG1196
      Location:53 → 1017
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    3. XM_047423034.1 → XP_047278990.1  structural maintenance of chromosomes protein 5 isoform X6

    4. XM_005251838.3 → XP_005251895.1  structural maintenance of chromosomes protein 5 isoform X2

      Conserved Domains (3) summary
      cd03277
      Location:951 → 1053
      ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins
      COG1196
      Location:53 → 1031
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl07863
      Location:286 → 364
      Phasin; Poly(hydroxyalcanoate) granule associated protein (phasin)
    5. XM_047423033.1 → XP_047278989.1  structural maintenance of chromosomes protein 5 isoform X5

    6. XM_047423035.1 → XP_047278991.1  structural maintenance of chromosomes protein 5 isoform X7

    7. XM_047423036.1 → XP_047278992.1  structural maintenance of chromosomes protein 5 isoform X8

    8. XM_017014507.2 → XP_016869996.1  structural maintenance of chromosomes protein 5 isoform X3

    9. XM_047423037.1 → XP_047278993.1  structural maintenance of chromosomes protein 5 isoform X9

      UniProtKB/TrEMBL
      B4E265
    10. XM_047423038.1 → XP_047278994.1  structural maintenance of chromosomes protein 5 isoform X10

    11. XM_047423039.1 → XP_047278995.1  structural maintenance of chromosomes protein 5 isoform X11

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      82425826..82521669
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362451.1 → XP_054218426.1  structural maintenance of chromosomes protein 5 isoform X1

    2. XM_054362454.1 → XP_054218429.1  structural maintenance of chromosomes protein 5 isoform X4

    3. XM_054362456.1 → XP_054218431.1  structural maintenance of chromosomes protein 5 isoform X6

    4. XM_054362452.1 → XP_054218427.1  structural maintenance of chromosomes protein 5 isoform X2

    5. XM_054362455.1 → XP_054218430.1  structural maintenance of chromosomes protein 5 isoform X5

    6. XM_054362457.1 → XP_054218432.1  structural maintenance of chromosomes protein 5 isoform X7

    7. XM_054362458.1 → XP_054218433.1  structural maintenance of chromosomes protein 5 isoform X8

    8. XM_054362453.1 → XP_054218428.1  structural maintenance of chromosomes protein 5 isoform X3

    9. XM_054362459.1 → XP_054218434.1  structural maintenance of chromosomes protein 5 isoform X9

      UniProtKB/TrEMBL
      B4E265
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