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

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, Oct 2024]
Expression: Ubiquitous expression in ovary (RPKM 12.4), lymph node (RPKM 10.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Human Smc5/6 recognises transcription-generated positive DNA supercoils.
Title: Human Smc5/6 recognises transcription-generated positive DNA supercoils.
The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress.
Title: The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress.
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.
The structural maintenance of chromosomes 5 is a possible biomarker for individualized treatment of colorectal cancer.
Title: The structural maintenance of chromosomes 5 is a possible biomarker for individualized treatment of colorectal cancer.
In-frame deletion of SMC5 related with the phenotype of primordial dwarfism, chromosomal instability and insulin resistance.
Title: In-frame deletion of SMC5 related with the phenotype of primordial dwarfism, chromosomal instability and insulin resistance.
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency.
Title: Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency.
Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy.
Title: Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (29)

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

Associated conditions

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC156606P1 (e-PCR)
- UniSTS:271408

D9S1695 (e-PCR)
- UniSTS:21104

D15S1477 (e-PCR)
- UniSTS:474482

SHGC-24172 (e-PCR)
- UniSTS:76687

STS-D29466 (e-PCR)
- UniSTS:4013

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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in cell division	IEA Inferred from Electronic Annotation more info
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 chromosome condensation	IEA Inferred from Electronic Annotation more info
involved_in chromosome segregation	IEA Inferred from Electronic Annotation more info
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair via homologous recombination	NAS Non-traceable Author Statement more info	PubMed
NOT involved_in double-strand break repair via nonhomologous end joining	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic cell cycle phase transition	IEA Inferred from Electronic Annotation more info
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 positive regulation of maintenance of mitotic sister chromatid cohesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
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 stem cell population maintenance	IEA Inferred from Electronic Annotation more info
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 cell junction	IDA Inferred from Direct Assay more info
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 cytoplasm	IEA Inferred from Electronic Annotation more info
located_in interchromatin granule	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	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 nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in sex chromosome	ISS Inferred from Sequence or Structural Similarity 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 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)

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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

70258978..70354873

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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]
XM_047423034.1 → XP_047278990.1 structural maintenance of chromosomes protein 5 isoform X6
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)
XM_047423033.1 → XP_047278989.1 structural maintenance of chromosomes protein 5 isoform X5
XM_047423035.1 → XP_047278991.1 structural maintenance of chromosomes protein 5 isoform X7
XM_047423036.1 → XP_047278992.1 structural maintenance of chromosomes protein 5 isoform X8
XM_017014507.2 → XP_016869996.1 structural maintenance of chromosomes protein 5 isoform X3
XM_047423037.1 → XP_047278993.1 structural maintenance of chromosomes protein 5 isoform X9
XM_047423038.1 → XP_047278994.1 structural maintenance of chromosomes protein 5 isoform X10
XM_047423039.1 → XP_047278995.1 structural maintenance of chromosomes protein 5 isoform X11

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

82425826..82521669

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054362451.1 → XP_054218426.1 structural maintenance of chromosomes protein 5 isoform X1
XM_054362454.1 → XP_054218429.1 structural maintenance of chromosomes protein 5 isoform X4
XM_054362456.1 → XP_054218431.1 structural maintenance of chromosomes protein 5 isoform X6
XM_054362452.1 → XP_054218427.1 structural maintenance of chromosomes protein 5 isoform X2
XM_054362455.1 → XP_054218430.1 structural maintenance of chromosomes protein 5 isoform X5
XM_054362457.1 → XP_054218432.1 structural maintenance of chromosomes protein 5 isoform X7
XM_054362458.1 → XP_054218433.1 structural maintenance of chromosomes protein 5 isoform X8
XM_054362453.1 → XP_054218428.1 structural maintenance of chromosomes protein 5 isoform X3
XM_054362459.1 → XP_054218434.1 structural maintenance of chromosomes protein 5 isoform X9