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NSMCE4A NSE4 homolog A, SMC5-SMC6 complex component [ Homo sapiens (human) ]

Gene ID: 54780, updated on 5-Mar-2024

Summary

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Official Symbol
NSMCE4Aprovided by HGNC
Official Full Name
NSE4 homolog A, SMC5-SMC6 complex componentprovided by HGNC
Primary source
HGNC:HGNC:25935
See related
Ensembl:ENSG00000107672 MIM:612987; AllianceGenome:HGNC:25935
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
NS4EA; NSE4A; C10orf86
Summary
Involved in positive regulation of response to DNA damage stimulus. Located in nuclear body. Part of Smc5-Smc6 complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in prostate (RPKM 10.0), fat (RPKM 9.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
10q26.13
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (121957091..121975217, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (122853434..122871558, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (123716606..123734732, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:123492224-123492816 Neighboring gene ribosomal protein S15a pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4140 Neighboring gene arginyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4141 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:123687446-123688312 Neighboring gene Sharpr-MPRA regulatory region 2750 Neighboring gene ATE1 antisense RNA 1 Neighboring gene uncharacterized LOC124902517 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:123734371-123735166 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:123778189-123779388 Neighboring gene transforming acidic coiled-coil containing protein 2 Neighboring gene Sharpr-MPRA regulatory region 10515 Neighboring gene Sharpr-MPRA regulatory regions 8460 and 2354 Neighboring gene MPRA-validated peak1120 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:123836619-123837120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:123844981-123845482 Neighboring gene Sharpr-MPRA regulatory regions 1076 and 11287 Neighboring gene uncharacterized LOC124902518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:123914119-123915090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:123931653-123932226 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:123933375-123933946 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:123938237-123938774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:123939851-123940388 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:123952053-123952808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:123955355-123956017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:123959504-123960449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:123960450-123961394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:123992934-123993434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:124005137-124006083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:124027705-124028206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:124050601-124051101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:124053014-124054004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4142 Neighboring gene BTB domain containing 16

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
  • 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. PJA1 Coordinates with the SMC5/6 Complex To Restrict DNA Viruses and Episomal Genes in an Interferon-Independent Manner. Xu W, et al. J Virol, 2018 Nov 15. PMID 30185588, Free PMC Article
  2. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. van der Crabben SN, et al. J Clin Invest, 2016 Aug 1. PMID 27427983, Free PMC Article
  3. Molecular Insights into the Architecture of the Human SMC5/6 Complex. Adamus M, et al. J Mol Biol, 2020 Jun 12. PMID 32389690
  4. Qri2/Nse4, a component of the essential Smc5/6 DNA repair complex. Hu B, et al. Mol Microbiol, 2005 Mar. PMID 15752197
  5. Human SMC5/6 complex promotes sister chromatid homologous recombination by recruiting the SMC1/3 cohesin complex to double-strand breaks. Potts PR, et al. EMBO J, 2006 Jul 26. PMID 16810316, Free PMC Article

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRIM31 directly binds to NSE4, suggesting the existence of a TRIM31-MAGEA1-NSE4 complex reminiscent of the NSE1-NSE3-NSE4 trimer.
    Title: The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex.
Submit: New GeneRIF Correction

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20003

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin looping NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in double-strand break repair via homologous recombination NAS
Non-traceable Author Statement
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 
Component Evidence Code Pubs
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, telomeric region NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
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
  

General protein information

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Preferred Names
non-structural maintenance of chromosomes element 4 homolog A
Names
NSE4 homolog, SMC5-SMC6 complex component A
non-SMC element 4 homolog A

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_001167865.2 → NP_001161337.1  non-structural maintenance of chromosomes element 4 homolog A isoform 2

    See identical proteins and their annotated locations for NP_001161337.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AL731566, BC062427
    UniProtKB/Swiss-Prot
    Q9NXX6
    Conserved Domains (2) summary
    pfam08743
    Location:286 → 373
    Nse4_C; Nse4 C-terminal
    pfam15412
    Location:133 → 185
    Nse4-Nse3_bdg; Binding domain of Nse4/EID3 to Nse3-MAGE

  2. NM_001411073.1 → NP_001398002.1  non-structural maintenance of chromosomes element 4 homolog A isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL731566
    Consensus CDS
    CCDS91366.1
    Related
    ENSP00000358013.5, ENST00000369017.5

  3. NM_017615.3 → NP_060085.2  non-structural maintenance of chromosomes element 4 homolog A isoform 1

    See identical proteins and their annotated locations for NP_060085.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK000010, AL731566, DA567626
    Consensus CDS
    CCDS7624.1
    UniProtKB/Swiss-Prot
    Q5SQQ5, Q6P673, Q8WY66, Q9BS90, Q9NXX6
    Related
    ENSP00000358019.3, ENST00000369023.8
    Conserved Domains (2) summary
    pfam08743
    Location:286 → 374
    Nse4_C; Nse4 C-terminal
    pfam15412
    Location:133 → 185
    Nse4-Nse3_bdg; Binding domain of Nse4/EID3 to Nse3-MAGE

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    121957091..121975217 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011539910.3 → XP_011538212.1  non-structural maintenance of chromosomes element 4 homolog A isoform X2

    See identical proteins and their annotated locations for XP_011538212.1

    Conserved Domains (1) summary
    pfam08743
    Location:127 → 215
    Nse4_C; Nse4 C-terminal

  2. XM_005269930.5 → XP_005269987.1  non-structural maintenance of chromosomes element 4 homolog A isoform X2

    See identical proteins and their annotated locations for XP_005269987.1

    Conserved Domains (1) summary
    pfam08743
    Location:127 → 215
    Nse4_C; Nse4 C-terminal

  3. XM_005269929.5 → XP_005269986.1  non-structural maintenance of chromosomes element 4 homolog A isoform X2

    See identical proteins and their annotated locations for XP_005269986.1

    Conserved Domains (1) summary
    pfam08743
    Location:127 → 215
    Nse4_C; Nse4 C-terminal

  4. XM_017016359.2 → XP_016871848.1  non-structural maintenance of chromosomes element 4 homolog A isoform X2

    Conserved Domains (1) summary
    pfam08743
    Location:127 → 215
    Nse4_C; Nse4 C-terminal

  5. XM_047425399.1 → XP_047281355.1  non-structural maintenance of chromosomes element 4 homolog A isoform X1

RNA

  1. XR_428706.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    122853434..122871558 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054366162.1 → XP_054222137.1  non-structural maintenance of chromosomes element 4 homolog A isoform X2

  2. XM_054366163.1 → XP_054222138.1  non-structural maintenance of chromosomes element 4 homolog A isoform X2

  3. XM_054366164.1 → XP_054222139.1  non-structural maintenance of chromosomes element 4 homolog A isoform X2

  4. XM_054366161.1 → XP_054222136.1  non-structural maintenance of chromosomes element 4 homolog A isoform X1

RNA

  1. XR_008488225.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXX6.2 GenPept UniProtKB/Swiss-Prot:Q9NXX6

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