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

    Gene ID: 54780, updated on 10-Dec-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 DNA damage response. Located in nuclear body. Part of Smc5-Smc6 complex. [provided by Alliance of Genome Resources, Dec 2024]
    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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    See NSMCE4A in Genome Data Viewer
    Location:
    10q26.13
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (121957091..121975217, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (122853434..122871558, complement)
    RS_2024_09 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 opposite strand, pseudogene 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: 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

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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. Qri2/Nse4, a component of the essential Smc5/6 DNA repair complex. Hu B, et al. Mol Microbiol, 2005 Mar. PMID 15752197
    4. Molecular Insights into the Architecture of the Human SMC5/6 Complex. Adamus M, et al. J Mol Biol, 2020 Jun 12. PMID 32389690
    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 (37) 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)

    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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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