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    EXD3 exonuclease 3'-5' domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 54932, updated on 2-Nov-2024

    Summary

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    Official Symbol
    EXD3provided by HGNC
    Official Full Name
    exonuclease 3'-5' domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:26023
    See related
    Ensembl:ENSG00000187609 MIM:620859; AllianceGenome:HGNC:26023
    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
    Nbr; mut-7
    Summary
    Predicted to enable 3'-5' exonuclease activity; metal ion binding activity; and nucleic acid binding activity. Predicted to be involved in nucleobase-containing compound metabolic process. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 2.6), fat (RPKM 2.4) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See EXD3 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137306896..137423162, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149544816..149673783, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140201348..140317614, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20605 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29350 Neighboring gene 9q34.3 TOR4A distal recombination region Neighboring gene torsin family 4 member A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140191021-140191688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140193329-140194222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140196022-140196940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140201529-140202446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140204820-140205742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140205743-140206664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140209101-140210036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20614 Neighboring gene NOTCH regulated ankyrin repeat protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140213503-140214138 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140214773-140215407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140215408-140216041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140245426-140245935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140245936-140246444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140262690-140263291 Neighboring gene MPRA-validated peak7347 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140264677-140264866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20616 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140306223-140306402 Neighboring gene Sharpr-MPRA regulatory region 4638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140311837-140312663 Neighboring gene uncharacterized LOC124902354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20619 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140323354-140324108 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140330497-140330751 Neighboring gene NADPH oxidase activator 1 Neighboring gene Sharpr-MPRA regulatory region 12030 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:140343721-140344920 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 8 Neighboring gene microRNA 7114 Neighboring gene NMDA receptor synaptonuclear signaling and neuronal migration factor

    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 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. [Bioinformatics analysis of expression and function of EXD3 gene in gastric cancer]. Sun D, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2019 Feb 28. PMID 30890511, Free PMC Article
    2. An empirical framework for binary interactome mapping. Venkatesan K, et al. Nat Methods, 2009 Jan. PMID 19060904, Free PMC Article
    3. TNF-α inhibits glucocorticoid receptor-induced gene expression by reshaping the GR nuclear cofactor profile. Dendoncker K, et al. Proc Natl Acad Sci U S A, 2019 Jun 25. PMID 31182584, Free PMC Article
    4. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Fei T, et al. Proc Natl Acad Sci U S A, 2017 Jun 27. PMID 28611215, Free PMC Article
    5. Towards a proteome-scale map of the human protein-protein interaction network. Rual JF, et al. Nature, 2005 Oct 20. PMID 16189514

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    • FLJ20433, FLJ30442, MGC74981, MGC131904

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5' exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in nucleobase-containing compound metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    exonuclease mut-7 homolog
    Names
    exonuclease 3'-5' domain-containing protein 3
    nibbler homolog
    testicular tissue protein Li 125

    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_001286823.2 → NP_001273752.1  exonuclease mut-7 homolog isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks several 3' exons but includes an alternate 3' exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is significantly shorter than isoform a.
      Source sequence(s)
      BC037355, BC069205, BX322799
      Consensus CDS
      CCDS75942.1
      UniProtKB/Swiss-Prot
      Q8N9H8
      Related
      ENSP00000431859.1, ENST00000479452.5

    2. NM_017820.5 → NP_060290.3  exonuclease mut-7 homolog isoform a

      See identical proteins and their annotated locations for NP_060290.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AI682614, AK094438, AL536907, BC131749, BX322799, HM005438
      Consensus CDS
      CCDS48066.1
      UniProtKB/Swiss-Prot
      A0A140VJP9, B8A4U7, C9JIQ9, E9PN82, Q2TAK4, Q6P1M1, Q8IXT8, Q8N3X4, Q8N9H8, Q8NHD1, Q96NP1, Q9NX53
      Related
      ENSP00000340474.4, ENST00000340951.9
      Conserved Domains (2) summary
      cd06146
      Location:373 → 568
      mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
      cl19501
      Location:631 → 850
      Mut7-C; Mut7-C RNAse domain

    RNA

    1. NR_104598.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) includes three additional exons in the 5' region, and lacks several 3' exons but includes an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC033079, BC069205, BX322799
      Related
      ENST00000460390.6

    2. NR_104599.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) shares two 5' exons but lacks the remaining exons found in variant 1, and it includes an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      BC039252, BC065002
      Related
      ENST00000465160.2

    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
      137306896..137423162 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423544.1 → XP_047279500.1  exonuclease mut-7 homolog isoform X4

    2. XM_047423543.1 → XP_047279499.1  exonuclease mut-7 homolog isoform X3

    3. XM_011518810.2 → XP_011517112.1  exonuclease mut-7 homolog isoform X2

      Conserved Domains (2) summary
      cd06146
      Location:497 → 693
      mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
      cl19501
      Location:756 → 852
      Mut7-C; Mut7-C RNAse domain

    4. XM_047423542.1 → XP_047279498.1  exonuclease mut-7 homolog isoform X1

    5. XM_024447588.2 → XP_024303356.1  exonuclease mut-7 homolog isoform X5

      Conserved Domains (2) summary
      cd06146
      Location:325 → 521
      mut-7_like_exo; DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins
      cl19501
      Location:584 → 680
      Mut7-C; Mut7-C RNAse domain

    6. XM_047423545.1 → XP_047279501.1  exonuclease mut-7 homolog isoform X6

    7. XM_047423546.1 → XP_047279502.1  exonuclease mut-7 homolog isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      149544816..149673783 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363186.1 → XP_054219161.1  exonuclease mut-7 homolog isoform X4

    2. XM_054363185.1 → XP_054219160.1  exonuclease mut-7 homolog isoform X3

    3. XM_054363183.1 → XP_054219158.1  exonuclease mut-7 homolog isoform X2

    4. XM_054363182.1 → XP_054219157.1  exonuclease mut-7 homolog isoform X1

    5. XM_054363184.1 → XP_054219159.1  exonuclease mut-7 homolog isoform X8

    6. XM_054363187.1 → XP_054219162.1  exonuclease mut-7 homolog isoform X5

    7. XM_054363188.1 → XP_054219163.1  exonuclease mut-7 homolog isoform X6

    8. XM_054363189.1 → XP_054219164.1  exonuclease mut-7 homolog isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N9H8.3 GenPept UniProtKB/Swiss-Prot:Q8N9H8

    Gene LinkOut

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

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