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

Gene ID: 54932, updated on 5-Mar-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 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. Predicted to be involved in nucleic acid phosphodiester bond hydrolysis. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
9q34.3
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137306896..137423162, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149544816..149673783, complement)
105.20220307 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
  • 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_2023_10

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

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