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    EXD1 exonuclease 3'-5' domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 161829, updated on 2-Nov-2024

    Summary

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    Official Symbol
    EXD1provided by HGNC
    Official Full Name
    exonuclease 3'-5' domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:28507
    See related
    Ensembl:ENSG00000178997 AllianceGenome:HGNC:28507
    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
    EXDL1
    Summary
    Predicted to enable RNA binding activity and protein homodimerization activity. Predicted to be involved in piRNA processing. Predicted to be located in P granule. Predicted to be part of PET complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 6.1) See more
    Orthologs
    mouse all
    NEW
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    Genomic context

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    See EXD1 in Genome Data Viewer
    Location:
    15q15.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (41182728..41230757, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (38988821..39036951, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (41474926..41522955, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene INO80 complex ATPase subunit Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:41407340-41408120 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:41408121-41408900 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:41409682-41410461 Neighboring gene CYCS pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:41443644-41444144 Neighboring gene NANOG hESC enhancer GRCh37_chr15:41472354-41472904 Neighboring gene CIBAR1 pseudogene 1 Neighboring gene RNA, 7SL, cytoplasmic 497, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9278 Neighboring gene MPRA-validated peak2306 silencer Neighboring gene calcineurin like EF-hand protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:41575083-41575824 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:41577309-41578048 Neighboring gene OIP5 antisense RNA 1 Neighboring gene Opa interacting protein 5

    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. Exonuclease Domain-Containing 1 Enhances MIWI2 piRNA Biogenesis via Its Interaction with TDRD12. Pandey RR, et al. Cell Rep, 2018 Sep 25. PMID 30257204
    2. PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway. Yang Z, et al. Mol Cell, 2016 Jan 7. PMID 26669262, Free PMC Article
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
    4. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article
    5. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    • MGC33637

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables 3'-5' exonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in meiotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in piRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in piRNA processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulatory ncRNA-mediated gene silencing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in P granule ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of PET complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of PET complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    piRNA biogenesis protein EXD1
    Names
    exonuclease 3'-5' domain-containing protein 1
    exonuclease 3'-5' domain-like-containing protein 1
    inactive exonuclease EXD1

    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_001286441.2 → NP_001273370.1  piRNA biogenesis protein EXD1 isoform 1

      See identical proteins and their annotated locations for NP_001273370.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC022408, AK302864, BC030628, DC404441
      Consensus CDS
      CCDS66738.1
      UniProtKB/Swiss-Prot
      Q8NHP7
      Related
      ENSP00000415056.2, ENST00000458580.7
      Conserved Domains (1) summary
      cd06148
      Location:147 → 345
      Egl_like_exo; DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

    2. NM_001385036.1 → NP_001371965.1  piRNA biogenesis protein EXD1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC012652, AC022408
      Conserved Domains (1) summary
      cd06148
      Location:124 → 322
      Egl_like_exo; DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

    3. NM_152596.4 → NP_689809.2  piRNA biogenesis protein EXD1 isoform 2

      See identical proteins and their annotated locations for NP_689809.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC022408, BC030628, DC404441
      Consensus CDS
      CCDS10072.1
      UniProtKB/Swiss-Prot
      A8K909, B7Z839, Q6ZW94, Q8NHP7
      Related
      ENSP00000321029.5, ENST00000314992.9
      Conserved Domains (1) summary
      cd06148
      Location:89 → 287
      Egl_like_exo; DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      41182728..41230757 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432210.1 → XP_047288166.1  piRNA biogenesis protein EXD1 isoform X3

      UniProtKB/Swiss-Prot
      A8K909, B7Z839, Q6ZW94, Q8NHP7

    2. XM_011521301.3 → XP_011519603.1  piRNA biogenesis protein EXD1 isoform X5

      Conserved Domains (1) summary
      cd06148
      Location:112 → 310
      Egl_like_exo; DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

    3. XM_011521298.3 → XP_011519600.1  piRNA biogenesis protein EXD1 isoform X1

      See identical proteins and their annotated locations for XP_011519600.1

      UniProtKB/Swiss-Prot
      Q8NHP7
      Conserved Domains (1) summary
      cd06148
      Location:147 → 345
      Egl_like_exo; DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

    4. XM_047432211.1 → XP_047288167.1  piRNA biogenesis protein EXD1 isoform X4

    5. XM_017021971.2 → XP_016877460.1  piRNA biogenesis protein EXD1 isoform X4

      Conserved Domains (1) summary
      cd06148
      Location:53 → 251
      Egl_like_exo; DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

    6. XM_047432209.1 → XP_047288165.1  piRNA biogenesis protein EXD1 isoform X2

    7. XM_017021970.2 → XP_016877459.1  piRNA biogenesis protein EXD1 isoform X4

      Conserved Domains (1) summary
      cd06148
      Location:53 → 251
      Egl_like_exo; DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

    8. XM_011521300.3 → XP_011519602.1  piRNA biogenesis protein EXD1 isoform X4

      Conserved Domains (1) summary
      cd06148
      Location:53 → 251
      Egl_like_exo; DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins

    9. XM_011521302.3 → XP_011519604.1  piRNA biogenesis protein EXD1 isoform X6

      See identical proteins and their annotated locations for XP_011519604.1

      Conserved Domains (1) summary
      cl10012
      Location:1 → 142
      DnaQ_like_exo; DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      38988821..39036951 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377399.1 → XP_054233374.1  piRNA biogenesis protein EXD1 isoform X1

    2. XM_054377401.1 → XP_054233376.1  piRNA biogenesis protein EXD1 isoform X3

    3. XM_054377406.1 → XP_054233381.1  piRNA biogenesis protein EXD1 isoform X5

    4. XM_054377405.1 → XP_054233380.1  piRNA biogenesis protein EXD1 isoform X4

    5. XM_054377404.1 → XP_054233379.1  piRNA biogenesis protein EXD1 isoform X4

    6. XM_054377400.1 → XP_054233375.1  piRNA biogenesis protein EXD1 isoform X2

    7. XM_054377403.1 → XP_054233378.1  piRNA biogenesis protein EXD1 isoform X4

    8. XM_054377402.1 → XP_054233377.1  piRNA biogenesis protein EXD1 isoform X4

    9. XM_054377407.1 → XP_054233382.1  piRNA biogenesis protein EXD1 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NHP7.4 GenPept UniProtKB/Swiss-Prot:Q8NHP7

    Gene LinkOut

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

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