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

Gene ID: 161829, updated on 5-Mar-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 gene silencing by RNA and piRNA metabolic process. Predicted to be located in P granule. Predicted to be part of PET complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward testis (RPKM 6.1) See more
Orthologs
mouse all
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Genomic context

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Location:
15q15.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (41182728..41230757, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (38988821..39036951, complement)
105.20220307 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
  • 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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NEW Try the new Transcript table

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_2023_10

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

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