EXD1 Gene (Protein Coding)

Exonuclease 3'-5' Domain Containing 1

GC15M041182
GIFtS:
34
See more...

Aliases for EXD1 Gene

Aliases for EXD1 Gene

  • Exonuclease 3'-5' Domain Containing 1 2 3 5
  • Exonuclease 3'-5' Domain-Like-Containing Protein 1 3 4
  • Exonuclease 3'-5' Domain-Containing Protein 1 3 4
  • PiRNA Biogenesis Protein EXD1 3 4
  • Inactive Exonuclease EXD1 3 4
  • EXDL1 3 4
  • Exonuclease 3'-5' Domain-Like 1 2
  • MGC33637 2
  • EXD1 5

External Ids for EXD1 Gene

Previous HGNC Symbols for EXD1 Gene

  • EXDL1

Previous GeneCards Identifiers for EXD1 Gene

  • GC15M039264
  • GC15M041474
  • GC15M018323

Summaries for EXD1 Gene

GeneCards Summary for EXD1 Gene

EXD1 (Exonuclease 3'-5' Domain Containing 1) is a Protein Coding gene. Diseases associated with EXD1 include Cerebral Creatine Deficiency Syndrome 3 and Cerebral Creatine Deficiency Syndrome. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and 3'-5' exonuclease activity. An important paralog of this gene is EXOSC10.

UniProtKB/Swiss-Prot Summary for EXD1 Gene

  • RNA-binding component of the PET complex, a multiprotein complex required for the processing of piRNAs during spermatogenesis. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposable elements, preventing their mobilization, which is essential for the germline integrity (By similarity). The PET complex is required during the secondary piRNAs metabolic process for the PIWIL2 slicing-triggered loading of PIWIL4 piRNAs. In the PET complex, EXD1 probably acts as an RNA adapter. EXD1 is an inactive exonuclease (By similarity).

Additional gene information for EXD1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for EXD1 Gene

Genomics for EXD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for EXD1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EXD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EXD1

Top Transcription factor binding sites by QIAGEN in the EXD1 gene promoter:
  • C/EBPbeta
  • CREB
  • deltaCREB
  • Evi-1
  • FOXJ2
  • FOXJ2 (long isoform)
  • FOXL1
  • RSRFC4

Genomic Locations for EXD1 Gene

Latest Assembly
chr15:41,182,725-41,231,074
(GRCh38/hg38)
Size:
48,350 bases
Orientation:
Minus strand

Previous Assembly
chr15:41,474,926-41,522,955
(GRCh37/hg19 by Entrez Gene)
Size:
48,030 bases
Orientation:
Minus strand

chr15:41,474,923-41,522,941
(GRCh37/hg19 by Ensembl)
Size:
48,019 bases
Orientation:
Minus strand

Genomic View for EXD1 Gene

Genes around EXD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EXD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EXD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for EXD1 Gene

Proteins for EXD1 Gene

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  • Protein details for EXD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NHP7-EXD1_HUMAN
    Recommended name:
    piRNA biogenesis protein EXD1
    Protein Accession:
    Q8NHP7
    Secondary Accessions:
    • A8K909
    • B7Z839
    • Q6ZW94

    Protein attributes for EXD1 Gene

    Size:
    514 amino acids
    Molecular mass:
    58335 Da
    Quaternary structure:
    • Homodimer (By similarity). Component of the PET complex, at least composed of EXD1, PIWIL2, TDRD12 and piRNAs (By similarity).

    Alternative splice isoforms for EXD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EXD1 Gene

Protein Expression for EXD1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for EXD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for EXD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EXD1 Gene

Domains & Families for EXD1 Gene

Gene Families for EXD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for EXD1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for EXD1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55584 (B7Z839_HUMAN)
  • Exonuclease 3'-5' domain-like-containing protein 1 (EXD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NHP7

UniProtKB/Swiss-Prot:

EXD1_HUMAN :
  • The 3'-5' exonuclease domain lacks the conserved Asp-Glu-Asp-Asp (DEDD) residues that coordinates divalent ions essential for exonuclease activity.
  • Belongs to the EXD1 family.
Domain:
  • The 3'-5' exonuclease domain lacks the conserved Asp-Glu-Asp-Asp (DEDD) residues that coordinates divalent ions essential for exonuclease activity.
Family:
  • Belongs to the EXD1 family.
genes like me logo Genes that share domains with EXD1: view

Function for EXD1 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for EXD1 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding component of the PET complex, a multiprotein complex required for the processing of piRNAs during spermatogenesis. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposable elements, preventing their mobilization, which is essential for the germline integrity (By similarity). The PET complex is required during the secondary piRNAs metabolic process for the PIWIL2 slicing-triggered loading of PIWIL4 piRNAs. In the PET complex, EXD1 probably acts as an RNA adapter. EXD1 is an inactive exonuclease (By similarity).

Phenotypes From GWAS Catalog for EXD1 Gene

Gene Ontology (GO) - Molecular Function for EXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding ISS --
GO:0005515 protein binding IPI 25416956
GO:0008408 NOT 3'-5' exonuclease activity IEA,ISS --
GO:0042803 protein homodimerization activity ISS --
genes like me logo Genes that share ontologies with EXD1: view
genes like me logo Genes that share phenotypes with EXD1: view

Animal Models for EXD1 Gene

MGI Knock Outs for EXD1:
  • Exd1 Exd1<tm1b(EUCOMM)Hmgu>
  • Exd1 Exd1<tm1Embrp>

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EXD1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for EXD1 Gene

Localization for EXD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EXD1 Gene

Cytoplasm. Note=Component of the meiotic nuage, also named P granule, a germ-cell-specific organelle required to repress transposon activity during meiosis. {ECO:0000250 UniProtKB:H9IUR0}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for EXD1 gene
Compartment Confidence
nucleus 2
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for EXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0043186 P granule ISS --
GO:1990923 PET complex IEA,ISS --
genes like me logo Genes that share ontologies with EXD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for EXD1 Gene

Pathways & Interactions for EXD1 Gene

PathCards logo

SuperPathways for EXD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for EXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006139 nucleobase-containing compound metabolic process IEA --
GO:0031047 gene silencing by RNA ISS --
GO:0034587 piRNA metabolic process IEA,ISS --
GO:0051321 meiotic cell cycle IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with EXD1: view

No data available for Pathways by source and SIGNOR curated interactions for EXD1 Gene

Drugs & Compounds for EXD1 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for EXD1 Gene

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mRNA/cDNA for EXD1 Gene

3 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EXD1

Alternative Splicing Database (ASD) splice patterns (SP) for EXD1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9
SP1: - - -
SP2:
SP3: -
SP4: - -

Relevant External Links for EXD1 Gene

GeneLoc Exon Structure for
EXD1

Expression for EXD1 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EXD1 Gene

mRNA expression in normal human tissues for EXD1 Gene
mRNA expression by BioGPS for EXD1 GenemRNA expression by GTEx for EXD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

mRNA differential expression in normal tissues according to GTEx for EXD1 Gene

This gene is overexpressed in Testis (x47.3).

Protein differential expression in normal tissues from HIPED for EXD1 Gene

This gene is overexpressed in Cerebrospinal fluid (67.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for EXD1 Gene



Protein tissue co-expression partners for EXD1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EXD1

SOURCE GeneReport for Unigene cluster for EXD1 Gene:

Hs.307999

Evidence on tissue expression from TISSUES for EXD1 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with EXD1: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EXD1 Gene

Orthologs for EXD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for EXD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia EXD1 30 31
  • 99.59 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia EXD1 30 31
  • 86.76 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia EXD1 30 31
  • 86.56 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Exd1 30
  • 79.43 (n)
Mouse
(Mus musculus)
 Mammalia Exd1 30 17 31
  • 78.05 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia EXD1 31
  • 55 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia EXD1 31
  • 37 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves EXD1 30
  • 60.58 (n)
Lizard
(Anolis carolinensis)
 Reptilia EXD1 31
  • 49 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia exd1 30
  • 59.66 (n)
Zebrafish
(Danio rerio)
 Actinopterygii exd1 30 31
  • 49.67 (n)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta egl 31
  • 9 (a)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea egal-1 31
  • 11 (a)
 OneToOne
Species where no ortholog for EXD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for EXD1 Gene

ENSEMBL:
Gene Tree for EXD1 (if available)
TreeFam:
Gene Tree for EXD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EXD1: view image

Paralogs for EXD1 Gene

Paralogs for EXD1 Gene

genes like me logo Genes that share paralogs with EXD1: view

Variants for EXD1 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EXD1 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
rs522063 - p.Thr489Ala

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for EXD1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for EXD1 Gene

Variant ID Type Subtype PubMed ID
dgv4499n54 CNV loss 21841781
nsv1039906 CNV loss 25217958
nsv1129379 OTHER inversion 24896259
nsv1138357 CNV deletion 24896259
nsv476391 CNV novel sequence insertion 20440878
nsv569231 CNV loss 21841781
nsv958016 CNV deletion 24416366

Variation tolerance for EXD1 Gene

Residual Variation Intolerance Score: 37.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.53; 29.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EXD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EXD1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EXD1 Gene

Disorders for EXD1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for EXD1 Gene - From: COP

Disorder Aliases PubMed IDs
cerebral creatine deficiency syndrome 3
  • ccds3
cerebral creatine deficiency syndrome
  • deficiency, cerebral creatine, syndrome
- elite association - COSMIC cancer census association via MalaCards
Search EXD1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for EXD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with EXD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EXD1 Gene

Publications for EXD1 Gene

  1. Exonuclease Domain-Containing 1 Enhances MIWI2 piRNA Biogenesis via Its Interaction with TDRD12. (PMID: 30257204) Pandey RR … Pillai RS (Cell reports 2018) 2 3
  2. PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway. (PMID: 26669262) Yang Z … Pillai RS (Molecular cell 2016) 2 3
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. (PMID: 30021884) Fasci D … Heck AJR (Molecular & cellular proteomics : MCP 2018) 3

ExternalLinks

View latest publications for EXD1 gene in Mastermind

Products for EXD1 Gene

Sources for EXD1 Gene