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Aliases for EXD1 Gene

Aliases for EXD1 Gene

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

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. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and 3-5 exonuclease activity.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for EXD1 Gene

Genomics for EXD1 Gene

GeneHancer (GH) Regulatory Elements for EXD1 Gene

Promoters and enhancers for EXD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15I041230 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 -0.3 -342 2.2 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC MEF2D SSRP1 GLIS1 CHP1 EXD1 MGA INO80 ENSG00000259211 LOC105370795 BAHD1 DNAJC17 VPS39 ZFYVE19
GH15I041282 Promoter/Enhancer 1.6 Ensembl ENCODE 11.4 -53.7 -53723 3.7 HDGF PKNOX1 CLOCK SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B OIP5-AS1 NDUFAF1 INO80 MGA GANC BAHD1 ENSG00000259211 RPAP1 DNAJC17 LOC105370795
GH15I040905 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10.3 +324.2 324154 3.7 HDGF ATF1 FOXA2 ARID4B SIN3A ZNF2 YY1 ZNF121 GLIS2 ZNF143 ENSG00000251161 LOC105370943 CHAC1 RHOV CHP1 EXD1 DLL4 GC15M040883
GH15I041259 Enhancer 1.1 Ensembl ENCODE 12.1 -28.3 -28328 2 PKNOX1 FOXA2 MLX ARID4B DMAP1 BRCA1 ZNF48 YY1 RXRA SP5 GC15M041261 GC15M041262 GC15M041263 GC15M041265 GC15M041266 GC15M041267 GC15M041269 PIR32693 GC15M041264 CHP1
GH15I040909 Enhancer 1.2 Ensembl ENCODE dbSUPER 10.3 +320.3 320340 2.4 ELF3 ZNF48 RARA YY1 RCOR1 THAP11 RXRA CEBPB ZNF398 ELF1 CHAC1 SPINT1 CHP1 EXD1 ZFYVE19 ENSG00000251161 DLL4 GC15M040883
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around EXD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EXD1 gene promoter:

Genomic Locations for EXD1 Gene

Genomic Locations for EXD1 Gene
chr15:41,182,725-41,231,074
(GRCh38/hg38)
Size:
48,350 bases
Orientation:
Minus strand
chr15:41,474,923-41,522,941
(GRCh37/hg19)

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 StructureGene Density

RefSeq DNA sequence for EXD1 Gene

Proteins for EXD1 Gene

  • 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

Post-translational modifications for EXD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

Suggested Antigen Peptide Sequences for EXD1 Gene

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

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).

Gene Ontology (GO) - Molecular Function for EXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding ISS --
GO:0005515 protein binding IPI 25416956
GO:0008408 NOT 3-5 exonuclease activity 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:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

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 ISS,IEA --
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

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 ISS,IEA --
GO:0051321 meiotic cell cycle 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

No Compound Related Data Available

Transcripts for EXD1 Gene

mRNA/cDNA for EXD1 Gene

(10) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(4) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for EXD1 Gene

Exonuclease 3-5 domain containing 1:
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for
EXD1

Expression for EXD1 Gene

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

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, PaxDb, and MOPED for EXD1 Gene



Protein tissue co-expression partners for EXD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of EXD1 Gene:

EXD1

SOURCE GeneReport for Unigene cluster for EXD1 Gene:

Hs.307999

Evidence on tissue expression from TISSUES for EXD1 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with EXD1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , 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 33 34
  • 99.59 (n)
dog
(Canis familiaris)
Mammalia EXD1 33 34
  • 86.76 (n)
cow
(Bos Taurus)
Mammalia EXD1 33 34
  • 86.56 (n)
rat
(Rattus norvegicus)
Mammalia Exd1 33
  • 79.43 (n)
mouse
(Mus musculus)
Mammalia Exd1 33 16 34
  • 78.05 (n)
oppossum
(Monodelphis domestica)
Mammalia EXD1 34
  • 55 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EXD1 34
  • 37 (a)
OneToOne
chicken
(Gallus gallus)
Aves EXD1 33
  • 60.58 (n)
lizard
(Anolis carolinensis)
Reptilia EXD1 34
  • 49 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia exd1 33
  • 59.66 (n)
zebrafish
(Danio rerio)
Actinopterygii exd1 33 34
  • 49.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta egl 34
  • 9 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea egal-1 34
  • 11 (a)
OneToOne
Species where no ortholog for EXD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

Paralogs for EXD1 Gene

No data available for Paralogs for EXD1 Gene

Variants for EXD1 Gene

Sequence variations from dbSNP and Humsavar for EXD1 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000114497 -- 41,191,710(-) T/C intron_variant
rs1000163484 -- 41,190,442(-) C/T intron_variant
rs1000169695 -- 41,196,830(-) A/C intron_variant
rs1000176898 -- 41,217,862(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000398413 -- 41,185,568(-) C/T intron_variant

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 Assay Products

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

Disorders for EXD1 Gene

Additional Disease Information for EXD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for EXD1 Gene.

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

Publications for EXD1 Gene

  1. 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 44 58
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  3. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58
  4. Analysis of the DNA sequence and duplication history of human chromosome 15. (PMID: 16572171) Zody MC … Nusbaum C (Nature 2006) 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4 58

Products for EXD1 Gene

Sources for EXD1 Gene

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