Free for academic non-profit institutions. Other users need a Commercial license

Aliases for EXD3 Gene

Aliases for EXD3 Gene

  • Exonuclease 3'-5' Domain Containing 3 2 3
  • Exonuclease 3-5 Domain-Containing Protein 3 3 4
  • Exonuclease 3-5 Domain Containing 3 5
  • Probable Exonuclease Mut-7 Homolog 3
  • Testicular Tissue Protein Li 125 3
  • Exonuclease Mut-7 Homolog 3
  • EC 3.1.-.- 4
  • Mut-7 3

External Ids for EXD3 Gene

Previous GeneCards Identifiers for EXD3 Gene

  • GC09M139322
  • GC09M140201
  • GC09M109660

Summaries for EXD3 Gene

GeneCards Summary for EXD3 Gene

EXD3 (Exonuclease 3'-5' Domain Containing 3) 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 EXD3 Gene

  • Possesses 3-5 exoribonuclease activity. Required for 3-end trimming of AGO1-bound miRNAs (By similarity).

Additional gene information for EXD3 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 EXD3 Gene

Genomics for EXD3 Gene

GeneHancer (GH) Regulatory Elements for EXD3 Gene

Promoters and enhancers for EXD3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J137422 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 656.5 -0.4 -425 3.3 HDGF PKNOX1 ARNT ARID4B SIN3A ZNF2 ZBTB7B YY1 ZNF766 CBX5 NOXA1 EXD3 NPDC1 AJM1 CACNA1B ENTPD8
GH09J136725 Promoter/Enhancer 1.6 Ensembl ENCODE 38.7 +695.8 695820 4.1 CLOCK MLX DMAP1 IRF4 YY1 ZNF213 ZNF143 SP3 NFYC SSRP1 SNHG7 GC09M136756 GC09M136758 GC09M136760 SNORA17A SNORA17B ENSG00000281808 DPH7 EHMT1 ANAPC2
GH09J137292 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 28.2 +122.9 122867 15.3 PKNOX1 FOXA2 ARNT ZFP64 SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF766 NRARP GC09M137300 EHMT1 DPH7 INPP5E ENTR1 ANAPC2 EXD3 MAN1B1 NDOR1
GH09J136839 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 24.1 +581.5 581514 4.5 HDGF PKNOX1 ARID4B SIN3A ZNF2 POLR2B ZNF213 E2F8 ZNF207 ZNF143 PHPT1 ANAPC2 DPH7 INPP5E EHMT1 EXD3 MAN1B1 ARRDC1-AS1 NDOR1 TRAF2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EXD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EXD3 gene promoter:
  • c-Jun
  • ATF-2
  • c-Fos
  • AP-1
  • c-Myb
  • Hand1
  • E47
  • GATA-3
  • Arnt

Genomic Locations for EXD3 Gene

Genomic Locations for EXD3 Gene
116,375 bases
Minus strand
116,367 bases
Minus strand

Genomic View for EXD3 Gene

Genes around EXD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EXD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EXD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EXD3 Gene

Proteins for EXD3 Gene

  • Protein details for EXD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Exonuclease mut-7 homolog
    Protein Accession:
    Secondary Accessions:
    • A0A140VJP9
    • B8A4U7
    • C9JIQ9
    • E9PN82
    • Q2TAK4
    • Q6P1M1
    • Q8IXT8
    • Q8N3X4
    • Q8NHD1
    • Q96NP1
    • Q9NX53

    Protein attributes for EXD3 Gene

    876 amino acids
    Molecular mass:
    96598 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available
    • Sequence=AAH39252.2; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=AAH65002.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=BAA91167.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=BAC04356.1; Type=Erroneous termination; Positions=759; Note=Translated as Ser.; Evidence={ECO:0000305}; Sequence=EAW88381.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for EXD3 Gene


neXtProt entry for EXD3 Gene

Post-translational modifications for EXD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for EXD3 Gene

Domains & Families for EXD3 Gene

Gene Families for EXD3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for EXD3 Gene

Suggested Antigen Peptide Sequences for EXD3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the mut-7 family.
  • Belongs to the mut-7 family.
genes like me logo Genes that share domains with EXD3: view

Function for EXD3 Gene

Molecular function for EXD3 Gene

UniProtKB/Swiss-Prot Function:
Possesses 3-5 exoribonuclease activity. Required for 3-end trimming of AGO1-bound miRNAs (By similarity).

Enzyme Numbers (IUBMB) for EXD3 Gene

Phenotypes From GWAS Catalog for EXD3 Gene

Gene Ontology (GO) - Molecular Function for EXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0004518 nuclease activity IEA --
GO:0004527 exonuclease activity IEA --
GO:0008408 3-5 exonuclease activity IBA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with EXD3: view
genes like me logo Genes that share phenotypes with EXD3: view

miRNA for EXD3 Gene

miRTarBase miRNAs that target EXD3

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EXD3 Gene

Localization for EXD3 Gene

Subcellular locations from

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 EXD3 gene
Compartment Confidence
nucleus 5
cytoskeleton 2
cytosol 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Focal adhesion sites (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with EXD3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for EXD3 Gene

Pathways & Interactions for EXD3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for EXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006139 nucleobase-containing compound metabolic process IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with EXD3: view

No data available for Pathways by source and SIGNOR curated interactions for EXD3 Gene

Drugs & Compounds for EXD3 Gene

No Compound Related Data Available

Transcripts for EXD3 Gene

Unigene Clusters for EXD3 Gene

Exonuclease 3-5 domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EXD3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23
SP2: - - -
SP3: -

Relevant External Links for EXD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for EXD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EXD3 Gene

Protein differential expression in normal tissues from HIPED for EXD3 Gene

This gene is overexpressed in Bone marrow stromal cell (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for EXD3 Gene

Protein tissue co-expression partners for EXD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of EXD3 Gene:


SOURCE GeneReport for Unigene cluster for EXD3 Gene:


Evidence on tissue expression from TISSUES for EXD3 Gene

  • Nervous system(4.3)
  • Lung(4.2)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with EXD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EXD3 Gene

Orthologs for EXD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for EXD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia EXD3 34 33
  • 77.1 (n)
(Bos Taurus)
Mammalia EXD3 34
  • 63 (a)
(Ornithorhynchus anatinus)
Mammalia EXD3 34
  • 46 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 45 (a)
-- 34
  • 35 (a)
(Gallus gallus)
Aves EXD3 34 33
  • 59.29 (n)
(Anolis carolinensis)
Reptilia EXD3 34
  • 43 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia exd3 33
  • 56.16 (n)
(Danio rerio)
Actinopterygii exd3 34 33
  • 53.27 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nbr 34 33
  • 40.78 (n)
(Caenorhabditis elegans)
Secernentea mut-7 34 33
  • 38.16 (n)
Y57A10A.13 34
  • 16 (a)
ZK1098.3 34
  • 15 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 38 (a)
Species where no ortholog for EXD3 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 EXD3 Gene

Gene Tree for EXD3 (if available)
Gene Tree for EXD3 (if available)
Evolutionary constrained regions (ECRs) for EXD3: view image

Paralogs for EXD3 Gene

No data available for Paralogs for EXD3 Gene

Variants for EXD3 Gene

Sequence variations from dbSNP and Humsavar for EXD3 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs35097575 benign, not specified 137,349,428(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000050037 -- 137,368,812(-) G/C genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000055878 -- 137,399,732(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000059934 -- 137,334,238(-) G/T genic_downstream_transcript_variant, intron_variant
rs1000080042 -- 137,400,904(-) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for EXD3 Gene

Variant ID Type Subtype PubMed ID
dgv1285e201 CNV deletion 23290073
dgv1286e201 CNV deletion 23290073
dgv13009n54 CNV loss 21841781
dgv13011n54 CNV loss 21841781
dgv2190e212 CNV gain 25503493
dgv25e24 CNV loss 17666407
dgv4176n106 CNV deletion 24896259
dgv4177n106 CNV deletion 24896259
esv1004393 CNV gain 20482838
esv1009301 CNV deletion 20482838
esv1107223 CNV insertion 17803354
esv1109653 CNV deletion 17803354
esv1174014 CNV insertion 17803354
esv1177905 CNV deletion 17803354
esv1197738 CNV insertion 17803354
esv1630433 CNV deletion 17803354
esv22353 CNV gain 19812545
esv2422220 CNV deletion 17116639
esv24763 CNV gain+loss 19812545
esv2630210 CNV deletion 19546169
esv2657904 CNV deletion 23128226
esv2664592 CNV deletion 23128226
esv2665135 CNV deletion 23128226
esv2672695 CNV deletion 23128226
esv27346 CNV gain+loss 19812545
esv2739421 CNV deletion 23290073
esv2739422 CNV deletion 23290073
esv2739423 CNV deletion 23290073
esv2739424 CNV deletion 23290073
esv2739426 CNV deletion 23290073
esv2739429 CNV deletion 23290073
esv2739431 CNV deletion 23290073
esv2739433 CNV deletion 23290073
esv2739434 CNV deletion 23290073
esv2739435 CNV deletion 23290073
esv2739436 CNV deletion 23290073
esv2739437 CNV deletion 23290073
esv2739438 CNV deletion 23290073
esv2739440 CNV deletion 23290073
esv2739441 CNV deletion 23290073
esv2739442 CNV deletion 23290073
esv2739443 CNV deletion 23290073
esv2739444 CNV deletion 23290073
esv2739445 CNV deletion 23290073
esv2742964 CNV deletion 23290073
esv2742965 CNV deletion 23290073
esv2759721 CNV loss 17122850
esv33008 CNV loss 17666407
esv33368 CNV gain 17666407
esv3352688 CNV insertion 20981092
esv3411436 CNV duplication 20981092
esv3545661 CNV deletion 23714750
esv3545662 CNV deletion 23714750
esv3545663 CNV deletion 23714750
esv3545664 CNV deletion 23714750
esv3573431 CNV loss 25503493
esv3622026 OTHER inversion 21293372
esv3622028 CNV loss 21293372
esv3622029 CNV loss 21293372
esv3622030 CNV loss 21293372
esv3622031 CNV loss 21293372
esv8361 CNV loss 19470904
esv997740 CNV insertion 20482838
nsv1037407 CNV gain 25217958
nsv1043075 CNV gain+loss 25217958
nsv1049808 CNV gain 25217958
nsv1050678 CNV gain 25217958
nsv1050826 CNV gain 25217958
nsv1075290 CNV deletion 25765185
nsv1075698 CNV deletion 25765185
nsv1075699 CNV deletion 25765185
nsv1076227 CNV deletion 25765185
nsv1076228 CNV deletion 25765185
nsv1077203 CNV deletion 25765185
nsv1079009 CNV insertion 25765185
nsv1111380 CNV tandem duplication 24896259
nsv1119619 CNV deletion 24896259
nsv1125982 CNV tandem duplication 24896259
nsv1136025 CNV deletion 24896259
nsv1141041 CNV deletion 24896259
nsv1142562 CNV tandem duplication 24896259
nsv1145962 CNV insertion 26484159
nsv1150357 CNV deletion 26484159
nsv1161918 CNV duplication 26073780
nsv416290 CNV deletion 16902084
nsv416338 CNV deletion 16902084
nsv416493 CNV deletion 16902084
nsv475364 CNV novel sequence insertion 20440878
nsv49 CNV insertion 15895083
nsv512129 CNV loss 21212237
nsv524322 CNV loss 19592680
nsv6770 CNV insertion 18451855
nsv6771 CNV insertion 18451855
nsv8583 CNV gain 18304495
nsv8584 CNV gain 18304495
nsv8585 CNV loss 18304495
nsv951207 CNV deletion 24416366
nsv951208 CNV deletion 24416366

Variation tolerance for EXD3 Gene

Residual Variation Intolerance Score: 99.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.48; 82.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EXD3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EXD3 Gene

Disorders for EXD3 Gene

Additional Disease Information for EXD3

No disorders were found for EXD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for EXD3 Gene

Publications for EXD3 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58
  3. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PMID: 21145461) Bennett EJ … Harper JW (Cell 2010) 3 58
  4. An empirical framework for binary interactome mapping. (PMID: 19060904) Venkatesan K … Vidal M (Nature methods 2009) 3 58
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K … Sugano S (Genome research 2006) 3 58

Products for EXD3 Gene

Sources for EXD3 Gene

Loading form....