Human Gene EXO5 (ENST00000296380.9) from GENCODE V44
  Description: Homo sapiens exonuclease 5 (EXO5), transcript variant 2, mRNA. (from RefSeq NM_022774)
RefSeq Summary (NM_022774): The protein encoded by this gene is a single-stranded DNA (ssDNA)-specific exonuclease that can slide along the DNA before cutting it. However, human replication protein A binds ssDNA and restricts sliding of the encoded protein, providing a 5'-directionality to the enzyme. This protein localizes to nuclear repair loci after DNA damage. [provided by RefSeq, Nov 2016].
Gencode Transcript: ENST00000296380.9
Gencode Gene: ENSG00000164002.12
Transcript (Including UTRs)
   Position: hg38 chr1:40,508,761-40,516,036 Size: 7,276 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chr1:40,514,545-40,515,666 Size: 1,122 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:40,508,761-40,516,036)mRNA (may differ from genome)Protein (373 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDMGIneXtProtOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: EXO5_HUMAN
DESCRIPTION: RecName: Full=Probable exonuclease V; Short=Exo V; EC=3.1.11.-; AltName: Full=Defects in morphology protein 1 homolog;
FUNCTION: Probable single strand DNA specific 5' exonuclease mitochondrial DNA replication and recombination (By similarity).
COFACTOR: Magnesium (By similarity).
SIMILARITY: Belongs to the EXO5 family.
SEQUENCE CAUTION: Sequence=CAI16298.1; Type=Erroneous gene model prediction; Sequence=CAI16299.1; Type=Erroneous gene model prediction; Sequence=CAI16300.1; Type=Erroneous gene model prediction; Sequence=CAI16301.1; Type=Erroneous gene model prediction; Sequence=CAI16302.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.97 RPKM in Spleen
Total median expression: 99.89 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -76.80205-0.375 Picture PostScript Text
3' UTR -92.20370-0.249 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019190 - Defects_morphology_1-like_mit

Pfam Domains:
PF09810 - Exonuclease V - a 5' deoxyribonuclease

ModBase Predicted Comparative 3D Structure on Q9H790
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0004518 nuclease activity
GO:0004527 exonuclease activity
GO:0008310 single-stranded DNA 3'-5' exodeoxyribonuclease activity
GO:0016787 hydrolase activity
GO:0042803 protein homodimerization activity
GO:0045145 single-stranded DNA 5'-3' exodeoxyribonuclease activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process:
GO:0006281 DNA repair
GO:0006974 cellular response to DNA damage stimulus
GO:0036297 interstrand cross-link repair
GO:0090305 nucleic acid phosphodiester bond hydrolysis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK021507 - Homo sapiens cDNA FLJ11445 fis, clone HEMBA1001375.
AK094092 - Homo sapiens cDNA FLJ36773 fis, clone ADRGL2000142.
AK024797 - Homo sapiens cDNA: FLJ21144 fis, clone CAS07955.
BC021969 - Homo sapiens defects in morphology 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:14947 IMAGE:3952573), complete cds.
AK023245 - Homo sapiens cDNA FLJ13183 fis, clone NT2RP3004145.
JD336584 - Sequence 317608 from Patent EP1572962.
JD462025 - Sequence 443049 from Patent EP1572962.
JD177049 - Sequence 158073 from Patent EP1572962.
JD407030 - Sequence 388054 from Patent EP1572962.
JD462582 - Sequence 443606 from Patent EP1572962.
LF206601 - JP 2014500723-A/14104: Polycomb-Associated Non-Coding RNAs.
MA442178 - JP 2018138019-A/14104: Polycomb-Associated Non-Coding RNAs.
JD519290 - Sequence 500314 from Patent EP1572962.
HQ448143 - Synthetic construct Homo sapiens clone IMAGE:100071528; CCSB006634_02 chromosome 1 open reading frame 176 (C1orf176) gene, encodes complete protein.
KJ899475 - Synthetic construct Homo sapiens clone ccsbBroadEn_08869 DEM1 gene, encodes complete protein.
JD474305 - Sequence 455329 from Patent EP1572962.
LF356439 - JP 2014500723-A/163942: Polycomb-Associated Non-Coding RNAs.
MA592016 - JP 2018138019-A/163942: Polycomb-Associated Non-Coding RNAs.
LF356438 - JP 2014500723-A/163941: Polycomb-Associated Non-Coding RNAs.
MA592015 - JP 2018138019-A/163941: Polycomb-Associated Non-Coding RNAs.
LF356437 - JP 2014500723-A/163940: Polycomb-Associated Non-Coding RNAs.
MA592014 - JP 2018138019-A/163940: Polycomb-Associated Non-Coding RNAs.
AF086542 - Homo sapiens full length insert cDNA clone ZE09H03.
JD172117 - Sequence 153141 from Patent EP1572962.
JD093805 - Sequence 74829 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C1orf176, D3DPV4, DEM1, ENST00000296380.1, ENST00000296380.2, ENST00000296380.3, ENST00000296380.4, ENST00000296380.5, ENST00000296380.6, ENST00000296380.7, ENST00000296380.8, EXO5_HUMAN, NM_022774, Q5SWM7, Q5SWM8, Q5SWM9, Q5SWN0, Q5SWN1, Q8WTW9, Q9H790, uc001cfp.1, uc001cfp.2, uc001cfp.3, uc001cfp.4, uc001cfp.5
UCSC ID: ENST00000296380.9
RefSeq Accession: NM_022774
Protein: Q9H790 (aka EXO5_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.