Aliases for USP29 Gene

Aliases for USP29 Gene

  • Ubiquitin Specific Peptidase 29 2 3 5
  • Ubiquitin-Specific-Processing Protease 29 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 29 3 4
  • Deubiquitinating Enzyme 29 3 4
  • Ubiquitin Thioesterase 29 3 4
  • Ubiquitin-Specific Processing Protease 3
  • Ubiquitin Specific Protease 29 2
  • Ubiquitin Thiolesterase 29 3
  • HOM-TES-84/86 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 51
  • USP29 5

External Ids for USP29 Gene

Previous GeneCards Identifiers for USP29 Gene

  • GC19P058538
  • GC19P058094
  • GC19P062316
  • GC19P062331
  • GC19P057631
  • GC19P053944

Summaries for USP29 Gene

GeneCards Summary for USP29 Gene

USP29 (Ubiquitin Specific Peptidase 29) is a Protein Coding gene. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include cysteine-type endopeptidase activity and thiol-dependent ubiquitin-specific protease activity. An important paralog of this gene is USP37.

Additional gene information for USP29 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP29 Gene

Genomics for USP29 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for USP29 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
GH19J057119 Promoter 0.4 EPDnew 600.7 +0.8 828 0.1 GABPB1 HSALNG0127807 USP29 ZIM3
GH19J057319 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 9.3 +202.0 201963 3 ARHGAP35 SP1 HNRNPL CREB1 ATF7 PRDM10 ZNF629 TFE3 ZNF692 POLR2A ZNF543 ZNF805 ZNF548 ZNF264 ZNF256 ZNF304 ZNF274 ZNF587B ZNF417 ZNF550
GH19J056972 Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.1 -143.5 -143513 8 HNRNPL CREB1 GATAD2A TFE3 SOX13 NFKBIZ RCOR2 RFX1 RBFOX2 POLR2A ZNF264 ZNF548 ZNF805 ZNF587B ZNF417 ZNF550 ZNF587 ZNF586 USP29 ZNF134
GH19J057095 Enhancer 1 Ensembl ENCODE CraniofacialAtlas 12 -22.2 -22231 2.5 GATAD2A ZNF7 RBFOX2 RXRB SOX13 CEBPB ZKSCAN8 TGIF2 FOXA2 KAT7 USP29 ZIM3 PEG3 ZIM2 AURKC ZNF805 ZNF418 ZNF814 ZNF417 ENSG00000176593
GH19J056983 Enhancer 1 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 9.1 -135.5 -135525 0.8 RFX1 RFX3 RAD21 ZMYM3 ZNF146 ZNF280D AURKC USP29 ZNF471 ZNF835 ZNF772 RF00017-3089 RF00005-077 ZIM2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP29 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP29

Top Transcription factor binding sites by QIAGEN in the USP29 gene promoter:
  • FOXD3
  • HNF-1
  • HNF-1A
  • p53
  • SRF
  • SRF (504 AA)

Genomic Locations for USP29 Gene

Genomic Locations for USP29 Gene
chr19:57,119,138-57,131,983
(GRCh38/hg38)
Size:
12,846 bases
Orientation:
Plus strand
chr19:57,630,506-57,643,294
(GRCh37/hg19)
Size:
12,789 bases
Orientation:
Plus strand

Genomic View for USP29 Gene

Genes around USP29 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP29 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP29 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP29 Gene

Proteins for USP29 Gene

  • Protein details for USP29 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBJ7-UBP29_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 29
    Protein Accession:
    Q9HBJ7

    Protein attributes for USP29 Gene

    Size:
    922 amino acids
    Molecular mass:
    104156 Da
    Quaternary structure:
    No Data Available

neXtProt entry for USP29 Gene

Selected DME Specific Peptides for USP29 Gene

Q9HBJ7:
  • NLGNTCYMN
  • GHYISDV
  • LIIHLKR

Post-translational modifications for USP29 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for USP29 Gene

Domains & Families for USP29 Gene

Gene Families for USP29 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for USP29 Gene

InterPro:
Blocks:
  • Ubiquitin thiolesterase, family 2
ProtoNet:

Suggested Antigen Peptide Sequences for USP29 Gene

GenScript: Design optimal peptide antigens:
  • Ubiquitin carboxyl-terminal hydrolase (A1L447_HUMAN)
  • Ubiquitin-specific-processing protease 29 (UBP29_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9HBJ7

UniProtKB/Swiss-Prot:

UBP29_HUMAN :
  • Belongs to the peptidase C19 family.
Family:
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP29: view

Function for USP29 Gene

Molecular function for USP29 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).; EC=3.4.19.12;.

Enzyme Numbers (IUBMB) for USP29 Gene

Phenotypes From GWAS Catalog for USP29 Gene

Gene Ontology (GO) - Molecular Function for USP29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IBA 21873635
GO:0004843 thiol-dependent ubiquitin-specific protease activity IBA 21873635
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with USP29: view
genes like me logo Genes that share phenotypes with USP29: view

Animal Models for USP29 Gene

MGI Knock Outs for USP29:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP29

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for USP29 Gene

Localization for USP29 Gene

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 USP29 gene
Compartment Confidence
nucleus 4
extracellular 2
cytosol 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
lysosome 1

Gene Ontology (GO) - Cellular Components for USP29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005634 nucleus IBA 21873635
GO:0005829 cytosol IBA 21873635
genes like me logo Genes that share ontologies with USP29: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for USP29 Gene

Pathways & Interactions for USP29 Gene

PathCards logo

SuperPathways for USP29 Gene

SuperPathway Contained pathways
1 Ubiquitin-Proteasome Dependent Proteolysis
-
genes like me logo Genes that share pathways with USP29: view

Pathways by source for USP29 Gene

1 Qiagen pathway for USP29 Gene
  • Ubiquitin-Proteasome Dependent Proteolysis

Gene Ontology (GO) - Biological Process for USP29 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000082 G1/S transition of mitotic cell cycle IBA 21873635
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0016579 protein deubiquitination IBA 21873635
genes like me logo Genes that share ontologies with USP29: view

No data available for SIGNOR curated interactions for USP29 Gene

Drugs & Compounds for USP29 Gene

(1) Drugs for USP29 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
genes like me logo Genes that share compounds with USP29: view

Transcripts for USP29 Gene

mRNA/cDNA for USP29 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP29

Alternative Splicing Database (ASD) splice patterns (SP) for USP29 Gene

No ASD Table

Relevant External Links for USP29 Gene

GeneLoc Exon Structure for
USP29

Expression for USP29 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for USP29 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for USP29 Gene

This gene is overexpressed in Testis (x49.0).

Protein differential expression in normal tissues from HIPED for USP29 Gene

This gene is overexpressed in Cerebrospinal fluid (32.0), Heart (16.3), Cervix (11.0), and Esophagus (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for USP29 Gene



Protein tissue co-expression partners for USP29 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USP29

SOURCE GeneReport for Unigene cluster for USP29 Gene:

Hs.515632
genes like me logo Genes that share expression patterns with USP29: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP29 Gene

Orthologs for USP29 Gene

This gene was present in the common ancestor of chordates.

Orthologs for USP29 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia USP29 30
  • 98.92 (n)
Mouse
(Mus musculus)
Mammalia Usp29 30 17 31
  • 64.65 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Usp29 30
  • 63.77 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 18 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii USP29 31
  • 31 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.2829 31
  • 25 (a)
OneToMany
Species where no ortholog for USP29 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)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Cow (Bos Taurus)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • 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 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for USP29 Gene

ENSEMBL:
Gene Tree for USP29 (if available)
TreeFam:
Gene Tree for USP29 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for USP29: view image

Paralogs for USP29 Gene

(2) SIMAP similar genes for USP29 Gene using alignment to 4 proteins:

  • UBP29_HUMAN
  • A1L447_HUMAN
  • M0QZL0_HUMAN
  • M0R2Y1_HUMAN
genes like me logo Genes that share paralogs with USP29: view

Variants for USP29 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP29 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
726289 Likely Benign: not provided 57,131,371(+) G/A MISSENSE_VARIANT
784552 Benign: not provided 57,129,296(+) G/A SYNONYMOUS_VARIANT
rs1027392 - p.Asn368Ser
rs3795003 - p.Glu586Lys

Additional dbSNP identifiers (rs#s) for USP29 Gene

Structural Variations from Database of Genomic Variants (DGV) for USP29 Gene

Variant ID Type Subtype PubMed ID
esv3644892 CNV gain 21293372
esv3893256 CNV loss 25118596
nsv1062392 CNV gain 25217958

Variation tolerance for USP29 Gene

Residual Variation Intolerance Score: 62.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.46; 64.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP29 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP29

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP29 Gene

Disorders for USP29 Gene

Additional Disease Information for USP29

No disorders were found for USP29 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP29 Gene

Publications for USP29 Gene

  1. Discovery of a novel, paternally expressed ubiquitin-specific processing protease gene through comparative analysis of an imprinted region of mouse chromosome 7 and human chromosome 19q13.4. (PMID: 10958632) Kim J … Stubbs L (Genome research 2000) 3 4 23
  2. Human and mouse proteases: a comparative genomic approach. (PMID: 12838346) Puente XS … López-Otín C (Nature reviews. Genetics 2003) 2 3
  3. WDR76 is a RAS binding protein that functions as a tumor suppressor via RAS degradation. (PMID: 30655611) Jeong WJ … Choi KY (Nature communications 2019) 3
  4. Induction of OTUD4 by viral infection promotes antiviral responses through deubiquitinating and stabilizing MAVS. (PMID: 30410068) Liuyu T … Zhong B (Cell research 2019) 3
  5. Ubiquitin-specific peptidase 2a (USP2a) deubiquitinates and stabilizes β-catenin. (PMID: 30323974) Kim J … Ma L (American journal of cancer research 2018) 3

Products for USP29 Gene

Sources for USP29 Gene