Aliases for USP49 Gene

Aliases for USP49 Gene

  • Ubiquitin Specific Peptidase 49 2 3 5
  • Ubiquitin-Specific-Processing Protease 49 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 49 3 4
  • Ubiquitin Specific Protease 49 2 3
  • Deubiquitinating Enzyme 49 3 4
  • Ubiquitin Thioesterase 49 3 4
  • Ubiquitin Thiolesterase 49 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 50
  • MGC20741 2
  • USP49 5

External Ids for USP49 Gene

Previous GeneCards Identifiers for USP49 Gene

  • GC06M041874
  • GC06M041919
  • GC06M041981
  • GC06M041876
  • GC06M041762
  • GC06M041484
  • GC06M041787
  • GC06M041795
  • GC06M041922
  • GC06M042304
  • GC06M043578

Summaries for USP49 Gene

GeneCards Summary for USP49 Gene

USP49 (Ubiquitin Specific Peptidase 49) is a Protein Coding gene. Among its related pathways are Deubiquitination and Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include histone binding and cysteine-type peptidase activity. An important paralog of this gene is USP44.

UniProtKB/Swiss-Prot Summary for USP49 Gene

  • Specifically deubiquitinates histone H2B at 'Lys-120' (H2BK120Ub). H2BK120Ub is a specific tag for epigenetic transcriptional activation and acts as a regulator of mRNA splicing. Deubiquitination is required for efficient cotranscriptional splicing of a large set of exons.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP49 Gene

Genomics for USP49 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for USP49 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 USP49 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP49

Top Transcription factor binding sites by QIAGEN in the USP49 gene promoter:
  • FAC1
  • GCNF
  • GCNF-1
  • HNF-1
  • HNF-1A
  • MyoD
  • NF-kappaB
  • NF-kappaB1
  • Pax-4a
  • Sp1

Genomic Locations for USP49 Gene

Latest Assembly
chr6:41,789,896-41,895,375
(GRCh38/hg38)
Size:
105,480 bases
Orientation:
Minus strand

Previous Assembly
chr6:41,757,634-41,863,113
(GRCh37/hg19 by Entrez Gene)
Size:
105,480 bases
Orientation:
Minus strand

chr6:41,757,634-41,863,099
(GRCh37/hg19 by Ensembl)
Size:
105,466 bases
Orientation:
Minus strand

Genomic View for USP49 Gene

Genes around USP49 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP49 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP49 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP49 Gene

Proteins for USP49 Gene

  • Protein details for USP49 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q70CQ1-UBP49_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 49
    Protein Accession:
    Q70CQ1
    Secondary Accessions:
    • Q5T3D9
    • Q5T3E0
    • Q96CK4

    Protein attributes for USP49 Gene

    Size:
    688 amino acids
    Molecular mass:
    79198 Da
    Quaternary structure:
    • Component of a complex with RUVBL1 and PSMC5.

    Alternative splice isoforms for USP49 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP49 Gene

Selected DME Specific Peptides for USP49 Gene

Q70CQ1:
  • NLGNTCYMN
  • QQDAQEFL

Post-translational modifications for USP49 Gene

  • Ubiquitination at Lys522
  • Modification sites at PhosphoSitePlus

Other Protein References for USP49 Gene

Domains & Families for USP49 Gene

Gene Families for USP49 Gene

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

Protein Domains for USP49 Gene

InterPro:
Blocks:
  • Ubiquitin thiolesterase, family 2
  • Zn-finger in ubiquitin thiolesterase

Suggested Antigen Peptide Sequences for USP49 Gene

GenScript: Design optimal peptide antigens:
  • Ubiquitin-specific-processing protease 49 (UBP49_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q70CQ1

UniProtKB/Swiss-Prot:

UBP49_HUMAN :
  • Belongs to the peptidase C19 family.
Family:
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP49: view

Function for USP49 Gene

Molecular function for USP49 Gene

UniProtKB/Swiss-Prot Function:
Specifically deubiquitinates histone H2B at 'Lys-120' (H2BK120Ub). H2BK120Ub is a specific tag for epigenetic transcriptional activation and acts as a regulator of mRNA splicing. Deubiquitination is required for efficient cotranscriptional splicing of a large set of exons.
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; Evidence={ECO:0000269|PubMed:14715245, ECO:0000269|PubMed:23824326};.

Enzyme Numbers (IUBMB) for USP49 Gene

Phenotypes From GWAS Catalog for USP49 Gene

Gene Ontology (GO) - Molecular Function for USP49 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IMP 23824326
GO:0004843 thiol-dependent ubiquitin-specific protease activity IDA 14715245
GO:0005515 protein binding IPI 19615732
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
genes like me logo Genes that share ontologies with USP49: view
genes like me logo Genes that share phenotypes with USP49: view

Animal Models for research

  • Taconic Biosciences Mouse Models for USP49

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for USP49

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP49 Gene

Localization for USP49 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP49 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 USP49 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1
mitochondrion 1
lysosome 1

Gene Ontology (GO) - Cellular Components for USP49 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with USP49: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for USP49 Gene

Pathways & Interactions for USP49 Gene

PathCards logo

SuperPathways for USP49 Gene

genes like me logo Genes that share pathways with USP49: view

Pathways by source for USP49 Gene

1 Qiagen pathway for USP49 Gene
  • Ubiquitin-Proteasome Dependent Proteolysis

Gene Ontology (GO) - Biological Process for USP49 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome IMP 23824326
GO:0006325 chromatin organization IEA --
GO:0006397 mRNA processing IEA --
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
genes like me logo Genes that share ontologies with USP49: view

No data available for SIGNOR curated interactions for USP49 Gene

Drugs & Compounds for USP49 Gene

No Compound Related Data Available

Transcripts for USP49 Gene

mRNA/cDNA for USP49 Gene

3 REFSEQ mRNAs :
7 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 USP49

Alternative Splicing Database (ASD) splice patterns (SP) for USP49 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP1:
SP2: -

Relevant External Links for USP49 Gene

GeneLoc Exon Structure for
USP49

Expression for USP49 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for USP49 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for USP49 Gene

This gene is overexpressed in Lung (64.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for USP49 Gene



Protein tissue co-expression partners for USP49 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USP49

SOURCE GeneReport for Unigene cluster for USP49 Gene:

Hs.665742

Evidence on tissue expression from TISSUES for USP49 Gene

  • Eye(4)
genes like me logo Genes that share expression patterns with USP49: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP49 Gene

Orthologs for USP49 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for USP49 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia USP49 29 30
  • 99.76 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia USP49 29 30
  • 90.88 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Usp49 29 16 30
  • 90.16 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia USP49 29 30
  • 89.82 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Usp49 29
  • 88.94 (n)
Oppossum
(Monodelphis domestica)
Mammalia USP49 30
  • 76 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia USP49 30
  • 73 (a)
OneToOne
Chicken
(Gallus gallus)
Aves USP49 29 30
  • 76.57 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia USP49 30
  • 73 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia usp49 29
  • 67.87 (n)
Zebrafish
(Danio rerio)
Actinopterygii usp49 29 30
  • 66.45 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea E01B7.1 30
  • 12 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP5 30
  • 15 (a)
ManyToMany
DOA4 30
  • 13 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 40 (a)
OneToMany
Species where no ortholog for USP49 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)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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 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 USP49 Gene

ENSEMBL:
Gene Tree for USP49 (if available)
TreeFam:
Gene Tree for USP49 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for USP49: view image
Alliance of Genome Resources:
Additional Orthologs for USP49

Paralogs for USP49 Gene

(1) SIMAP similar genes for USP49 Gene using alignment to 5 proteins:

  • UBP49_HUMAN
  • A6PVU2_HUMAN
  • A6PVU3_HUMAN
  • H7BZI7_HUMAN
  • Q5T3E1_HUMAN
genes like me logo Genes that share paralogs with USP49: view

Variants for USP49 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP49 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs111948785 Benign: not provided 41,806,602(-) G/T
NM_001286554.1(USP49):c.382C>A (p.Leu128Met)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for USP49 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 USP49 Gene

Variant ID Type Subtype PubMed ID
nsv1114800 CNV deletion 24896259

Variation tolerance for USP49 Gene

Residual Variation Intolerance Score: 14.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.02; 50.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP49 Gene

Human Gene Mutation Database (HGMD)
USP49
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP49
Leiden Open Variation Database (LOVD)
USP49

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP49 Gene

Disorders for USP49 Gene

Additional Disease Information for USP49

No disorders were found for USP49 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP49 Gene

Publications for USP49 Gene

  1. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. (PMID: 14715245) Quesada V … López-Otín C (Biochemical and biophysical research communications 2004) 2 3 4
  2. USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing. (PMID: 23824326) Zhang Z … Wang H (Genes & development 2013) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. Gene expression and cell identity controlled by anaphase-promoting complex. (PMID: 32076268) Oh E … Rape M (Nature 2020) 3
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for USP49 Gene

Sources for USP49 Gene