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Aliases for USP49 Gene

Aliases for USP49 Gene

  • Ubiquitin Specific Peptidase 49 2 3 5
  • Ubiquitin-Specific-Processing Protease 49 4
  • Ubiquitin Specific Protease 49 2
  • Deubiquitinating Enzyme 49 4
  • Ubiquitin Thioesterase 49 4
  • EC 3.4.19.12 4
  • EC 3.1.2.15 61

External Ids for USP49 Gene

Previous GeneCards Identifiers for USP49 Gene

  • GC06M041874
  • GC06M041919
  • GC06M041981
  • GC06M041876
  • GC06M041762
  • GC06M041484
  • GC06M041787

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 Metabolism of proteins. 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 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 , fRNAdb sequence ontologies and piRNA Summary for USP49 Gene

Genomics for USP49 Gene

Regulatory Elements for USP49 Gene

Enhancers for USP49 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G041934 1.8 FANTOM5 ENCODE dbSUPER 22.8 -43.3 -43345 8.9 CREB3L1 AGO1 ZFP64 DMAP1 YY1 ZNF143 SP3 NFYC TBX21 PPARGC1A ENSG00000124593 USP49 FRS3 MED20 ENSG00000207371 BYSL RNU6-761P PRICKLE4 TOMM6 ENSG00000206977
GH06G042312 1.9 FANTOM5 Ensembl ENCODE dbSUPER 15.2 -420.0 -419995 6.5 ATF1 SIN3A ZNF121 GLIS2 GATA2 FOS CAVIN1 JUNB MEF2D CREB3 USP49 CUL9 GUCA1B BICRAL BYSL TRERF1 LOC105375061 GC06M042412
GH06G042291 1.7 FANTOM5 Ensembl ENCODE dbSUPER 15.2 -398.7 -398676 5.3 SIN3A ZNF48 FOS KDM4B JUNB REST KAT8 GLIS1 STAT3 SETDB1 USP49 CUL9 BICRAL ENSG00000206977 TAF8 LOC105375061 GC06M042412
GH06G041965 1.5 Ensembl ENCODE dbSUPER 15.7 -71.3 -71283 3.0 HDGF ATF1 PKNOX1 ARNT AGO1 ZFP64 SIN3A ZNF766 GATA2 ELK1 USP49 MED20 RNU6-761P ENSG00000207371 BYSL ENSG00000206977 ENSG00000124593 FRS3 LOC105375060
GH06G042020 2 FANTOM5 Ensembl ENCODE dbSUPER 11.5 -130.0 -130036 8.8 HDGF FOXA2 PKNOX1 CREB3L1 ARNT WRNIP1 SIN3A ZNF766 ZNF143 ZNF207 ENSG00000124593 MED20 CCND3 TAF8 USP49 FRS3 PRICKLE4 ENSG00000207371 BYSL TOMM6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP49 on UCSC Golden Path with GeneCards custom track

Promoters for USP49 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000196895 -39 1601 HDGF PKNOX1 CREB3L1 ARNT SIN3A YBX1 DMAP1 ZBTB7B ZNF143 KLF13

Genomic Location for USP49 Gene

Chromosome:
6
Start:
41,789,896 bp from pter
End:
41,895,361 bp from pter
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

Suggested Antigen Peptide Sequences for USP49 Gene

GenScript: Design optimal peptide antigens:

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 CatalyticActivity:
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).
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.

Enzyme Numbers (IUBMB) 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 Model Products

  • Taconic Biosciences Mouse Models for USP49

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP49

Flow Cytometry Products

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
mitochondrion 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 --
genes like me logo Genes that share ontologies with USP49: view

Pathways & Interactions for USP49 Gene

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

Pathways by source for USP49 Gene

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:0006397 mRNA processing IEA --
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with USP49: view

No data available for SIGNOR curated interactions for USP49 Gene

Transcripts for USP49 Gene

Unigene Clusters for USP49 Gene

Ubiquitin specific peptidase 49:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for USP49

Flow Cytometry Products

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
ECgene alternative splicing isoforms for
USP49

Expression for USP49 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of USP49 Gene:

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

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 35 34
  • 99.76 (n)
OneToOne
dog
(Canis familiaris)
Mammalia USP49 34 35
  • 90.88 (n)
mouse
(Mus musculus)
Mammalia Usp49 16 35 34
  • 90.16 (n)
cow
(Bos Taurus)
Mammalia USP49 35 34
  • 89.82 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp49 34
  • 88.94 (n)
oppossum
(Monodelphis domestica)
Mammalia USP49 35
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP49 35
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP49 35 34
  • 76.57 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP49 35
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp49 34
  • 67.87 (n)
zebrafish
(Danio rerio)
Actinopterygii usp49 35 34
  • 66.45 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea E01B7.1 35
  • 12 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP5 35
  • 15 (a)
ManyToMany
DOA4 35
  • 13 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 40 (a)
OneToMany
Species where no ortholog for USP49 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)
  • 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 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)

Paralogs for USP49 Gene

Paralogs for USP49 Gene

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

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

Variants for USP49 Gene

Sequence variations from dbSNP and Humsavar for USP49 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000017938 -- 41,813,724(+) TGCAC(C/T)TCACC intron-variant
rs1000029524 -- 41,860,734(+) CTCAA(C/T)CTCCT intron-variant
rs1000033636 -- 41,872,028(+) CGTAA(A/G)CAAAA intron-variant, upstream-variant-2KB
rs1000074818 -- 41,831,206(+) CCAAC(A/G)TGGTG intron-variant
rs1000087244 -- 41,871,659(+) ATCTG(C/T)AAGAT intron-variant, upstream-variant-2KB

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)

Relevant External Links for USP49 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP49

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

Disorders for USP49 Gene

Relevant External Links for USP49

Genetic Association Database (GAD)
USP49
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. … Lopez-Otin C. (Biochem. Biophys. Res. Commun. 2004) 2 3 4 64
  2. USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing. (PMID: 23824326) Zhang Z. … Wang H. (Genes Dev. 2013) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. USP18 recruits USP20 to promote innate antiviral response through deubiquitinating STING/MITA. (PMID: 27801882) Zhang M. … Zhong B. (Cell Res. 2016) 3 64
  5. A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. (PMID: 25036637) Taipale M. … Lindquist S. (Cell 2014) 3 64

Products for USP49 Gene

Sources for USP49 Gene

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