Human Gene USP49 (ENST00000373006.5_5) from GENCODE V47lift37
  Description: ubiquitin specific peptidase 49, transcript variant 2 (from RefSeq NM_018561.5)
Gencode Transcript: ENST00000373006.5_5
Gencode Gene: ENSG00000164663.15_12
Transcript (Including UTRs)
   Position: hg19 chr6:41,765,383-41,863,099 Size: 97,717 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr6:41,766,415-41,774,721 Size: 8,307 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:41,765,383-41,863,099)mRNA (may differ from genome)Protein (640 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBP49_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin carboxyl-terminal hydrolase 49; EC=3.4.19.12; AltName: Full=Deubiquitinating enzyme 49; AltName: Full=Ubiquitin thioesterase 49; AltName: Full=Ubiquitin-specific-processing protease 49;
CATALYTIC ACTIVITY: 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).
SIMILARITY: Belongs to the peptidase C19 family.
SIMILARITY: Contains 1 UBP-type zinc finger.

-  Primer design for this transcript
 

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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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.88 RPKM in Testis
Total median expression: 27.43 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -44.90222-0.202 Picture PostScript Text
3' UTR -320.501032-0.311 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
IPR018200 - Pept_C19ubi-hydrolase_C_CS
IPR001394 - Peptidase_C19
IPR013083 - Znf_RING/FYVE/PHD
IPR001607 - Znf_UBP

Pfam Domains:
PF00443 - Ubiquitin carboxyl-terminal hydrolase
PF02148 - Zn-finger in ubiquitin-hydrolases and other protein
PF13423 - Ubiquitin carboxyl-terminal hydrolase

SCOP Domains:
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
54001 - Cysteine proteinases
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q70CQ1
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004197 cysteine-type endopeptidase activity
GO:0004843 thiol-dependent ubiquitin-specific protease activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity
GO:0042393 histone binding
GO:0046872 metal ion binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006325 chromatin organization
GO:0006397 mRNA processing
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0008380 RNA splicing
GO:0016579 protein deubiquitination
GO:0035616 histone H2B conserved C-terminal lysine deubiquitination

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC014176 - Homo sapiens ubiquitin specific peptidase 49, mRNA (cDNA clone MGC:20741 IMAGE:4579283), complete cds.
AJ586139 - Homo sapiens mRNA for ubiquitin-specific proteinase 49 (USP49 gene).
JD345395 - Sequence 326419 from Patent EP1572962.
JD178616 - Sequence 159640 from Patent EP1572962.
JD145916 - Sequence 126940 from Patent EP1572962.
JD482629 - Sequence 463653 from Patent EP1572962.
JD093698 - Sequence 74722 from Patent EP1572962.
JD184338 - Sequence 165362 from Patent EP1572962.
JD268552 - Sequence 249576 from Patent EP1572962.
JD088892 - Sequence 69916 from Patent EP1572962.
JD510987 - Sequence 492011 from Patent EP1572962.
JD171107 - Sequence 152131 from Patent EP1572962.
JD292296 - Sequence 273320 from Patent EP1572962.
JD310155 - Sequence 291179 from Patent EP1572962.
JD511788 - Sequence 492812 from Patent EP1572962.
JD197657 - Sequence 178681 from Patent EP1572962.
JD388490 - Sequence 369514 from Patent EP1572962.
JD498189 - Sequence 479213 from Patent EP1572962.
JD281801 - Sequence 262825 from Patent EP1572962.
JD482659 - Sequence 463683 from Patent EP1572962.
JD145923 - Sequence 126947 from Patent EP1572962.
JD043320 - Sequence 24344 from Patent EP1572962.
JD286871 - Sequence 267895 from Patent EP1572962.
JD533256 - Sequence 514280 from Patent EP1572962.
JD512822 - Sequence 493846 from Patent EP1572962.
JD412845 - Sequence 393869 from Patent EP1572962.
JD197837 - Sequence 178861 from Patent EP1572962.
JD212443 - Sequence 193467 from Patent EP1572962.
JD542573 - Sequence 523597 from Patent EP1572962.
JD512821 - Sequence 493845 from Patent EP1572962.
JD534145 - Sequence 515169 from Patent EP1572962.
JD393714 - Sequence 374738 from Patent EP1572962.
JD040135 - Sequence 21159 from Patent EP1572962.
JD061697 - Sequence 42721 from Patent EP1572962.
JD061696 - Sequence 42720 from Patent EP1572962.
JD361147 - Sequence 342171 from Patent EP1572962.
JD177521 - Sequence 158545 from Patent EP1572962.
JD447025 - Sequence 428049 from Patent EP1572962.
JD238482 - Sequence 219506 from Patent EP1572962.
JD483095 - Sequence 464119 from Patent EP1572962.
JD223102 - Sequence 204126 from Patent EP1572962.
JD185687 - Sequence 166711 from Patent EP1572962.
JD144743 - Sequence 125767 from Patent EP1572962.
JD058539 - Sequence 39563 from Patent EP1572962.
JD259115 - Sequence 240139 from Patent EP1572962.
JD143534 - Sequence 124558 from Patent EP1572962.
JD228675 - Sequence 209699 from Patent EP1572962.
JD275760 - Sequence 256784 from Patent EP1572962.
JD159033 - Sequence 140057 from Patent EP1572962.
JD105704 - Sequence 86728 from Patent EP1572962.
JD380102 - Sequence 361126 from Patent EP1572962.
JD179804 - Sequence 160828 from Patent EP1572962.
JD481479 - Sequence 462503 from Patent EP1572962.
JD512794 - Sequence 493818 from Patent EP1572962.
JD412817 - Sequence 393841 from Patent EP1572962.
JD197820 - Sequence 178844 from Patent EP1572962.
JD212427 - Sequence 193451 from Patent EP1572962.
JD406221 - Sequence 387245 from Patent EP1572962.
JD294448 - Sequence 275472 from Patent EP1572962.
JD294814 - Sequence 275838 from Patent EP1572962.
JF432543 - Synthetic construct Homo sapiens clone IMAGE:100073766 ubiquitin specific peptidase 49 (USP49) gene, encodes complete protein.
KJ893479 - Synthetic construct Homo sapiens clone ccsbBroadEn_02873 USP49 gene, encodes complete protein.
JD378384 - Sequence 359408 from Patent EP1572962.
AK021462 - Homo sapiens cDNA FLJ11400 fis, clone HEMBA1000673.
AF119901 - Homo sapiens PRO2831 mRNA, complete cds.
JD048594 - Sequence 29618 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q70CQ1 (Reactome details) participates in the following event(s):

R-HSA-5696960 USP49 deubiquitinates H2B
R-HSA-5689880 Ub-specific processing proteases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000373006.1, ENST00000373006.2, ENST00000373006.3, ENST00000373006.4, NM_018561, Q5T3D9, Q5T3E0, Q70CQ1, Q96CK4, UBP49_HUMAN, uc318kkd.1, uc318kkd.2
UCSC ID: ENST00000373006.5_5
RefSeq Accession: NM_018561.5
Protein: Q70CQ1 (aka UBP49_HUMAN or UB49_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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