Protein interactions - USP13 - The Human Protein Atlas

GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	USP13
Synonyms	IsoT-3
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin specific peptidase 13
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Metabolic proteins Plasma proteins
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.	Intracellular
Protein evidence	Evidence at protein level (all genes)

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression analysis and annotation data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.	Skeletal myocytes - Muscle structure & formation (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.	Cell type enhanced (Alveolar cells type 2, Cardiomyocytes, Myonuclei, Oligodendrocyte progenitor cells, Oligodendrocytes, Thymic myoid cells)
Tissue expression cluster (RNA)ⁱ The RNA data was used to cluster genes according to their expression across tissues. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity.	Skeletal muscle - Striated muscle contraction (mainly)
Tissue specificity (RNA)ⁱ The RNA specificity category is based on mRNA expression levels in the consensus dataset which is calculated from the RNA expression levels in samples from HPA and GTEX. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected.	Group enriched (Heart muscle, Skeletal muscle, Tongue)
Subcellular locationⁱ Main subcellular location based on data generated in the subcellular section of the Human Protein Atlas.	Localized to the Nucleoplasm, Cytosol
Secretome annotationⁱ All genes with at least one predicted secreted isoform have been annotated and classified with the aim to determine if the corresponding protein(s) are: secreted into blood locally secreted or actually being attached to membrane or retained in intracellular locations like mitochondria, endoplasmatic reticulum (ER), Golgi apparatus or lysosomes.	Not available

GENE INFORMATIONⁱ Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Chromosome	3
Cytoband	q26.33
Chromosome location (bp)	179653032 - 179804366
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	23
Ensembl	ENSG00000058056 (version 109)
Entrez gene	8975
HGNC	HGNC:12611
UniProt	Q92995
GeneCards	USP13

ASSAYSⁱ

Interaction

Metabolic

INTERACTIONⁱ

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e.g. Brain enriched, Localized to mitochondria, Skeletal muscle - Striated muscle contraction

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Number of interactions:

Interaction	# Consensus	# IntAct	# BioGrid	# OpenCell	# BioPlex
SMC1A	17	13	71	23	11
TRIM55	1	2	19	0	0
TRIM63	8	10	36	0	0

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View all protein interaction data in IntAct

Interaction	# Consensus	# IntAct	# BioGrid	# OpenCell	# BioPlex
ATXN3	3	74	64	1	0
DAZAP2	10	124	17	0	2
TARDBP	16	141	74	7	0
TRIM55	1	2	19	0	0
TRIM63	8	10	36	0	0

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Interaction	# Consensus	# IntAct	# BioGrid	# OpenCell	# BioPlex
AMFR	13	12	65	0	15
ATG5	11	18	33	2	9
BAG6	8	11	69	6	0
CCND1	14	17	56	0	11
CLK3	14	34	45	5	0
CSNK2A1	99	67	249	184	22
CTNNB1	47	85	285	13	13
G3BP1	35	15	146	69	1
HMGB1	14	21	61	0	1
MCL1	9	14	35	0	5
MDC1	7	7	73	0	0
METTL3	2	1	13	7	0
MYC	66	90	1269	2	0
OGDH	1	2	14	0	2
PDS5A	7	7	24	3	12
PTEN	11	18	130	0	0
RAD21	9	10	46	7	7
RHBDF2	0	0	4	0	0
SIAH2	3	3	41	0	0
SMC1A	17	13	71	23	11
SMC3	9	9	74	4	5
SQSTM1	32	40	312	2	0
STAG2	10	10	26	9	0
TOPBP1	4	4	51	0	0
TRIM55	1	2	19	0	0
TRIM63	8	10	36	0	0
TWIST1	5	22	25	0	0
UBC	35	59	463	4	0
UBL4A	6	10	27	4	6
UFD1	3	4	21	2	0
UIMC1	3	3	23	0	0
USP5	1	3	34	0	0
VCP	57	56	348	43	5
WAPL	7	7	25	3	0
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Subcell location

Predicted location

Cell type specificity

Protein class

Number of interactions:

Interaction	# Consensus	# IntAct	# BioGrid	# OpenCell	# BioPlex
SMC1A	17	13	71	23	11

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Subcell location

Predicted location

Cell type specificity

Protein class

Number of interactions:

Interaction	# Consensus	# IntAct	# BioGrid	# OpenCell	# BioPlex
DDX28	6	1	15	0	31
REC8	2	2	2	0	9

METABOLIC SUMMARYⁱ In this summary the pathway/subsystems to which the gene belongs is shown together with the associated cellular compartment for the reactions based on metabolite information. The number of proteins and metabolites in the pathway is shown as well as the number of reactions for the selected gene. By clicking on a pathway in the summary table the associated metabolic network map is shown, together with a gene-tissue heatmap that shows the expression of genes in that pathway in different tissues.
Gene USP13 is associated with 1 reactions in 1 different subsystems, and present in the compartments: Cytosol. Provided by metabolicatlas.org
Pathway / Subsystem	Subsystem-associated compartments	# proteins	# metabolites	# reactions for this protein
Isolated	Cytosol, Mitochondria, Peroxisome, Endoplasmic reticulum, Extracellular, Nucleus, Golgi apparatus	524	320	1

PROTEIN INFORMATIONⁱ The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database. The Splice variant identifier links to the Ensembl website protein summary for the selected splice variant. The data in the Swissprot and TrEMBL columns links to corresponding pages in the UniProt database. The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide and number of predicted transmembrane region(s) according to in-house majority decision methods based on sets of predictors are also reported.
Splice variant	SwissProt	TrEMBL	Protein class	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
USP13-201	Q92995	A0A0A6YZ17	Enzymes Metabolic proteins Predicted intracellular proteins Plasma proteins Mapped to neXtProt Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014) Show all	863 aa 97.3 kDa	No	0
USP13-203	Q92995		Enzymes Metabolic proteins Predicted intracellular proteins Plasma proteins Mapped to neXtProt Protein evidence (Ezkurdia et al 2014) Show all	798 aa 90.4 kDa	No	0
USP13-204		H7C5J3	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	299 aa 34.2 kDa	No	0
USP13-206		A0A7P0Z4M1	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	15 aa 1.7 kDa	No	0
USP13-209		A0A7P0TBG5	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	145 aa 16.5 kDa	No	0
USP13-212		A0A7P0TB18	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	64 aa 7.2 kDa	No	0
USP13-214		A0A7P0T8B2	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	40 aa 4.5 kDa	No	0
USP13-215		A0A7P0TB48	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	71 aa 8.1 kDa	No	0
USP13-216		A0A7P0TAJ9	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	226 aa 24.9 kDa	No	0
USP13-222		A0A7P0T8S4	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	53 aa 5.9 kDa	No	0
USP13-226		A0A7P0TB69	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	819 aa 92.1 kDa	No	0
USP13-230		A0A7P0T9S5	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	83 aa 9.5 kDa	No	0
USP13-236		A0A7P0T9N7	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	65 aa 6.7 kDa	No	0
USP13-237		A0A7P0TB82	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	131 aa 14.1 kDa	No	0
USP13-238		A0A7P0TAJ4	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	80 aa 8.8 kDa	No	0
USP13-240		A0A7P0TAP9	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	862 aa 97.2 kDa	No	0
USP13-244		A0A7P0T8Y7	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	71 aa 7.4 kDa	No	0
USP13-249		A0A7P0T873	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	92 aa 10.6 kDa	No	0
USP13-251		A0A7P0TB92	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	103 aa 11.3 kDa	No	0
USP13-256		A0A7P0T9V0	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	52 aa 5.8 kDa	No	0
USP13-259		A0A7P0Z4C0	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	75 aa 8 kDa	No	0
USP13-265		A0A7P0T9H6	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	89 aa 10.2 kDa	No	0
USP13-271		A0A7P0T863	Metabolic proteins Predicted intracellular proteins Protein evidence (Ezkurdia et al 2014)	76 aa 8.4 kDa	No	0
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