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Gene: USP39 (ubiquitin specific peptidase 39) Pan paniscus

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Symbol:

USP39

Name:

ubiquitin specific peptidase 39

RGD ID:

11746488

Description:

ENCODES a protein that exhibits cysteine-type deubiquitinase activity (ortholog); INVOLVED IN mRNA processing (inferred); mRNA splicing, via spliceosome (inferred); protein deubiquitination (inferred); ASSOCIATED WITH Colonic Neoplasms (ortholog); Experimental Neoplasms (ortholog); hereditary spastic paraplegia 31 (ortholog); FOUND IN nucleoplasm (inferred); nucleus (inferred); spliceosomal complex (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

U4/U6.U5 tri-snRNP-associated protein 2; ubiquitin carboxyl-terminal hydrolase 39

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly

Position:

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	12	40,733,638 - 40,779,733 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	40,736,399 - 40,782,484 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	85,655,633 - 85,701,775 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	87,219,121 - 87,251,931 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	87,215,366 - 87,251,931 (+)	Ensembl	panpan1.1		panPan2

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
USP39	Bonobo	hereditary spastic paraplegia 31		ISO	RGD:1317682	8554872	ClinVar Annotator: match by term: Hereditary spastic paraplegia 31	ClinVar	PMID:18321925\|PMID:18644145\|PMID:22062632\|PMID:22703882\|PMID:24986827\|PMID:28492532

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
USP39	Bonobo	Colonic Neoplasms		ISO	RGD:1317682	9068941	CTD Direct Evidence: marker/mechanism	CTD	PMID:34822033
USP39	Bonobo	Experimental Neoplasms		ISO	RGD:1317682	9068941	CTD Direct Evidence: marker/mechanism	CTD	PMID:34822033

Biological Process

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
USP39	Bonobo	mRNA processing	involved_in	IEA	InterPro:IPR033809	150520179		InterPro	GO_REF:0000002
USP39	Bonobo	mRNA processing	involved_in	IEA	UniProtKB-KW:KW-0507	150520179		UniProt	GO_REF:0000043
USP39	Bonobo	mRNA splicing, via spliceosome	involved_in	IEA	UniProtKB:Q53GS9\|ensembl:ENSP00000312981	150520179		Ensembl	GO_REF:0000107
USP39	Bonobo	protein deubiquitination	involved_in	IEA	InterPro:IPR001394	150520179		InterPro	GO_REF:0000002
USP39	Bonobo	RNA splicing	involved_in	IEA	UniProtKB-KW:KW-0508	150520179		UniProt	GO_REF:0000043
USP39	Bonobo	spliceosomal complex assembly	involved_in	IEA	InterPro:IPR033809	150520179		InterPro	GO_REF:0000002
USP39	Bonobo	spliceosomal complex assembly	involved_in	IEA	UniProtKB:Q53GS9\|ensembl:ENSP00000312981	150520179		Ensembl	GO_REF:0000107

Cellular Component

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
USP39	Bonobo	nucleoplasm	located_in	IEA	UniProtKB:Q53GS9\|ensembl:ENSP00000312981	150520179		Ensembl	GO_REF:0000107
USP39	Bonobo	nucleus	located_in	IEA	UniProtKB:Q53GS9\|ensembl:ENSP00000312981	150520179		Ensembl	GO_REF:0000107
USP39	Bonobo	nucleus	located_in	IEA	UniProtKB-KW:KW-0539	150520179		UniProt	GO_REF:0000043
USP39	Bonobo	nucleus	located_in	IEA	UniProtKB-SubCell:SL-0191	150520179		UniProt	GO_REF:0000044
USP39	Bonobo	spliceosomal complex	part_of	IEA	UniProtKB-KW:KW-0747	150520179		UniProt	GO_REF:0000043
USP39	Bonobo	U4/U6 x U5 tri-snRNP complex	part_of	IEA	UniProtKB:Q53GS9\|ensembl:ENSP00000312981	150520179		Ensembl	GO_REF:0000107

Molecular Function

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
USP39	Bonobo	cysteine-type deubiquitinase activity	NOT\|enables	ISO	RGD:1317682	9068941	PMID:18728397	FlyBase	PMID:18728397
USP39	Bonobo	cysteine-type deubiquitinase activity	enables	IEA	InterPro:IPR001394	150520179		InterPro	GO_REF:0000002
USP39	Bonobo	metal ion binding	enables	IEA	UniProtKB-KW:KW-0479	150520179		UniProt	GO_REF:0000043
USP39	Bonobo	protein binding	enables	ISO	UniProtKB:Q5S007	9068941	PMID:29513927, PMID:31046837	IntAct	PMID:29513927\|PMID:31046837
USP39	Bonobo	protein binding	enables	ISO	UniProtKB:Q96SB4	9068941	PMID:23602568, PMID:32707033	IntAct	PMID:23602568\|PMID:32707033
USP39	Bonobo	zinc ion binding	enables	IEA	InterPro:IPR001607	150520179		InterPro	GO_REF:0000002
USP39	Bonobo	zinc ion binding	enables	IEA	UniProtKB-KW:KW-0863	150520179		UniProt	GO_REF:0000043

PMID:22301074

USP39
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	12	40,733,638 - 40,779,733 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	40,736,399 - 40,782,484 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	85,655,633 - 85,701,775 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	87,219,121 - 87,251,931 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	87,215,366 - 87,251,931 (+)	Ensembl	panpan1.1		panPan2

USP39
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	85,602,861 - 85,649,283 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	85,602,856 - 85,649,283 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	85,829,984 - 85,876,406 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	85,696,794 - 85,729,917 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	85,754,940 - 85,788,063	NCBI
Celera	2	85,671,566 - 85,704,705 (+)	NCBI		Celera
Cytogenetic Map	2	p11.2	NCBI
HuRef	2	85,727,104 - 85,773,387 (+)	NCBI		HuRef
CHM1_1	2	85,759,771 - 85,806,166 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	85,604,921 - 85,651,339 (+)	NCBI		T2T-CHM13v2.0

Usp39
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	72,295,749 - 72,322,190 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	72,295,661 - 72,322,167 (-)	Ensembl		GRCm39 Ensembl
GRCm38	6	72,318,676 - 72,345,208 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	72,318,678 - 72,345,184 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	72,268,670 - 72,295,169 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	72,248,185 - 72,274,684 (-)	NCBI		MGSCv36	mm8
Celera	6	74,408,796 - 74,435,299 (-)	NCBI		Celera
Cytogenetic Map	6	C1	NCBI
cM Map	6	32.27	NCBI

Usp39
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	105,932,140 - 105,964,551 (-)	NCBI		GRCr8
mRatBN7.2	4	104,373,948 - 104,406,359 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	104,373,955 - 104,406,359 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	109,754,240 - 109,786,619 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	105,529,358 - 105,561,736 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	104,143,607 - 104,176,020 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	100,181,408 - 100,211,425 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	100,181,455 - 100,213,858 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	164,952,169 - 164,982,100 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	105,623,922 - 105,650,275 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	105,868,446 - 105,900,853 (-)	NCBI
Celera	4	93,527,956 - 93,554,280 (-)	NCBI		Celera
Cytogenetic Map	4	q32	NCBI

Usp39
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955424	1,867,850 - 1,894,157 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955424	1,867,910 - 1,893,338 (-)	NCBI	ChiLan1.0	ChiLan1.0

USP39
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	17	39,437,908 - 39,470,579 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	17	39,438,329 - 39,470,549 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	17	39,109,745 - 39,141,965 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	17	40,184,513 - 40,217,215 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	17	40,184,513 - 40,217,432 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	17	39,314,066 - 39,346,743 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	17	39,386,575 - 39,418,768 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	17	39,785,977 - 39,818,386 (-)	NCBI		UU_Cfam_GSD_1.0

Usp39
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024406292	79,196,882 - 79,233,019 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936712	1,625,802 - 1,661,533 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936712	1,625,429 - 1,661,561 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

USP39
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	59,121,048 - 59,156,442 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	59,121,381 - 59,156,597 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	62,195,078 - 62,215,382 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

USP39
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	14	21,507,666 - 21,554,819 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	21,508,104 - 21,541,553 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	90,913,997 - 90,971,480 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Usp39
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624749	17,501,219 - 17,526,712 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624749	17,500,781 - 17,526,755 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.


RefSeq Transcripts	XM_034953474	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_034953475	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_034953476	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JARIFH020000012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSPPAT00000033726 ⟹ ENSPPAP00000011071

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	2A	87,215,366 - 87,251,457 (+)	Ensembl

Ensembl Acc Id:

ENSPPAT00000033732 ⟹ ENSPPAP00000011077

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	2A	87,215,366 - 87,251,457 (+)	Ensembl

Ensembl Acc Id:

ENSPPAT00000033736 ⟹ ENSPPAP00000011081

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	2A	87,219,121 - 87,251,931 (+)	Ensembl

Ensembl Acc Id:

ENSPPAT00000033755 ⟹ ENSPPAP00000011100

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	2A	87,219,225 - 87,251,457 (+)	Ensembl

Ensembl Acc Id:

ENSPPAT00000033757 ⟹ ENSPPAP00000011102

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	2A	87,219,225 - 87,250,686 (+)	Ensembl

Ensembl Acc Id:

ENSPPAT00000033761 ⟹ ENSPPAP00000011106

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	2A	87,219,225 - 87,250,686 (+)	Ensembl

RefSeq Acc Id:

XM_034953474 ⟹ XP_034809365

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	12	40,733,638 - 40,766,552 (-)	NCBI
NHGRI_mPanPan1	2A	40,736,399 - 40,769,302 (-)	NCBI
Mhudiblu_PPA_v0	2A	85,668,839 - 85,701,775 (+)	NCBI

RefSeq Acc Id:

XM_034953475 ⟹ XP_034809366

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	12	40,733,638 - 40,766,592 (-)	NCBI
NHGRI_mPanPan1	2A	40,736,399 - 40,769,353 (-)	NCBI
Mhudiblu_PPA_v0	2A	85,668,845 - 85,701,775 (+)	NCBI

RefSeq Acc Id:

XM_034953476 ⟹ XP_034809367

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	12	40,733,638 - 40,779,733 (-)	NCBI
NHGRI_mPanPan1	2A	40,736,399 - 40,782,484 (-)	NCBI
Mhudiblu_PPA_v0	2A	85,655,633 - 85,701,775 (+)	NCBI


Protein RefSeqs	XP_034809365	(Get FASTA)	NCBI Sequence Viewer
	XP_034809366	(Get FASTA)	NCBI Sequence Viewer
	XP_034809367	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSPPAP00000011071.1
	ENSPPAP00000011077.1
	ENSPPAP00000011081.1
	ENSPPAP00000011100.1
	ENSPPAP00000011102.1
	ENSPPAP00000011106.1

RefSeq Acc Id:	XP_034809367 ⟸ XM_034953476
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_034809365 ⟸ XM_034953474
- Peptide Label:	isoform X1
- UniProtKB:	A0A2R9A6V0 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_034809366 ⟸ XM_034953475
- Peptide Label:	isoform X1
- UniProtKB:	A0A2R9A6V0 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSPPAP00000011081 ⟸ ENSPPAT00000033736

Ensembl Acc Id:

ENSPPAP00000011077 ⟸ ENSPPAT00000033732

Protein Domains

UBP-type USP

Database	Acc Id	Source(s)
Ensembl Genes	ENSPPAG00000028703	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSPPAT00000033726.1	UniProtKB/TrEMBL
	ENSPPAT00000033732.1	UniProtKB/TrEMBL
	ENSPPAT00000033736.1	UniProtKB/TrEMBL
	ENSPPAT00000033755.1	UniProtKB/TrEMBL
	ENSPPAT00000033757.1	UniProtKB/TrEMBL
	ENSPPAT00000033761.1	UniProtKB/TrEMBL
Gene3D-CATH	3.30.40.10	UniProtKB/TrEMBL
	Cysteine proteinases	UniProtKB/TrEMBL
InterPro	Papain-like_cys_pep_sf	UniProtKB/TrEMBL
	Peptidase_C19_UCH	UniProtKB/TrEMBL
	Ub_carboxyl-term_hydrolase	UniProtKB/TrEMBL
	USP39	UniProtKB/TrEMBL
	USP_dom	UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/TrEMBL
	Znf_UBP	UniProtKB/TrEMBL
NCBI Gene	USP39	ENTREZGENE
PANTHER	PTHR21646:SF16	UniProtKB/TrEMBL
	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE	UniProtKB/TrEMBL
Pfam	UCH	UniProtKB/TrEMBL
	zf-UBP	UniProtKB/TrEMBL
PROSITE	USP_3	UniProtKB/TrEMBL
	ZF_UBP	UniProtKB/TrEMBL
SMART	ZnF_UBP	UniProtKB/TrEMBL
Superfamily-SCOP	RING/U-box	UniProtKB/TrEMBL
	SSF54001	UniProtKB/TrEMBL
UniProt	A0A2R9A1E6_PANPA	UniProtKB/TrEMBL
	A0A2R9A1H1_PANPA	UniProtKB/TrEMBL
	A0A2R9A5X6_PANPA	UniProtKB/TrEMBL
	A0A2R9A6U6_PANPA	UniProtKB/TrEMBL
	A0A2R9A6V0	ENTREZGENE, UniProtKB/TrEMBL
	A0A2R9A6X0_PANPA	UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailable


InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailable


Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
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MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable

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