Usp39 (ubiquitin specific peptidase 39)

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Gene: Usp39 (ubiquitin specific peptidase 39) Rattus norvegicus

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Symbol:

Usp39

Name:

ubiquitin specific peptidase 39

RGD ID:

1308103

Description:

Predicted to enable zinc ion binding activity. Predicted to be involved in spliceosomal complex assembly. Predicted to be located in nucleoplasm. Predicted to be part of U4/U6 x U5 tri-snRNP complex. Orthologous to human USP39 (ubiquitin specific peptidase 39); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC297336; U4/U6.U5 tri-snRNP-associated protein 2; ubiquitin carboxyl-terminal hydrolase 39; ubiquitin specific protease 39

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	USP39 (ubiquitin specific peptidase 39)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, PhylomeDB, Treefam
Mus musculus (house mouse):	Usp39 (ubiquitin specific peptidase 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Usp39 (ubiquitin specific peptidase 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	USP39 (ubiquitin specific peptidase 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	USP39 (ubiquitin specific peptidase 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Usp39 (ubiquitin specific peptidase 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	USP39 (ubiquitin specific peptidase 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	USP39 (ubiquitin specific peptidase 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Usp39 (ubiquitin specific peptidase 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	SYCE1L (synaptonemal complex central element protein 1 like)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	USP39 (ubiquitin specific peptidase 39)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Usp39 (ubiquitin specific peptidase 39)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	usp39 (ubiquitin specific peptidase 39)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SAD1	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Usp39	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	usp-39	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	usp39	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

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

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Colonic Neoplasms (ISO)

Experimental Neoplasms (ISO)

hereditary spastic paraplegia 31 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4-amino-2,6-dinitrotoluene (EXP)

acrolein (ISO)

acrylamide (EXP,ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

cisplatin (ISO)

deoxynivalenol (ISO)

dexamethasone (ISO)

Dibutyl phosphate (ISO)

flutamide (EXP)

FR900359 (ISO)

gentamycin (EXP)

indometacin (ISO)

ivermectin (ISO)

lead(0) (ISO)

mercury atom (ISO)

mercury(0) (ISO)

methyl methanesulfonate (ISO)

N-methyl-4-phenylpyridinium (ISO)

nefazodone (EXP)

nimesulide (EXP)

ozone (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

pirinixic acid (ISO)

reactive oxygen species (ISO)

resveratrol (ISO)

sodium arsenite (ISO)

tetrachloromethane (EXP,ISO)

trimellitic anhydride (ISO)

Triptolide (EXP)

trovafloxacin (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

mRNA splicing, via spliceosome (ISO)

protein deubiquitination (IEA)

spliceosomal complex assembly (ISO)

Cellular Component

nucleoplasm (IEA,ISO)

nucleus (ISO)

spliceosomal complex (IEA)

U4/U6 x U5 tri-snRNP complex (ISO)

Molecular Function

cysteine-type deubiquitinase activity (ISO)

protein binding (ISO)

zinc ion binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

spliceosome pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
2.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:11350945	PMID:12477932	PMID:22082260	PMID:26912367

Genomics

Comparative Map Data

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
(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
(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
(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
(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

Variants

Variants in Usp39
98 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	95
Count of miRNA genes:	83
Interacting mature miRNAs:	88
Transcripts:	ENSRNOT00000015562
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1582232	Gluco25	Glucose level QTL 25	3.6	0.0023	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	85253748	148090731	Rat
631689	Scl4	Serum cholesterol level QTL 4	1.9	0.008	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	4	95174120	140174120	Rat
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	38465774	146803430	Rat
1578655	Bmd11	Bone mineral density QTL 11	11		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	4	90850165	135850165	Rat
1357342	Bw40	Body weight QTL 40		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	4	76647384	117676292	Rat
631556	Bp135	Blood pressure QTL 135		0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	78881294	117676292	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	70362013	132642728	Rat
70167	Bw22	Body weight QTL 22	3.1		body mass (VT:0001259)	body weight (CMO:0000012)	4	76647384	117676292	Rat
1549839	Bw52	Body weight QTL 52		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	61697658	115089733	Rat
70177	Xhs1	X-ray hypersensitivity QTL 1	25.1		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	82798864	152731274	Rat
724522	Bp146	Blood pressure QTL 146	2.2	0.0021	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	73630210	118630210	Rat
61476	Aia3	Adjuvant induced arthritis QTL 3	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	86730991	131730991	Rat
1641919	Alc22	Alcohol consumption QTL 22		0.0005	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	81192555	126192555	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	44463908	148090542	Rat
2300179	Bmd50	Bone mineral density QTL 50	5.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	4	60928534	105928534	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	50119848	146803430	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	4	62933508	114921294	Rat
1578670	Bss14	Bone structure and strength QTL 14	16.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	4	87327165	132327165	Rat
2317588	Eae27	Experimental allergic encephalomyelitis QTL 27			nervous system integrity trait (VT:0010566)	percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)	4	103194805	112478794	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	39524264	116179656	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	56647873	149491524	Rat
1578657	Bss12	Bone structure and strength QTL 12	8.9		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	4	60220938	105220938	Rat
1578658	Bss13	Bone structure and strength QTL 13	8		femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	4	60220938	105220938	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	11320076	180699135	Rat
6478684	Anxrr30	Anxiety related response QTL 30		0.00087	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
1578662	Bss15	Bone structure and strength QTL 15	19.6		femur width (VT:1000666)	femoral neck width (CMO:0001695)	4	87327165	132327165	Rat
2302051	Pia28	Pristane induced arthritis QTL 28	5.3	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)	4	73630210	118630210	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	59948935	154902892	Rat
2312567	Glom19	Glomerulus QTL 19	1.9	0.006	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	4	45456990	146803430	Rat
738015	Pia9	Pristane induced arthritis QTL 9	4.5	0.048	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	80694870	125694870	Rat
6478772	Anxrr49	Anxiety related response QTL 49		0.15488	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
634335	Anxrr16	Anxiety related response QTL 16	7.22		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	93308457	167139447	Rat
631646	Stl4	Serum triglyceride level QTL 4	6.5	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	4	73169846	132642728	Rat
634334	Xhs3	X-ray hypersensitivity QTL 3	10		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	84728680	129854654	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	44463908	148090542	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	4	70808386	115808386	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5214602	146446691	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	83428419	177635233	Rat
631662	Hcar2	Hepatocarcinoma resistance QTL 2	3.1	0.0003	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	78878504	123878504	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	44463720	155883716	Rat
61418	Pia5	Pristane induced arthritis QTL 5	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	62277855	128289560	Rat
631651	Bp124	Blood pressure QTL 124	3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	62879517	107879517	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
1358202	Gluco11	Glucose level QTL 11	2.4	0.02	adipocyte glucose uptake trait (VT:0004185)	absolute change in adipocyte glucose uptake (CMO:0000873)	4	85379421	167139601	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	56698790	126192555	Rat
2306899	Bp338	Blood pressure QTL 338		0.071	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	81006124	120102625	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	64528739	157573521	Rat
6478743	Anxrr40	Anxiety related response QTL 40		0.83076	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
12798523	Anxrr56	Anxiety related response QTL 56	2.83	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	85253748	150276390	Rat
61434	Cia3	Collagen induced arthritis QTL 3	4.8		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	103194656	148194656	Rat
12798520	Anxrr55	Anxiety related response QTL 55	4.45	0.01	locomotor behavior trait (VT:0001392)	number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)	4	32583980	114627242	Rat

Markers in Region

RH130860

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	104,373,961 - 104,374,167 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	100,181,462 - 100,181,667	NCBI	Rnor6.0
Rnor_5.0	4	164,952,223 - 164,952,428	UniSTS	Rnor5.0
RGSC_v3.4	4	105,623,976 - 105,624,181	UniSTS	RGSC3.4
Celera	4	93,528,010 - 93,528,215	UniSTS
RH 3.4 Map	4	632.15	UniSTS
Cytogenetic Map	4	q33	UniSTS

D6Wsu157e

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	104,373,956 - 104,374,117 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	100,181,457 - 100,181,617	NCBI	Rnor6.0
Rnor_5.0	4	164,952,218 - 164,952,378	UniSTS	Rnor5.0
RGSC_v3.4	4	105,623,971 - 105,624,131	UniSTS	RGSC3.4
Celera	4	93,528,005 - 93,528,165	UniSTS
Cytogenetic Map	4	q33	UniSTS

Expression

RNA-SEQ Expression

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

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106597	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001398741	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063285778	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC133017	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC166516	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473957	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000015562 ⟹ ENSRNOP00000015563

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	104,373,955 - 104,406,359 (-)	Ensembl
Rnor_6.0 Ensembl	4	100,181,455 - 100,213,858 (-)	Ensembl

RefSeq Acc Id:

NM_001106597 ⟹ NP_001100067

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	105,932,140 - 105,964,551 (-)	NCBI
mRatBN7.2	4	104,373,948 - 104,406,359 (-)	NCBI
Rnor_6.0	4	100,181,408 - 100,207,761 (-)	NCBI
Rnor_5.0	4	164,952,169 - 164,982,100 (-)	NCBI
RGSC_v3.4	4	105,623,922 - 105,650,275 (-)	RGD
Celera	4	93,527,956 - 93,554,280 (-)	RGD

Sequence:

show sequence

GGCGCGGAAGCTCCTAACCGGTGGTGGCGATGTCTAGCCGGTCCAAGCGGCAGTCTCATGGTTC
TACCCGTGGGAAGCGCGAGTCCGAGTCTCGAGGTAGCTCGGGTCGCATCAAGAAGGAGCGAGAC
CGCGAGAAGGAGCCCGAGGCGGCGAGCTCCCGGGGTAGTCCGGTCCGCGTGAAGCGGGAGGCCG
AGCCGACTCCGCGAGAGGTCCCGGCGCCCGTGCTCCCGGTTGTGCGGGTGAAGCGTGAGCGTGA
GGCCGACGAGGACTCGGAGCCCGAGCGGGAGGTGCGAGCAAAGAATGGCCGAGTGGATTCTGAA
GACCGGAGGAGTCGTCACTGTCCATACTTGGATACTATTAATAGGAGTGTGCTGGACTTCGACT
TTGAGAAACTCTGTTCCATTTCTCTCTCGCACATCAATGCATATGCCTGCCTGGTGTGTGGCAA
GTACTTTCAAGGCCGGGGTTTAAAGTCTCATGCCTACATCCACAGTGTCCAGTTCAGCCACCAT
GTCTTCCTCAACCTCCACACTCTCAAGTTTTACTGCCTTCCTGACAACTATGAGATCATCGATT
CCTCGCTGGAGGATATTACATATGTGTTGAAGCCTACTTTCACAAAGCAGCAAATTGCAAACTT
GGACAAGCAAGCCAAATTGTCCCGGGCATATGATGGTACCACTTACCTGCCAGGGATTGTGGGA
CTGAACAACATAAAAGCCAACGACTATGCAAATGCTGTGCTGCAGGCACTATCTAACGTTCCTC
CTCTTCGGAACTACTTCCTGGAGGAGGACAATTATAAGAACATCAAGCGTCCTCCGGGGGATAT
CATGTTCTTGTTGGTCCAGCGTTTTGGAGAGCTGATGAGAAAGCTCTGGAACCCCCGAAACTTC
AAGGCACATGTTTCTCCTCATGAGATGCTTCAGGCCGTCGTACTTTGCAGCAAGAAGACTTTCC
AAATTACCAAACAAGGGGATGGAGTTGACTTCCTGTCTTGGTTTCTGAATGCTCTGCACTCAGC
TCTGGGAGGCACCAAGAAGAAGAAAAAGACTATTGTGAATGATGTTTTCCAGGGATCAATGAGA
ATTTTCACCAAAAAGCTTCCTCATCCTGATCTGCCAGCGGAAGAGAAAGAGCAGCTGCTCCATA
ATGAGGAGTACCAAGAGACAATGGTGGAGTCCACGTTCATGTACCTGACGCTCGACCTTCCCAC
TGCTCCACTCTATAAGGACGAGAAGGAGCAGCTCATTATCCCGCAAGTGCCACTCTTCAACATC
CTGGCCAAGTTCAACGGCATCACGGAGAAGGAATACAAGACTTATAAGGAGAACTTCCTGAAGC
GCTTCCAGCTCACCAAGCTGCCTCCATATCTAATCTTTTGCATCAAGAGATTTACAAAGAACAA
CTTCTTCGTGGAGAAGAATCCAACAATTGTCAATTTCCCTATCACAAATGTGGATCTGAGAGAA
TACTTATCTGAAGAAGTCCAAGCAGTCCACAAGAACACCACCTATGACCTCATCGCCAACATTG
TGCATGATGGCAAGCCTTCTGAGGGCTCCTACAGGATCCATGTGCTTCATCATGGGACAGGCAA
GTGGTATGAACTACAAGACCTCCAGGTGACGGACATTCTGCCCCAGATGATCACCCTGTCTGAG
GCGTACATTCAGCACATGCCTTCCCTTTCAGCATCAGCAGGCAGAACTCTTACAGATGGATGCC
TTATTTGAATTGCTGCAAGTATCAAAGAACAGAAAGTTCCGTGGAAACATCAAGTCTTGAGATT
CTAGGAGTAAACATGGAGTCAGCAGCACCCTTATGCCATAGGTAGATGGTTTTCCTGTAGTTCC
CTCCATCTCCTCGTGGGACCTTTGGGATGGATTAAATGTCCTCCTGTTTTTAAACCAGGCTCTT
GTTTTATAGACCTCATTTAGGCTTGTTAAGAGTT

hide sequence

RefSeq Acc Id:

NM_001398741 ⟹ NP_001385670

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	105,932,140 - 105,964,551 (-)	NCBI
mRatBN7.2	4	104,373,948 - 104,406,359 (-)	NCBI

RefSeq Acc Id:

XM_063285778 ⟹ XP_063141848

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	105,932,144 - 105,962,047 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001100067	(Get FASTA)	NCBI Sequence Viewer
	NP_001385670	(Get FASTA)	NCBI Sequence Viewer
	XP_063141848	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI66516	(Get FASTA)	NCBI Sequence Viewer
	EDL91020	(Get FASTA)	NCBI Sequence Viewer
	EDL91021	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000015563.5

RefSeq Acc Id:	NP_001100067 ⟸ NM_001106597
- Peptide Label:	isoform 1
- UniProtKB:	A6IAA2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSSRSKRQSHGSTRGKRESESRGSSGRIKKERDREKEPEAASSRGSPVRVKREAEPTPREVPAP VLPVVRVKREREADEDSEPEREVRAKNGRVDSEDRRSRHCPYLDTINRSVLDFDFEKLCSISLS HINAYACLVCGKYFQGRGLKSHAYIHSVQFSHHVFLNLHTLKFYCLPDNYEIIDSSLEDITYVL KPTFTKQQIANLDKQAKLSRAYDGTTYLPGIVGLNNIKANDYANAVLQALSNVPPLRNYFLEED NYKNIKRPPGDIMFLLVQRFGELMRKLWNPRNFKAHVSPHEMLQAVVLCSKKTFQITKQGDGVD FLSWFLNALHSALGGTKKKKKTIVNDVFQGSMRIFTKKLPHPDLPAEEKEQLLHNEEYQETMVE STFMYLTLDLPTAPLYKDEKEQLIIPQVPLFNILAKFNGITEKEYKTYKENFLKRFQLTKLPPY LIFCIKRFTKNNFFVEKNPTIVNFPITNVDLREYLSEEVQAVHKNTTYDLIANIVHDGKPSEGS YRIHVLHHGTGKWYELQDLQVTDILPQMITLSEAYIQHMPSLSASAGRTLTDGCLI hide sequence

Ensembl Acc Id:

ENSRNOP00000015563 ⟸ ENSRNOT00000015562

RefSeq Acc Id:	NP_001385670 ⟸ NM_001398741
- Peptide Label:	isoform 2
- UniProtKB:	F7F1N8 (UniProtKB/TrEMBL), B2GV41 (UniProtKB/TrEMBL), A0A9K3Y7X0 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_063141848 ⟸ XM_063285778
- Peptide Label:	isoform X1
- UniProtKB:	A0A9K3Y7X0 (UniProtKB/TrEMBL), B2GV41 (UniProtKB/TrEMBL), F7F1N8 (UniProtKB/TrEMBL)

Protein Domains

UBP-type USP

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-B2GV41-F1-model_v2	AlphaFold	B2GV41	1-564	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13693124

Promoter ID:

EPDNEW_R3649

Type:

initiation region

Name:

Usp39_1

Description:

ubiquitin specific peptidase 39

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	100,207,746 - 100,207,806	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308103	AgrOrtholog
BioCyc Gene	G2FUF-44153	BioCyc
Ensembl Genes	ENSRNOG00000010930	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000015562.7	UniProtKB/TrEMBL
Gene3D-CATH	3.30.40.10	UniProtKB/TrEMBL
	Cysteine proteinases	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7131845	IMAGE-MGC_LOAD
InterPro	Papain_like_cys_pep_sf	UniProtKB/TrEMBL
	Peptidase_C19	UniProtKB/TrEMBL
	Ub_carboxyl-term_hydrolase	UniProtKB/TrEMBL
	UCH/PAN2	UniProtKB/TrEMBL
	USP39	UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/TrEMBL
	Znf_UBP	UniProtKB/TrEMBL
KEGG Report	rno:297336	UniProtKB/TrEMBL
MGC_CLONE	MGC:188093	IMAGE-MGC_LOAD
NCBI Gene	297336	ENTREZGENE
PANTHER	PTHR21646:SF16	UniProtKB/TrEMBL
	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE	UniProtKB/TrEMBL
Pfam	UCH	UniProtKB/TrEMBL
	zf-UBP	UniProtKB/TrEMBL
PhenoGen	Usp39	PhenoGen
PROSITE	UCH_2_3	UniProtKB/TrEMBL
	ZF_UBP	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000010930	RatGTEx
SMART	ZnF_UBP	UniProtKB/TrEMBL
Superfamily-SCOP	RING/U-box	UniProtKB/TrEMBL
	SSF54001	UniProtKB/TrEMBL
UniProt	A0A9K3Y7X0	ENTREZGENE, UniProtKB/TrEMBL
	A6IAA2	ENTREZGENE, UniProtKB/TrEMBL
	B2GV41	ENTREZGENE, UniProtKB/TrEMBL
	F7F1N8	ENTREZGENE
UniProt Secondary	F7F1N8	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-04	Usp39	ubiquitin specific peptidase 39	Usp39_predicted	ubiquitin specific protease 39 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-12	Usp39_predicted	ubiquitin specific protease 39 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)