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Gene: Usp39 (ubiquitin specific peptidase 39) Chinchilla lanigera

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Symbol:

Usp39

Name:

ubiquitin specific peptidase 39

RGD ID:

8900455

Description:

ENCODES a protein that exhibits cysteine-type deubiquitinase activity (ortholog); INVOLVED IN mRNA splicing, via spliceosome (ortholog); spliceosomal complex assembly (ortholog); ASSOCIATED WITH Colonic Neoplasms (ortholog); Experimental Neoplasms (ortholog); hereditary spastic paraplegia 31 (ortholog); FOUND IN nucleoplasm (ortholog); nucleus (ortholog); U4/U6 x U5 tri-snRNP complex (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

U4/U6.U5 tri-snRNP-associated protein 2

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

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

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Usp39	Chinchilla	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	Chinchilla	Colonic Neoplasms		ISO	RGD:1317682	9068941	CTD Direct Evidence: marker/mechanism	CTD	PMID:34822033
Usp39	Chinchilla	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	Chinchilla	mRNA splicing, via spliceosome	involved_in	ISO	RGD:1317682	9068941	PMID:11350945	UniProt	PMID:11350945
Usp39	Chinchilla	spliceosomal complex assembly	involved_in	ISO	RGD:1317682	9068941	PMID:11350945	UniProt	PMID:11350945

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	Chinchilla	nucleoplasm	located_in	ISO	RGD:1317682	9068941		HPA	GO_REF:0000052
Usp39	Chinchilla	nucleus	located_in	ISO	RGD:1317682	9068941	PMID:11350945, PMID:26912367	UniProt	PMID:11350945\|PMID:26912367
Usp39	Chinchilla	U4/U6 x U5 tri-snRNP complex	part_of	ISO	RGD:1317682	9068941	PMID:30975767	ComplexPortal	PMID:30975767
Usp39	Chinchilla	U4/U6 x U5 tri-snRNP complex	part_of	ISO	RGD:1317682	9068941	PMID:11350945, PMID:26912367	UniProt	PMID:11350945\|PMID:26912367

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	Chinchilla	cysteine-type deubiquitinase activity	NOT\|enables	ISO	RGD:1317682	9068941	PMID:18728397	FlyBase	PMID:18728397
Usp39	Chinchilla	protein binding	enables	ISO	UniProtKB:Q5S007	9068941	PMID:29513927, PMID:31046837	IntAct	PMID:29513927\|PMID:31046837
Usp39	Chinchilla	protein binding	enables	ISO	UniProtKB:Q96SB4	9068941	PMID:23602568, PMID:32707033	IntAct	PMID:23602568\|PMID:32707033

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

PMID:22301074

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
(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
(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

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_005385418	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01024249	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDI01219635	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSCLAT00000010046 ⟹ ENSCLAP00000009916

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955424	1,867,850 - 1,894,157 (-)	Ensembl

RefSeq Acc Id:

XM_005385418 ⟹ XP_005385475

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955424	1,867,910 - 1,893,338 (-)	NCBI

Sequence:

show sequence

CTCAAGCGTGCCCGGCGCCTGCGCCGGATCCCTCGGCCGGTAGTAGCGATGTCTAGTCGATCTAAACGGGAGTCTCGTGGTTCCACCCGCGGGAAGCGCGAGTCCGAGTGGCGGAGCAGCTCGGGTCG
CGTGAAGCGGGAGCGAGATCGGGAGCGGGAGCCCGAGGCGCCAGGCTCTCGGGGCAGCCCGGTGCGCGTGAAGCGAGAGGTCGAGCCGGCGAGCGTGCGCGATGTCCCCGCGCCCCCAGTCCCGGCGG
TGCGGGTGAAGCGGGAGCGCGAGGCCGACGAGGACTCGGAGCCCGAGCGGGAGGTGCGAGCGAAGAATGGCCGTGTGGATTCTGAGGACCGGAGGAGCCGCCACTGCCCATACCTGGATACCATTAAC
AGGAGCGTGCTGGATTTTGACTTTGAGAAACTGTGTTCTATCTCCCTCTCGCATATCAATGCATACGCCTGTCTGGTGTGCGGCAAGTACTTTCAAGGCCGGGGCTTGAAGTCTCACGCCTACATTCA
CAGCGTCCAGTTTAGCCACCATGTCTTCTTGAACCTCCACACCCTCAAGTTTTACTGCCTTCCAGACAACTATGAGATCATCGATTCCTCACTGGAGGATATCACGTATGTGTTGAAGCCTACTTTCA
CAAAGCAGCAGATTGCAAACTTGGACAAGCAAGCCAAACTGTCCCGGGCATATGATGGTACCACTTACCTACCGGGTATCGTGGGACTGAATAACATAAAGGCCAACGACTATGCCAATGCTGTCCTT
CAGGCTCTGTCTAATGTTCCTCCCCTCCGGAACTACTTCCTGGAAGAAGATAATTATAAGAACATCAAGCGCCCCCCAGGGGATATCATGTTCCTGCTGGTGCAGCGTTTTGGAGAGCTCATGAGAAA
GCTGTGGAACCCTCGGAATTTTAAGGCGCACGTCTCTCCCCACGAGATGCTTCAGGCTGTTGTCCTTTGTAGCAAAAAGACTTTTCAGATCACCAAACAAGGGGATGGCGTTGACTTCCTGTCTTGGT
TTCTGAATGCCCTGCACTCCGCTCTGGGGGGCACAAAGAAGAAAAAGAAGACGATTGTGACCGATGTTTTCCAAGGGTCCATGAGGATCTTCACTAAAAAGCTTCCCCATCCTGACCTGCCAGCAGAG
GAGAAAGAGCAGCTGCTCCATAATGACGAGTACCAGGAGACAATGGTGGAGTCCACGTTTATGTACCTGACGCTGGACCTCCCTACTGCCCCGCTCTACAAGGATGAGAAGGAGCAGCTTATTATTCC
CCAGGTGCCGCTCTTCAACATCCTGGCCAAGTTCAACGGCATCACGGAGAAGGAGTATAAGACTTACAAAGAGAACTTCCTGAAGCGCTTCCAGCTCACCAAGCTGCCTCCATATCTAATCTTTTGTA
TCAAGAGATTCACTAAGAACAACTTCTTTGTGGAGAAGAATCCAACGATTGTCAACTTCCCTATTACAAACGTGGATCTGAGAGAATACTTGTCTGAAGAAGTGCAAGCAGTCCACAAGAACACCACC
TATGACCTCATCGCCAACATCGTGCACGACGGCAAGCCCTCCGAGGGCTCCTACCGCATCCACGTGCTGCATCACGGCACTGGCAAATGGTACGAATTACAAGACCTCCAGGTGACGGACATCCTGCC
CCAGATGATCACGCTGTCGGAGGCTTACATTCAGATTTGGAAAAGGAGGGATAACGATGAAGTCAACCAGCAGGGGGCTTGAAGGAGGCATCCAGGGCTTCGGCAGGGCGCAGTAAGAATACTGAAGC
TGTCGCTGAGCACAGCCTGACTGCAGATTGCCTGGCTCAGCCCTGTTTTTGTGGGTTCTGCCGACACCAGAGCACTAGAGGGGCCCATCTGCCTGGGATGGCCCTGTGCTGTCCCTGTTTTTCGATCA
GGTTATTGTACATCGACGTCCCTTTCTCCTTCCTGTCTGTCTCCCTTTTAGCTTCAGCACGCAAAACTTTTTCCAGACGGCCGTAATTTATTTCTGTGTAGACTGGCGTATCTCAAGGGCAGACAGCG
TCTTACAGACATCAAGCCTTGGGGTTCTGGGAATAAGAGTGTGAAGACAGTGACGTAAGTCGTCTATTGTAGGAAGATGATTTTCTCTTTCCTTTCATTTCTTGATGTGTTTTTTGAAATGGATTAAA
CATTCTCCTGTTCTTAAA

hide sequence


Protein RefSeqs	XP_005385475	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000009916
	ENSCLAP00000009916.1

RefSeq Acc Id:

XP_005385475 ⟸ XM_005385418

- UniProtKB:

A0A8C2V560 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSSRSKRESRGSTRGKRESEWRSSSGRVKRERDREREPEAPGSRGSPVRVKREVEPASVRDVPAPPVPAVRVKREREADEDSEPEREVRAKNGRVDSEDRRSRHCPYLDTINRSVLDFDFEKLCSISL
SHINAYACLVCGKYFQGRGLKSHAYIHSVQFSHHVFLNLHTLKFYCLPDNYEIIDSSLEDITYVLKPTFTKQQIANLDKQAKLSRAYDGTTYLPGIVGLNNIKANDYANAVLQALSNVPPLRNYFLEE
DNYKNIKRPPGDIMFLLVQRFGELMRKLWNPRNFKAHVSPHEMLQAVVLCSKKTFQITKQGDGVDFLSWFLNALHSALGGTKKKKKTIVTDVFQGSMRIFTKKLPHPDLPAEEKEQLLHNDEYQETMV
ESTFMYLTLDLPTAPLYKDEKEQLIIPQVPLFNILAKFNGITEKEYKTYKENFLKRFQLTKLPPYLIFCIKRFTKNNFFVEKNPTIVNFPITNVDLREYLSEEVQAVHKNTTYDLIANIVHDGKPSEG
SYRIHVLHHGTGKWYELQDLQVTDILPQMITLSEAYIQIWKRRDNDEVNQQGA

hide sequence

Ensembl Acc Id:

ENSCLAP00000009916 ⟸ ENSCLAT00000010046

Protein Domains

UBP-type USP

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000006866	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000010046	ENTREZGENE
	ENSCLAT00000010046.1	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	A0A8C2V560	ENTREZGENE, 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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