Trim39 (tripartite motif-containing 39)

Gene: Trim39 (tripartite motif-containing 39) Rattus norvegicus

Analyze

Symbol:

Trim39

Name:

tripartite motif-containing 39

RGD ID:

1303115

Description:

Predicted to enable identical protein binding activity and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle phase transition; and regulation of signal transduction. Predicted to be located in mitochondrion and nucleus. Predicted to be active in cytosol. Orthologous to human TRIM39 (tripartite motif containing 39); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

E3 ubiquitin-protein ligase TRIM39; RING finger protein 23; RING-type E3 ubiquitin transferase TRIM39; Rnf23; tripartite motif protein 39; tripartite motif-containing protein 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):	TRIM39 (tripartite motif containing 39)	HGNC	Ensembl, HomoloGene, Inparanoid, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Trim39 (tripartite motif-containing 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TRIM39 (tripartite motif containing 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TRIM39 (tripartite motif containing 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	TRIM39 (tripartite motif containing 39)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Trim39 (tripartite motif-containing 39)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	btr02 (bloodthirsty-related gene family, member 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA)
Danio rerio (zebrafish):	btr26 (bloodthirsty-related gene family, member 26)	Alliance	DIOPT (Hieranoid\|OMA\|OrthoInspector\|SonicParanoid)
Danio rerio (zebrafish):	btr30 (bloodthirsty-related gene family, member 30)	Alliance	DIOPT (Hieranoid\|OMA\|PhylomeDB)
Caenorhabditis elegans (roundworm):	B0281.8	Alliance	DIOPT (Ensembl Compara\|InParanoid)
Caenorhabditis elegans (roundworm):	ZK1240.5	Alliance	DIOPT (Ensembl Compara\|InParanoid)
Caenorhabditis elegans (roundworm):	ZK1240.9	Alliance	DIOPT (Ensembl Compara\|InParanoid)
Caenorhabditis elegans (roundworm):	nhl-3	Alliance	DIOPT (Ensembl Compara\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ZK1240.8	Alliance	DIOPT (Ensembl Compara\|InParanoid)
Caenorhabditis elegans (roundworm):	ZK1240.3	Alliance	DIOPT (Ensembl Compara\|InParanoid)

Related Pseudogenes:

Trim39-ps

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	20	2,008,528 - 2,022,383 (+)	NCBI		GRCr8
mRatBN7.2	20	2,003,320 - 2,017,175 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	1,983,533 - 2,020,117 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	20	2,043,510 - 2,057,364 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	2,047,022 - 2,060,876 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	2,000,908 - 2,014,763 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	20	2,500,691 - 2,514,546 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	2,500,689 - 2,514,546 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	20	4,530,743 - 4,544,598 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	2,091,969 - 2,105,824 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	20	2,091,968 - 2,105,824 (+)	NCBI
Celera	20	2,710,987 - 2,724,842 (+)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

megacolon (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-methylcholine (ISO)

3-methylcholanthrene (ISO)

6-propyl-2-thiouracil (EXP)

acrolein (ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

amitrole (EXP)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenous acid (ISO)

benzene (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (EXP)

carbon nanotube (ISO)

copper atom (EXP)

copper(0) (EXP)

cyclosporin A (ISO)

diarsenic trioxide (ISO)

Dibutyl phosphate (ISO)

endosulfan (EXP)

furan (EXP)

ketamine (EXP)

metformin (ISO)

methimazole (EXP)

methyl methanesulfonate (ISO)

ozone (ISO)

paracetamol (ISO)

perfluorohexanesulfonic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

pirinixic acid (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

temozolomide (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

trovafloxacin (ISO)

tungsten (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

apoptotic process (IEA)

mitotic G2 DNA damage checkpoint signaling (IEA,ISO,ISS)

negative regulation of canonical NF-kappaB signal transduction (IEA,ISO,ISS)

negative regulation of proteasomal ubiquitin-dependent protein catabolic process (IBA,IEA,ISO,ISS)

negative regulation of ubiquitin-dependent protein catabolic process (ISO)

phosphorelay signal transduction system (IEA)

positive regulation of apoptotic signaling pathway (IBA,IEA,ISO)

protein stabilization (IBA,IEA,ISO,ISS)

protein ubiquitination (IBA,IEA)

regulation of cell cycle G1/S phase transition (IEA,ISO,ISS)

Cellular Component

cytoplasm (IBA)

cytosol (IBA,IEA,ISO)

mitochondrion (IEA,ISO)

nucleus (IEA,ISO,ISS)

Molecular Function

identical protein binding (IEA,ISO)

protein binding (ISO)

ubiquitin protein ligase activity (IBA)

zinc ion binding (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	GOA pipeline	RGD automated data pipeline
4.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
6.	Information Derived from GenBank Report	RGD, Sept. 2003

Additional References at PubMed

PMID:15060004	PMID:16189514	PMID:19100260	PMID:21516116	PMID:22493164	PMID:23213251	PMID:25416956	PMID:26363554

Genomics

Comparative Map Data

Trim39
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	20	2,008,528 - 2,022,383 (+)	NCBI		GRCr8
mRatBN7.2	20	2,003,320 - 2,017,175 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	1,983,533 - 2,020,117 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	20	2,043,510 - 2,057,364 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	2,047,022 - 2,060,876 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	2,000,908 - 2,014,763 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	20	2,500,691 - 2,514,546 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	2,500,689 - 2,514,546 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	20	4,530,743 - 4,544,598 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	2,091,969 - 2,105,824 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	20	2,091,968 - 2,105,824 (+)	NCBI
Celera	20	2,710,987 - 2,724,842 (+)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

TRIM39
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	30,326,469 - 30,343,729 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	30,326,479 - 30,343,729 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	30,294,246 - 30,311,506 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	30,403,019 - 30,419,485 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	6	30,403,018 - 30,419,484	NCBI
Celera	6	31,892,811 - 31,909,701 (+)	NCBI		Celera
Cytogenetic Map	6	p22.1	NCBI
HuRef	6	30,092,745 - 30,109,636 (+)	NCBI		HuRef
CHM1_1	6	30,296,698 - 30,313,590 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	6	30,190,674 - 30,207,940 (+)	NCBI		T2T-CHM13v2.0

Trim39
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	36,569,764 - 36,582,896 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	36,569,765 - 36,583,139 (-)	Ensembl		GRCm39 Ensembl
GRCm38	17	36,258,872 - 36,272,004 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	36,258,873 - 36,272,247 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	36,395,818 - 36,408,949 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	35,866,925 - 35,880,057 (-)	NCBI		MGSCv36	mm8
Celera	17	39,731,391 - 39,744,522 (-)	NCBI		Celera
Cytogenetic Map	17	B1	NCBI
cM Map	17	19.01	NCBI

TRIM39
(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	5	44,919,935 - 44,937,249 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	40,882,956 - 40,900,270 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	30,104,381 - 30,121,649 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	30,975,260 - 30,992,628 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	30,975,260 - 30,995,764 (+)	Ensembl	panpan1.1		panPan2

TRIM39
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	23,047,520 - 23,062,487 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	23,047,048 - 23,062,974 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	26,716,866 - 26,733,939 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Variants

Variants in Trim39
7 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	126
Count of miRNA genes:	110
Interacting mature miRNAs:	113
Transcripts:	ENSRNOT00000001021
Prediction methods:	Miranda, Rnahybrid
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
724519	Bp144	Blood pressure QTL 144		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	20	1	3624629	Rat
1354642	Despr15	Despair related QTL 15		0.0027	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	20	1	24159021	Rat
1600382	Edcs3	Endometrial carcinoma susceptibility QTL3	3.5	0.003	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	20	1	25159026	Rat
2317851	Alcrsp22	Alcohol response QTL 22	3.2	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	27339237	Rat
1641893	Alcrsp7	Alcohol response QTL 7			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	27339237	Rat
8694189	Bw153	Body weight QTL 153	3.13	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	20	1	29191651	Rat
9590275	Scort15	Serum corticosterone level QTL 15	3.48	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	29191651	Rat
7411650	Foco23	Food consumption QTL 23	20.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	29191651	Rat
9590109	Sffal8	Serum free fatty acids level QTL 8	5.32	0.01	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	20	1	29191651	Rat
9589155	Insul32	Insulin level QTL 32	6.38	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	29191651	Rat
6893685	Bw111	Body weight QTL 111	2.7	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	20	1	32578807	Rat
7411668	Foco32	Food consumption QTL 32	8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	36600972	Rat
9590252	Scort12	Serum corticosterone level QTL 12	20.46	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	36600972	Rat
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	1527842	46527842	Rat
2306850	Pia40	Pristane induced arthritis QTL 40		0.0001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	1527959	5304575	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	1530655	46530655	Rat

Markers in Region

RH137959

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	2,005,768 - 2,005,957 (+)	MAPPER	mRatBN7.2
Rnor_6.0	20	2,503,140 - 2,503,328	NCBI	Rnor6.0
Rnor_5.0	20	4,533,192 - 4,533,380	UniSTS	Rnor5.0
RGSC_v3.4	20	2,094,418 - 2,094,606	UniSTS	RGSC3.4
Celera	20	2,713,436 - 2,713,624	UniSTS
RH 3.4 Map	20	15.8	UniSTS
Cytogenetic Map	20	p12	UniSTS

BF415953

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	2,016,686 - 2,016,818 (+)	MAPPER	mRatBN7.2
Rnor_6.0	20	2,514,058 - 2,514,189	NCBI	Rnor6.0
Rnor_5.0	20	4,544,110 - 4,544,241	UniSTS	Rnor5.0
RGSC_v3.4	20	2,105,336 - 2,105,467	UniSTS	RGSC3.4
Celera	20	2,724,354 - 2,724,485	UniSTS
RH 3.4 Map	20	21.9	UniSTS
Cytogenetic Map	20	p12	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2	2	14	4	19	4			65	18	38	11
Low	1	41	43	37		37	8	11	9	17	3		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_213562	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601635	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601636	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC120486	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BX883050	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474093	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000020	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000001021 ⟹ ENSRNOP00000001021

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	2,003,862 - 2,016,953 (+)	Ensembl
Rnor_6.0 Ensembl	20	2,500,689 - 2,514,546 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000077291

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	2,501,252 - 2,503,330 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000079307 ⟹ ENSRNOP00000068699

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	2,501,252 - 2,505,315 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000084559 ⟹ ENSRNOP00000069344

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	2,003,320 - 2,013,052 (+)	Ensembl
Rnor_6.0 Ensembl	20	2,501,292 - 2,509,888 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000086884

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	2,501,292 - 2,511,032 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000087695 ⟹ ENSRNOP00000074583

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	2,004,128 - 2,020,117 (+)	Ensembl
Rnor_6.0 Ensembl	20	2,503,134 - 2,510,593 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000091981

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	2,505,240 - 2,510,468 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000092094 ⟹ ENSRNOP00000073185

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	2,503,401 - 2,513,427 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000098868 ⟹ ENSRNOP00000083277

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	1,983,533 - 2,012,274 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000118924 ⟹ ENSRNOP00000094860

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	1,983,533 - 2,017,175 (+)	Ensembl

RefSeq Acc Id:

NM_213562 ⟹ NP_998727

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	2,008,528 - 2,022,383 (+)	NCBI
mRatBN7.2	20	2,003,320 - 2,017,175 (+)	NCBI
Rnor_6.0	20	2,500,691 - 2,514,546 (+)	NCBI
Rnor_5.0	20	4,530,743 - 4,544,598 (+)	NCBI
RGSC_v3.4	20	2,091,969 - 2,105,824 (+)	RGD
Celera	20	2,710,987 - 2,724,842 (+)	RGD

Sequence:

show sequence

GGATAGGGCGCACCTCGGTCCACAGCCAAGATAACTTACCTACTACCGCTTCACCGTAAGCTAA
ATGCTAAACCTTAGCCAGTCGGAAGTGACGTGCAACACGGCCTCTCAGTTATAATGGCAGAGAC
AAGTCTGTTAGAGGCTGGAGCCTCTGCAGCCTCCACAGCCGCTGCTCTGGAGAACTTGCAGGTA
GAGGCAAGCTGTTCTGTGTGCCTGGAGTACCTGAAGGAGCCGGTTATCATTGAATGTGGGCACA
ACTTCTGCAAAGCGTGTATTACCCGCTGGTGGGAGGACCTAGAGCGGGACTTCCCTTGCCCTGT
CTGTCGGAAGACATCCCGATACCGGAGCCTCAGGCCTAACCGACAGCTAGGCAGCATGGTGGAA
ATAGCCAAGCAGCTCCAGACGGTCAAGCGGAAGATCAGAGACGAAAGCCTCTGCTCCCAGCACC
ATGAACCCCTTAGCCTTTTCTGCTACGAAGACCAGGAGGCTGTCTGTCTGATATGTGCAATTTC
CCATACCCACCGGGCCCATACGGTCGTGCCGATGGACGATGCTACACAGGAGTACAAGGAGAAA
CTTCAGAAGTGCCTGGAGCCCCTGGAACAGAAGCTGCAGGAGATCACCTGCTGCAAAGCCTCAG
AAGAAAGGAAACCAGGGGAACTCAAGAGACTGGTAGAGAGCCGCCGGCAGCAGATCCTAAAGGA
GTTTGAGGAGCTGCACAGGCGACTGGACGAGGAACAGCAGACGCTGCTCTCCCGGCTGGAGGAG
GAAGAACAGGACATTCTACAGAGACTTCGAGAAAACGCTGCTCACCTTGGGGATAGGCGCCGGG
ACCTTGCCCACTTAGCTGCTGAGGTGGAGGGCAAGTGCTTACAGTCAGGCTTCGAGATGCTTAA
GGATGTGAAAAGTACCCTAGAAAAATGTGAGAAGGTGAAGACCATGGAGGTGACTTCAGTATCT
ATAGAGCTGGAAAAGAACTTCAGCCATTTCCCCCGGCAGTACTTTGCCCTAAGGAAAATTCTTA
AACAGCTAATTGCGGATGTGACCCTGGACCCTGAGACGGCTCATCCTAACCTTGTCCTGTCAGA
GGATCGGAAAAGTGTCAAGTTTGTGGAGACAAGACTCCGAGACCTCCCTGACACACCACAGCGT
TTCACTTTCTACCCTTGTGTCTTAGCTACTGAAGGCTTCACCTCAGGTCGACACTACTGGGAGG
TGGAGGTGGGTGACAAGACCCACTGGGCAGTAGGAGTATGCCGGGACTCTGTGAGCAGGAAGGG
TGAACTGACTCCACTCCCGGAGACTGGCTACTGGCGTGTTCGGCTGTGGAATGGGGACAAGTAT
GCAGCCACCACCACGCCTTTTACCCCTTTGCACATCAAGGTGAAACCTAAGCGGGTAGGCATAT
TCCTAGACTATGAGGCTGGCACACTGTCTTTTTACAACGTCACAGACCGCTCACATATCTACAC
CTTCACTGATACTTTCACTGAAAAACTTTGGCCCCTCTTCTACCCAGGGATCCGAGCCGGTCGG
AAGAATGCTGCACCACTTACCATCAGACCCCCAACGGATTGGGAATGACAAGAGATGCAGTTGA
ATTGGGGTGAGGCAGGGTCAAGAGCAGCGGGCCTTCCTAACTGGCCCACTGGAAAACCTTGGTG
TCTGCGTGGTTCCAGTCTTGAGCCATCTTGAGAAACCACCTCGTCTGTGGGATGGTTTGTGTGA
AGGAGAAAGATAGGACTGGGCTGCATGACCAAGCACAGATGTGTCTCCCTCCTAACTAGTGGGA
GTGTGGACTCCCAGGGTCCAGGTTTCCTAGTGCACAAGGACAGGTTGAGAAAGAAAAGGCTTTT
CCAGAAACCAAGTCTATTGGAAAGGGTCTTAATTTGCTTAAAATGCAGGGAACAGAAACCTTTA
AAAGGCTTCTATGACTCAGAATAGCCTTGTTCTTGTGGAAGTGCGTAGGGATCTGTACACATAC
CTCTGTGTGGAAGATGAGTGGCAGTGGCTGTCATGAGTCTAGGAGTTGAGGGGCTTTTCTGGGG
GCAGAGATTGAGCATTAAAGTTAGGAGAGGAATCAGGGAAAAGGCTGAAGGAGTGTTTCTAGAA
ATGAATGAAGGGAACGGGGATTTCTTTGATCTCTTTTCTTAGGGTAATGTTAATCATTACCCTT
AGGATTAGCCAGAGGTTCAGATCTGGGAGAAGGAAAGGGTGGGAAGAAAGGAGAATCCGTGTCC
CAAAGGCTTGGGTTATTCCTGGTTCCTGCAGTTGGCTGTCTCTAAAAAGTAGGCTCCTCTCGTT
CCCTTCTAAAGGTGAGATGGAAGCGATTCTGCAAGACACACATCTGCCCTTCCATTGTTCCCAA
GGCAACTTGGAGAGGAGTCAGATGTTAAAGGAGACAGAACGGTGTAGCCAAAGCTCTGGCCTTA
AAGAATGTTACTAAGTTGTCCACCTTGTCCCCTGGCTCAAATGTCTAAGGAAAGAAGGGAAGAT
AATGGAGTCTTCCTCACCCCACGACAGCAGGGTAGAAGAGGGTGGTTTGTGTTACAAAGGGCCA
GATGACGGCTAAGCCTCTGTTTCCATCCTCCACCCTTTGACATTCCCCTTTTCAGAGAATGTAA
ATTATCTTAATTTTAGGCCAAAATAAACGACCCATAGGGTACATATTTTGTCACAAAAGGTAAC
GTGATGCATGCCAAACCAAACAGCCTGGATTATCTGCTGCCTGGGTAATCTTCACACAAGACTG
AGACAAGAAACTGCATTGAGGGTATTCAGTTCCTCCTACCACCTCAACAGGACTTTGTCCACTC
TCCTCTTACCTTTGTGCCTTGACTGTGGTTCTTTGTGGCAAGATAATTTGGTTGGTGAAAATAT
GGAACAAAGGATCCACTAATGTGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_998727	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	CAE84052	(Get FASTA)	NCBI Sequence Viewer
	EDL84593	(Get FASTA)	NCBI Sequence Viewer
	EDL84594	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000001021.4
	ENSRNOP00000069344.2
	ENSRNOP00000074583.2
	ENSRNOP00000083277.1
	ENSRNOP00000094860
	ENSRNOP00000094860.1
	ENSRNOP00055012419
	ENSRNOP00060004161
	ENSRNOP00065042001
GenBank Protein	Q6MFZ5	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_998727 ⟸ NM_213562

- UniProtKB:

Q6MFZ5 (UniProtKB/Swiss-Prot), A6KR95 (UniProtKB/TrEMBL), A0A8L2PYM6 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAETSLLEAGASAASTAAALENLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDF
PCPVCRKTSRYRSLRPNRQLGSMVEIAKQLQTVKRKIRDESLCSQHHEPLSLFCYEDQEAVCLI
CAISHTHRAHTVVPMDDATQEYKEKLQKCLEPLEQKLQEITCCKASEERKPGELKRLVESRRQQ
ILKEFEELHRRLDEEQQTLLSRLEEEEQDILQRLRENAAHLGDRRRDLAHLAAEVEGKCLQSGF
EMLKDVKSTLEKCEKVKTMEVTSVSIELEKNFSHFPRQYFALRKILKQLIADVTLDPETAHPNL
VLSEDRKSVKFVETRLRDLPDTPQRFTFYPCVLATEGFTSGRHYWEVEVGDKTHWAVGVCRDSV
SRKGELTPLPETGYWRVRLWNGDKYAATTTPFTPLHIKVKPKRVGIFLDYEAGTLSFYNVTDRS
HIYTFTDTFTEKLWPLFYPGIRAGRKNAAPLTIRPPTDWE

hide sequence

RefSeq Acc Id:

ENSRNOP00000068699 ⟸ ENSRNOT00000079307

RefSeq Acc Id:

ENSRNOP00000073185 ⟸ ENSRNOT00000092094

RefSeq Acc Id:

ENSRNOP00000069344 ⟸ ENSRNOT00000084559

RefSeq Acc Id:

ENSRNOP00000074583 ⟸ ENSRNOT00000087695

RefSeq Acc Id:

ENSRNOP00000001021 ⟸ ENSRNOT00000001021

RefSeq Acc Id:

ENSRNOP00000083277 ⟸ ENSRNOT00000098868

RefSeq Acc Id:

ENSRNOP00000094860 ⟸ ENSRNOT00000118924

Protein Domains

B box-type B30.2/SPRY HPt RING-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q6MFZ5-F1-model_v2	AlphaFold	Q6MFZ5	1-488	view protein structure

Transcriptome

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

Promoters

RGD ID:

13701280

Promoter ID:

EPDNEW_R11802

Type:

single initiation site

Name:

Trim39_1

Description:

tripartite motif-containing 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	20	2,501,315 - 2,501,375	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1303115	AgrOrtholog
BioCyc Gene	G2FUF-4941	BioCyc
Ensembl Genes	ENSRNOG00000000785	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOG00055009162	UniProtKB/Swiss-Prot
	ENSRNOG00060003475	UniProtKB/Swiss-Prot
	ENSRNOG00065029568	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000001021.6	UniProtKB/TrEMBL
	ENSRNOT00000084559.2	UniProtKB/TrEMBL
	ENSRNOT00000087695.2	UniProtKB/TrEMBL
	ENSRNOT00000098868.1	UniProtKB/TrEMBL
	ENSRNOT00000118924	ENTREZGENE
	ENSRNOT00000118924.1	UniProtKB/TrEMBL
	ENSRNOT00055015504	UniProtKB/Swiss-Prot
	ENSRNOT00060005703	UniProtKB/Swiss-Prot
	ENSRNOT00065051056	UniProtKB/Swiss-Prot
Gene3D-CATH	2.60.120.920	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	3.30.40.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Classic Zinc Finger	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	B30.2/SPRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	B30.2/SPRY_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Butyrophylin_SPRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ConA-like_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PRY/SPRY_TRIM39	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Sig_transdc_His_kin_Hpt_dom	UniProtKB/TrEMBL
	SPRY_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_B-box	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_RING	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Znf_RING_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:309591	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	309591	ENTREZGENE
PANTHER	E3 UBIQUITIN-PROTEIN LIGASE TRIM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	E3 UBIQUITIN-PROTEIN LIGASE TRIM39	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SPRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	zf-B_box	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	zf-C3HC4_4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Trim39	PhenoGen
PRINTS	BUTYPHLNCDUF	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	B302_SPRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HPT	UniProtKB/TrEMBL
	ZF_BBOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ZF_RING_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ZF_RING_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000000785	RatGTEx
	ENSRNOG00055009162	RatGTEx
	ENSRNOG00060003475	RatGTEx
	ENSRNOG00065029568	RatGTEx
SMART	BBOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	RING	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SPRY	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	B-box zinc-binding domain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	RING/U-box	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SSF49899	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JV44_RAT	UniProtKB/TrEMBL
	A0A0G2K8F1_RAT	UniProtKB/TrEMBL
	A0A8I5ZVL9_RAT	UniProtKB/TrEMBL
	A0A8I6GLC5_RAT	UniProtKB/TrEMBL
	A0A8L2PYM6	ENTREZGENE, UniProtKB/TrEMBL
	A6KR95	ENTREZGENE, UniProtKB/TrEMBL
	Q6MFZ5	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-31	Trim39	tripartite motif-containing 39	Trim39	tripartite motif protein 39	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-02-14	Trim39	tripartite motif protein 39			Symbol and Name status set to provisional	70820	PROVISIONAL

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)

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Imported Disease Annotations - ClinVar