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Gene: Trim54 (tripartite motif-containing 54) Rattus norvegicus

Analyze

Symbol:

Trim54

Name:

tripartite motif-containing 54

RGD ID:

1306453

Description:

Predicted to enable microtubule binding activity and ubiquitin protein ligase activity. Predicted to be involved in innate immune response. Predicted to act upstream of or within negative regulation of microtubule depolymerization. Predicted to be located in Z disc and microtubule. Predicted to be part of microtubule associated complex. Predicted to be active in cytoplasm. Orthologous to human TRIM54 (tripartite motif containing 54); INTERACTS WITH 17beta-estradiol; 2,2',5,5'-tetrachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC362708; ring finger protein 30; Rnf30; tripartite motif-containing protein 54

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):	TRIM54 (tripartite motif containing 54)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Trim54 (tripartite motif-containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Trim54 (tripartite motif containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TRIM54 (tripartite motif containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TRIM54 (tripartite motif containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Trim54 (tripartite motif containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TRIM54 (tripartite motif containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	TRIM54 (tripartite motif containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Trim54 (tripartite motif containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Trim54 (tripartite motif containing 54)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	TRIM54 (tripartite motif containing 54)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Trim54 (tripartite motif-containing 54)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	trim54 (tripartite motif containing 54)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	Y47G6A.14	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	trim54	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	30,959,306 - 30,978,475 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	6	30,959,306 - 30,978,475 (-)	Ensembl				GRCr8
mRatBN7.2	6	25,239,340 - 25,258,511 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	25,239,340 - 25,258,511 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	6	25,540,163 - 25,559,346 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	25,856,057 - 25,875,204 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	25,334,941 - 25,354,308 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	26,603,364 - 26,623,950 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	26,603,369 - 26,624,092 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	6	36,419,744 - 36,439,076 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	25,218,008 - 25,237,575 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	24,730,464 - 24,749,611 (-)	NCBI		Celera
RGSC_v3.1	6	25,220,960 - 25,240,528 (-)	NCBI
Cytogenetic Map	6	q14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP,ISO)

2,2',5,5'-tetrachlorobiphenyl (EXP)

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

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

aflatoxin B1 (EXP,ISO)

alpha-Zearalanol (EXP)

amphetamine (EXP)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

beta-lapachone (ISO)

bisphenol A (EXP)

C60 fullerene (EXP)

CGP 52608 (ISO)

chloroprene (EXP)

copper(II) sulfate (ISO)

corticosterone (EXP)

crocidolite asbestos (ISO)

doxorubicin (ISO)

Echimidine (EXP)

endosulfan (EXP)

GW 4064 (ISO)

Heliotrine (EXP)

ketamine (EXP)

mono(2-ethylhexyl) phthalate (ISO)

Muraglitazar (EXP)

N-nitrosodiethylamine (EXP)

naphthalene (ISO)

okadaic acid (ISO)

orphenadrine (EXP)

ozone (EXP)

paracetamol (EXP,ISO)

paraquat (EXP)

PCB138 (EXP)

perfluorooctane-1-sulfonic acid (EXP)

perfluorooctanoic acid (EXP)

pioglitazone (ISO)

rotenone (EXP)

S-nitrosoglutathione (ISO)

sodium arsenite (ISO)

Soman (EXP)

sulforaphane (ISO)

sunitinib (ISO)

Tesaglitazar (EXP)

thiram (ISO)

titanium dioxide (ISO)

trichloroethene (EXP)

valproic acid (EXP,ISO)

zinc atom (EXP)

zinc(0) (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell differentiation (IEA)

innate immune response (IBA)

negative regulation of microtubule depolymerization (ISO)

Cellular Component

cytoplasm (IBA)

cytoskeleton (IEA)

microtubule (IEA)

microtubule associated complex (IEA,ISO)

Z disc (IEA)

Molecular Function

metal ion binding (IEA)

microtubule 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 MGI mouse gene data--August 2006	MGD 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.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:10953002	PMID:15489334	PMID:38042492

Genomics

Comparative Map Data

Trim54
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	30,959,306 - 30,978,475 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	6	30,959,306 - 30,978,475 (-)	Ensembl				GRCr8
mRatBN7.2	6	25,239,340 - 25,258,511 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	25,239,340 - 25,258,511 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	6	25,540,163 - 25,559,346 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	25,856,057 - 25,875,204 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	25,334,941 - 25,354,308 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	26,603,364 - 26,623,950 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	26,603,369 - 26,624,092 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	6	36,419,744 - 36,439,076 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	25,218,008 - 25,237,575 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	24,730,464 - 24,749,611 (-)	NCBI		Celera
RGSC_v3.1	6	25,220,960 - 25,240,528 (-)	NCBI
Cytogenetic Map	6	q14	NCBI

TRIM54
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	27,282,429 - 27,307,435 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	27,282,366 - 27,309,400 (+)	Ensembl			hg38	GRCh38
GRCh37	2	27,505,297 - 27,530,303 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	27,359,104 - 27,383,811 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	2	27,417,250 - 27,441,957	NCBI
Celera	2	27,351,621 - 27,377,411 (+)	NCBI		Celera
Cytogenetic Map	2	p23.3	NCBI
HuRef	2	27,247,000 - 27,272,529 (+)	NCBI		HuRef
CHM1_1	2	27,435,215 - 27,460,253 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	27,322,074 - 27,349,850 (+)	NCBI		T2T-CHM13v2.0

Trim54
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	31,273,956 - 31,294,970 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	31,274,056 - 31,294,974 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	5	31,116,612 - 31,137,626 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	31,116,712 - 31,137,630 (+)	Ensembl			mm10	GRCm38
MGSCv37	5	31,418,985 - 31,439,999 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	5	31,393,293 - 31,414,207 (+)	NCBI		MGSCv36	mm8
Celera	5	28,595,527 - 28,616,535 (+)	NCBI		Celera
Cytogenetic Map	5	B1	NCBI
cM Map	5	17.06	NCBI

Trim54
(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_004955469	9,258,946 - 9,277,275 (+)	Ensembl
ChiLan1.0	NW_004955469	9,258,946 - 9,277,275 (+)	NCBI	ChiLan1.0	ChiLan1.0

TRIM54
(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	99,205,024 - 99,234,825 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	99,208,992 - 99,238,793 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	27,281,950 - 27,309,495 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	27,370,903 - 27,397,214 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	27,370,903 - 27,397,214 (+)	Ensembl			panPan2	panpan1.1

TRIM54
(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	21,257,660 - 21,278,410 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	17	21,257,706 - 21,278,274 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	17	21,149,470 - 21,170,217 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	17	21,578,911 - 21,599,695 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	17	21,578,929 - 21,599,695 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	17	21,265,637 - 21,286,390 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	17	21,276,455 - 21,295,890 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	17	21,323,359 - 21,344,115 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Trim54
(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	65,560,242 - 65,578,438 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936493	5,256,282 - 5,279,022 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936493	5,261,127 - 5,279,040 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TRIM54
(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	111,834,181 - 111,852,744 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	3	111,836,038 - 111,852,468 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

TRIM54
(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	80,305,297 - 80,330,844 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	80,305,727 - 80,330,063 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666045	31,821,234 - 31,847,093 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Trim54
(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_004624738	9,373,017 - 9,392,947 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624738	9,372,535 - 9,393,195 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Trim54
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	7	22,948,052 - 22,966,654 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Trim54
44 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	87
Count of miRNA genes:	74
Interacting mature miRNAs:	77
Transcripts:	ENSRNOT00000008113
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
8552962	Pigfal16	Plasma insulin-like growth factor 1 level QTL 16	9.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	1975879	46975879	Rat
10401812	Kidm54	Kidney mass QTL 54			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	20097635	65097635	Rat
8552910	Pigfal5	Plasma insulin-like growth factor 1 level QTL 5	4.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	22653889	67653889	Rat
10401800	Kidm49	Kidney mass QTL 49			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	20097635	65097635	Rat
1300164	Rf15	Renal function QTL 15	3.12		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	3239989	48239989	Rat
9589129	Insul24	Insulin level QTL 24	19.06	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	6	1975879	46975879	Rat
7411603	Foco13	Food consumption QTL 13	5.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1975879	46975879	Rat
1598843	Cm63	Cardiac mass QTL 63	2.6		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	1	44788383	Rat
7411542	Bw127	Body weight QTL 127	5.5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	1975879	46975879	Rat
2292616	Ept15	Estrogen-induced pituitary tumorigenesis QTL 15	4.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	6	1	44788383	Rat
9589048	Scfw3	Subcutaneous fat weight QTL 3	4.57	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	6	1975879	46975879	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	26618314	86868070	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	20859430	113082285	Rat
2301964	Bp323	Blood pressure QTL 323	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	86868070	Rat
2293709	Bss23	Bone structure and strength QTL 23	5.18	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	6	3239989	48239989	Rat
2293650	Bss31	Bone structure and strength QTL 31	5.05	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	6	3239989	48239989	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	26618314	86868070	Rat
1300128	Rf16	Renal function QTL 16	3.89		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	1	40163351	Rat
1641898	Colcr4	Colorectal carcinoma resistance QTL4	3.71	0.0007	intestine integrity trait (VT:0010554)	well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)	6	30937632	75937632	Rat
70199	Coreg1	Compensatory renal growth QTL 1	11.8		kidney mass (VT:0002707)	compensatory renal growth score (CMO:0001894)	6	14599473	63457687	Rat
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	16089372	61967788	Rat
1358190	Ept1	Estrogen-induced pituitary tumorigenesis QTL 1	4.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	6	1	44788383	Rat
2293656	Bss28	Bone structure and strength QTL 28	6.79	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	6	3239989	48239989	Rat
1359023	Bp272	Blood pressure QTL 272	2.5		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	22288257	32981219	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	22288257	67288257	Rat

Markers in Region

AA800245

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	6	30,959,425 - 30,959,987 (+)	Marker Load Pipeline
mRatBN7.2	6	25,239,459 - 25,240,021 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	26,603,484 - 26,604,045	NCBI	Rnor6.0
Rnor_5.0	6	36,419,864 - 36,420,425	UniSTS	Rnor5.0
RGSC_v3.4	6	25,218,128 - 25,218,689	UniSTS	RGSC3.4
Celera	6	24,730,584 - 24,731,145	UniSTS
Cytogenetic Map	6	q14	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	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
11	12	67	120	80	80	50	21	50	6	220	120	10	93	31	65	30	4	4

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001013217	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC083706	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000008113 ⟹ ENSRNOP00000008113

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	6	30,959,306 - 30,978,475 (-)	Ensembl
mRatBN7.2 Ensembl	6	25,239,340 - 25,258,511 (-)	Ensembl
Rnor_6.0 Ensembl	6	26,603,369 - 26,624,092 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000097701 ⟹ ENSRNOP00000081253

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	25,239,340 - 25,247,870 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000116436 ⟹ ENSRNOP00000078088

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	25,239,836 - 25,258,511 (-)	Ensembl

RefSeq Acc Id:

NM_001013217 ⟹ NP_001013235

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	30,959,306 - 30,978,475 (-)	NCBI
mRatBN7.2	6	25,239,340 - 25,258,511 (-)	NCBI
Rnor_6.0	6	26,603,364 - 26,623,950 (-)	NCBI
Rnor_5.0	6	36,419,744 - 36,439,076 (-)	NCBI
RGSC_v3.4	6	25,218,008 - 25,237,575 (-)	RGD
Celera	6	24,730,464 - 24,749,611 (-)	RGD

Sequence:

show sequence

GGAAATAGCCCAGGGAGAGAGGAGCTGTTAGAGGAAGGGACAGGAAGCACCGCTCTTTCCAGAG
GGAGCAATATCAGGGATCCCAAGAATCTACAGTCAGCCTAAACTGACAGCGGAAGGGCGCGCAG
GCAGGGGGAGAGAAGGCCAGCAACAGGGCCACAGCAAGGCACCAGAGCACCGCGGGATGAACTT
CACGGTGGGTTTCAAGCCGCTGCTGGGGGATGCACACAACATGGACAACCTGGAGAAGCAGCTC
ATCTGCCCCATCTGCCTGGAGATGTTCTCCAAGCCCGTGGTGATCTTGCCGTGCCAACACAACC
TGTGCCGCAAGTGTGCCAACGACGTCTTCCAGGCCTCTAACCCTCTGTGGCAATCCCGGGGCTC
CACAACTGTGTCTTCAGGAGGACGTTTCCGCTGCCCATCTTGTAGGCACGAGGTTGTCCTGGAC
CGGCATGGCGTCTACGGCCTGCAGCGGAACCTGCTAGTGGAGAATATTATTGACATCTACAAAC
AGGAGTCCTCCCGGCCACTGCACTCCAAGGCTGAACAGCACCTTATGTGTGAGGAACATGAAGA
CGAGAAGATTAACATCTACTGTCTGAGCTGTGAGGTGCCCACCTGCTCTCTCTGCAAGGTCTTT
GGCGCCCACAAGGACTGTGAGGTGGCCCCTCTGCCCACCATTTACAAACGCCAGAAGAGTGAGC
TGAGTGACGGCATCGCGATGCTGGTGGCAGGCAACGACCGTGTGCAGGCAGTGATCACGCAGAT
GGAGGAGGTGTGCCAGACCATTGAGGACAACAGCCGCAGACAGAAACAACTGTTAAACCAGAAG
TTCGAGACCCTGTGCGCGGTTTTGGAGGAGCGCAAGGGCGAGTTGCTTCAAGCGCTGGCTCGGG
TGCAAGAGGAGAAGCTGCAGCGCGTGCGTAGCCTCATCCGCCAGTACGGAGACCACTTGGAGGC
CTCCTCTAAGCTGGTGGAGTCCGCCATCCAGTCCATGGAGGAGCCGCAGATGGCTCTCTACCTC
CAGCAGGCCAAGGAGCTGATCAACAAGGTCGGGGCAATGTCGAAGGTGGAGCTGGCTGGACGGC
CGGAGCCAGGCTATGAGAGCATGGAGCAATTCTCTGTGATCGTGGAGCACGTGGCGGAAATGTT
GCGGACCATCGACTTCCAGCCGGGCGCCTCTGGGGATGAAGAGGATGACGAGGTGACTTTGGAC
GGGGAAGAGGGCAACACAGGGCTGGAGGAGGAGCGGCTGGACGGGCCAGAAGGTTTGCACTGAT
CCGACTCTGATCCAGAGCGCACGCCCGGGAGCCAAGGGATGCTGAGGATCTGCGCAGAGACCAT
CGCGCTACCCATCTCGGCCTCCACCCCCAGGGATGGTTCTCAATAAAGAACTCATGTGTCCCAC
GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001013235	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH83706	(Get FASTA)	NCBI Sequence Viewer
	EDM02931	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000008113
	ENSRNOP00000008113.5
GenBank Protein	Q5XIH6	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001013235 ⟸ NM_001013217

- UniProtKB:

Q5XIH6 (UniProtKB/Swiss-Prot), A6HA76 (UniProtKB/TrEMBL), A0A8I5Y850 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MNFTVGFKPLLGDAHNMDNLEKQLICPICLEMFSKPVVILPCQHNLCRKCANDVFQASNPLWQS
RGSTTVSSGGRFRCPSCRHEVVLDRHGVYGLQRNLLVENIIDIYKQESSRPLHSKAEQHLMCEE
HEDEKINIYCLSCEVPTCSLCKVFGAHKDCEVAPLPTIYKRQKSELSDGIAMLVAGNDRVQAVI
TQMEEVCQTIEDNSRRQKQLLNQKFETLCAVLEERKGELLQALARVQEEKLQRVRSLIRQYGDH
LEASSKLVESAIQSMEEPQMALYLQQAKELINKVGAMSKVELAGRPEPGYESMEQFSVIVEHVA
EMLRTIDFQPGASGDEEDDEVTLDGEEGNTGLEEERLDGPEGLH

hide sequence

Ensembl Acc Id:

ENSRNOP00000008113 ⟸ ENSRNOT00000008113

Ensembl Acc Id:

ENSRNOP00000081253 ⟸ ENSRNOT00000097701

Ensembl Acc Id:

ENSRNOP00000078088 ⟸ ENSRNOT00000116436

Protein Domains

B box-type COS RING-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5XIH6-F1-model_v2	AlphaFold	Q5XIH6	1-364	view protein structure

Transcriptome

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

Promoters

RGD ID:

13694447

Promoter ID:

EPDNEW_R4970

Type:

multiple initiation site

Name:

Trim54_1

Description:

tripartite motif-containing 54

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	6	26,624,063 - 26,624,123	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1306453	AgrOrtholog
BioCyc Gene	G2FUF-38345	BioCyc
Ensembl Genes	ENSRNOG00000006146	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000008113	ENTREZGENE
	ENSRNOT00000008113.7	UniProtKB/Swiss-Prot
Gene3D-CATH	1.20.5.170	UniProtKB/Swiss-Prot
	3.30.40.10	UniProtKB/Swiss-Prot
	Classic Zinc Finger	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7190356	IMAGE-MGC_LOAD
InterPro	COS_domain	UniProtKB/Swiss-Prot
	TRIM/RBCC	UniProtKB/Swiss-Prot
	TRIM54/TRIM55	UniProtKB/Swiss-Prot
	TRIM54_RING-HC	UniProtKB/Swiss-Prot
	Znf-RING_LisH	UniProtKB/Swiss-Prot
	Znf_B-box	UniProtKB/Swiss-Prot
	Znf_RING	UniProtKB/Swiss-Prot
	Znf_RING/FYVE/PHD	UniProtKB/Swiss-Prot
	Znf_RING_CS	UniProtKB/Swiss-Prot
KEGG Report	rno:362708	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:94590	IMAGE-MGC_LOAD
NCBI Gene	362708	ENTREZGENE
PANTHER	E3 UBIQUITIN-PROTEIN LIGASE TRIM	UniProtKB/Swiss-Prot
Pfam	zf-B_box	UniProtKB/Swiss-Prot
	zf-RING_UBOX	UniProtKB/Swiss-Prot
PhenoGen	Trim54	PhenoGen
PROSITE	COS	UniProtKB/Swiss-Prot
	ZF_BBOX	UniProtKB/Swiss-Prot
	ZF_RING_1	UniProtKB/Swiss-Prot
	ZF_RING_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000006146	RatGTEx
SMART	BBOX	UniProtKB/Swiss-Prot
	RING	UniProtKB/Swiss-Prot
Superfamily-SCOP	B-box zinc-binding domain	UniProtKB/Swiss-Prot
	RING/U-box	UniProtKB/Swiss-Prot
UniProt	A0A8I5Y850	ENTREZGENE
	A6HA76	ENTREZGENE, UniProtKB/TrEMBL
	Q5XIH6	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2006-03-30	Trim54	tripartite motif-containing 54	Rnf30	ring finger protein 30	Symbol and Name updated	1299863	APPROVED
2005-12-06	Rnf30	ring finger protein 30	Rnf30_predicted	ring finger protein 30 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Rnf30_predicted	ring finger protein 30 (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)

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