Trim28 (tripartite motif-containing 28)

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Gene: Trim28 (tripartite motif-containing 28) Rattus norvegicus

Analyze

Symbol:

Trim28

Name:

tripartite motif-containing 28

RGD ID:

620289

Description:

Predicted to enable several functions, including promoter-specific chromatin binding activity; protein domain specific binding activity; and ubiquitin-like protein transferase activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of DNA methylation-dependent heterochromatin assembly; and regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within several processes, including negative regulation of nucleobase-containing compound metabolic process; negative regulation of single stranded viral RNA replication via double stranded DNA intermediate; and regulation of genetic imprinting. Predicted to be located in euchromatin; heterochromatin; and nucleus. Predicted to be part of RNA polymerase II transcription regulator complex. Predicted to be active in chromatin and nucleoplasm. Orthologous to human TRIM28 (tripartite motif containing 28); PARTICIPATES IN p53 signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

E3 SUMO-protein ligase TRIM28; Kap1; KRAB-associated protein 1; Krip1; nuclear corepressor KAP-1; RING-type E3 ubiquitin transferase TIF1-beta; TIF1-beta; Tif1b; transcription intermediary factor 1-beta; tripartite motif protein 28; tripartite motif-containing protein 28

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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):	TRIM28 (tripartite motif containing 28)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Trim28 (tripartite motif-containing 28)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Trim28 (tripartite motif containing 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TRIM28 (tripartite motif containing 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TRIM28 (tripartite motif containing 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Trim28 (tripartite motif containing 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TRIM28 (tripartite motif containing 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	TRIM28 (tripartite motif containing 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Trim28 (tripartite motif containing 28)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	TRIM28 (tripartite motif containing 28)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Mus musculus (house mouse):	Trim28 (tripartite motif-containing 28)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Drosophila melanogaster (fruit fly):	bon	Alliance	DIOPT (InParanoid\|OrthoInspector\|PANTHER\|PhylomeDB)

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
mRatBN7.2	1	73,652,441 - 73,659,388 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	1	73,652,709 - 73,659,380 (+)	Ensembl
Rnor_6.0	1	65,544,369 - 65,551,043 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	65,544,373 - 65,551,043 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	66,355,602 - 66,362,276 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	72,892,399 - 72,899,070 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	72,973,571 - 72,973,906 (-)	NCBI
Celera	1	60,180,424 - 60,187,048 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

atherosclerosis (ISO)

Colorectal Neoplasms (ISO)

nephroblastoma (ISO)

prostate cancer (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

(S)-nicotine (ISO)

1,2-dimethylhydrazine (ISO)

1,4-dichlorobenzene (ISO)

1-chloro-2,4-dinitrobenzene (ISO)

17alpha-ethynylestradiol (EXP)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (ISO)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-amino-14,16-dimethyloctadecan-3-ol (ISO)

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

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

aphidicolin (ISO)

aristolochic acid (ISO)

arsenite(3-) (ISO)

benzatropine (ISO)

bisphenol A (EXP,ISO)

bleomycin A2 (ISO)

C60 fullerene (EXP)

caffeine (ISO)

camptothecin (ISO)

cannabidiol (ISO)

captan (ISO)

chromium(6+) (ISO)

cisplatin (ISO)

clofibrate (ISO)

clozapine (ISO)

cocaine (EXP)

Cuprizon (ISO)

deoxynivalenol (ISO)

diazinon (ISO)

dibutyl phthalate (ISO)

dicrotophos (ISO)

diethylstilbestrol (EXP)

doxorubicin (ISO)

elemental selenium (ISO)

enzyme inhibitor (ISO)

ethanol (ISO)

folic acid (ISO)

folpet (ISO)

gentamycin (EXP)

haloperidol (ISO)

hydrogen peroxide (ISO)

ivermectin (ISO)

L-ascorbic acid (ISO)

lead(0) (ISO)

lead(2+) (ISO)

methotrexate (ISO)

methyl methanesulfonate (ISO)

miconazole (ISO)

N-acetyl-L-cysteine (ISO)

nicotine (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

pirinixic acid (ISO)

piroxicam (ISO)

potassium chromate (ISO)

resveratrol (ISO)

selenium atom (ISO)

sodium dichromate (ISO)

tetrachloromethane (ISO)

thimerosal (ISO)

thioacetamide (EXP)

trichloroethene (ISO)

uranium atom (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chromatin organization (IEA)

convergent extension involved in axis elongation (ISO)

DNA methylation involved in embryo development (ISO)

DNA repair (ISO)

embryo implantation (ISO)

embryonic placenta morphogenesis (ISO)

epithelial to mesenchymal transition (ISO,ISS)

in utero embryonic development (ISO)

innate immune response (IBA,ISO)

negative regulation of DNA demethylation (ISO)

negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

negative regulation of transcription, DNA-templated (IBA,ISO)

positive regulation of DNA binding (ISO)

positive regulation of DNA methylation-dependent heterochromatin assembly (ISO,ISS)

positive regulation of DNA repair (ISO)

positive regulation of protein import into nucleus (ISO,ISS)

positive regulation of transcription, DNA-templated (IBA,ISO,ISS)

protein autophosphorylation (ISO)

protein phosphorylation (ISO)

protein sumoylation (IBA,IEA,ISO)

protein ubiquitination (IEA)

Ras protein signal transduction (ISO,ISS)

regulation of genetic imprinting (ISO)

suppression of viral release by host (ISO)

Cellular Component

chromatin (IBA,ISO)

euchromatin (ISO)

heterochromatin (ISO)

nucleolus (ISO)

nucleoplasm (IBA,ISO)

nucleus (ISO,ISS)

protein-containing complex (ISO)

RNA polymerase II transcription regulator complex (IBA,ISO,ISS)

Molecular Function

chromatin binding (ISO)

chromo shadow domain binding (ISO)

DNA binding (IBA,ISO)

Krueppel-associated box domain binding (ISO,ISS)

promoter-specific chromatin binding (IBA,ISO,ISS)

protein binding (ISO)

protein kinase activity (ISO)

SUMO transferase activity (ISO)

transcription coactivator activity (ISO,ISS)

transcription corepressor activity (IBA,ISO)

ubiquitin protein ligase binding (ISO)

ubiquitin-protein transferase activity (IBA,ISO)

zinc ion binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

p53 signaling pathway (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Huang Z, etal., J Biol Chem 1999 Mar 19;274(12):7640-8.
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
7.	RGD automated data pipeline
8.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:8769649	PMID:8986806	PMID:9016654	PMID:10562550	PMID:10653693	PMID:11226167	PMID:11331580	PMID:11331592	PMID:12477932	PMID:15469996	PMID:15882967	PMID:17178852
PMID:17273560	PMID:17298944	PMID:17512541	PMID:18082607	PMID:18248090	PMID:19270682	PMID:19321449	PMID:20164836	PMID:21518874	PMID:22082260	PMID:22110054	PMID:22495301
PMID:22681889	PMID:22801370	PMID:22871113	PMID:23665872	PMID:24623306	PMID:24625528	PMID:25002582	PMID:27029610	PMID:30053369

Genomics

Comparative Map Data

Trim28
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	73,652,441 - 73,659,388 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	1	73,652,709 - 73,659,380 (+)	Ensembl
Rnor_6.0	1	65,544,369 - 65,551,043 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	65,544,373 - 65,551,043 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	66,355,602 - 66,362,276 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	72,892,399 - 72,899,070 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	72,973,571 - 72,973,906 (-)	NCBI
Celera	1	60,180,424 - 60,187,048 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

TRIM28
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	58,544,064 - 58,550,715 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	19	58,544,064 - 58,550,722 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	59,055,431 - 59,062,082 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	63,747,648 - 63,753,894 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	19	63,747,647 - 63,753,894	NCBI
Celera	19	56,099,015 - 56,105,261 (+)	NCBI
Cytogenetic Map	19	q13.43	NCBI
HuRef	19	55,366,200 - 55,372,319 (+)	NCBI		HuRef
CHM1_1	19	59,049,665 - 59,055,911 (+)	NCBI		CHM1_1

Trim28
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	12,758,079 - 12,764,959 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	7	12,733,041 - 12,764,962 (+)	Ensembl
GRCm38	7	13,024,152 - 13,031,032 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	12,999,114 - 13,031,035 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	13,609,501 - 13,616,381 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	11,924,340 - 11,931,208 (+)	NCBI			mm8
Celera	7	10,651,338 - 10,658,223 (+)	NCBI		Celera
Cytogenetic Map	7	A1	NCBI

Trim28
(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	NW_004955584	1,148,903 - 1,156,001 (+)	NCBI	ChiLan1.0	ChiLan1.0

TRIM28
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	19	64,369,979 - 64,377,144 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	64,371,477 - 64,377,144 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	19	55,557,130 - 55,563,802 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

TRIM28
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	99,408,920 - 99,415,432 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	99,408,925 - 99,415,146 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	99,786,699 - 99,813,478 (-)	NCBI
ROS_Cfam_1.0	1	100,001,554 - 100,028,322 (-)	NCBI
ROS_Cfam_1.0 Ensembl	1	100,022,040 - 100,028,984 (-)	Ensembl
UMICH_Zoey_3.1	1	99,646,919 - 99,673,683 (-)	NCBI
UNSW_CanFamBas_1.0	1	99,359,536 - 99,386,515 (-)	NCBI
UU_Cfam_GSD_1.0	1	100,114,388 - 100,141,157 (-)	NCBI

Trim28
(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_024405118	217,986,447 - 217,992,258 (-)	NCBI
SpeTri2.0	NW_004937062	126,832 - 132,938 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TRIM28
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	63,094,648 - 63,101,532 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	63,094,382 - 63,101,532 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

TRIM28
(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	6	50,820,188 - 50,826,376 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	6	50,819,833 - 50,827,010 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666045	4,125,654 - 4,132,206 (+)	NCBI	Vero_WHO_p1.0

Trim28
(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 1.0	NW_004624832	49,324 - 56,113 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH137168

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	73,659,062 - 73,659,270 (-)	MAPPER	mRatBN7.2
Rnor_6.0	1	65,544,483 - 65,544,690	NCBI	Rnor6.0
Rnor_5.0	1	66,355,716 - 66,355,923	UniSTS	Rnor5.0
RGSC_v3.4	1	72,892,510 - 72,892,717	UniSTS	RGSC3.4
Celera	1	60,180,535 - 60,180,742	UniSTS
Cytogenetic Map	1	q21	UniSTS

RH143061

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	73,648,021 - 73,648,135 (-)	MAPPER	mRatBN7.2
Rnor_6.0	1	65,555,613 - 65,555,726	NCBI	Rnor6.0
Rnor_5.0	1	66,366,846 - 66,366,959	UniSTS	Rnor5.0
RGSC_v3.4	1	72,903,644 - 72,903,757	UniSTS	RGSC3.4
Celera	1	60,191,344 - 60,191,457	UniSTS
RH 3.4 Map	4	624.54	UniSTS
Cytogenetic Map	1	q21	UniSTS

RH126533

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	73,659,159 - 73,659,362 (-)	MAPPER	mRatBN7.2
Rnor_6.0	1	65,544,391 - 65,544,593	NCBI	Rnor6.0
Rnor_5.0	1	66,355,624 - 66,355,826	UniSTS	Rnor5.0
RGSC_v3.4	1	72,892,418 - 72,892,620	UniSTS	RGSC3.4
Celera	1	60,180,443 - 60,180,645	UniSTS
Cytogenetic Map	1	q21	UniSTS

Trim28

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	42,845,774 - 42,846,639 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	43,889,372 - 43,890,236	NCBI	Rnor6.0
Rnor_5.0	14	46,101,219 - 46,102,083	UniSTS	Rnor5.0
RGSC_v3.4	18	44,661,266 - 44,662,130	UniSTS	RGSC3.4
Celera	18	41,074,256 - 41,075,120	UniSTS
Cytogenetic Map	18	q11	UniSTS
Cytogenetic Map	1	q21	UniSTS
Cytogenetic Map	14	p11	UniSTS

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
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	509108	86060548	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5925874	115540829	Rat
1300167	Hrtrt2	Heart rate QTL 2	4.35		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	11481312	75088344	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	11481312	82174945	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11481312	82174945	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11481312	82174945	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11481312	82174945	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	22340647	102268831	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	28879780	78430678	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	30882023	123479925	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32356093	162846471	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	32737273	90665040	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32737458	199368955	Rat
1354599	Bw29	Body weight QTL 29	3.46	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	33449848	78449848	Rat
1354643	Foco2	Food consumption QTL 2	7.17	0.0001	eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	1	33449848	78449848	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	34836858	79836858	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	34836858	79836858	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	34836858	79836858	Rat
1331732	Srn4	Serum renin concentration QTL 4	4.467		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	1	35239598	78430678	Rat
1331792	Rf29	Renal function QTL 29	4.589		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	1	35239598	78430678	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43284731	118944897	Rat
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43284731	118944897	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43284731	118944897	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43284731	118944897	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43284731	118944897	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	43284731	118944897	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43284731	118944897	Rat
2302059	Pia36	Pristane induced arthritis QTL 36	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	43333002	88333002	Rat
1331778	Rf28	Renal function QTL 28	4.66		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	1	45803140	78430678	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	48963584	144267916	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	49361465	82174945	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	49393172	94393172	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49393172	159356837	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49393289	199050459	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	53863041	90532583	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	53895117	82174945	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	53895117	82174945	Rat
61342	Bp27	Blood pressure QTL 27	3.4	0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	56732668	98773277	Rat
2300164	Bmd44	Bone mineral density QTL 44	5.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	1	56949932	101949932	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	57336763	151090257	Rat
1300121	Hrtrt1	Heart rate QTL 1	3.7		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	65789093	115540829	Rat
7421628	Bp361	Blood pressure QTL 361		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	66023617	118608521	Rat
631512	Scl6	Serum cholesterol level QTL 6	9.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	72197680	90508767	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	130
Count of miRNA genes:	98
Interacting mature miRNAs:	107
Transcripts:	ENSRNOT00000029996
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.

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	3	43	57	41	19	41	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053916	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006228108	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC166843	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000029	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U95041	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000029996 ⟹ ENSRNOP00000031061

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	73,652,709 - 73,659,380 (+)	Ensembl
Rnor_6.0 Ensembl	1	65,544,373 - 65,551,043 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000100960 ⟹ ENSRNOP00000090373

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	73,652,709 - 73,659,380 (+)	Ensembl

RefSeq Acc Id:

NM_053916 ⟹ NP_446368

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	73,652,709 - 73,659,381 (+)	NCBI
Rnor_6.0	1	65,544,372 - 65,551,043 (-)	NCBI
Rnor_5.0	1	66,355,602 - 66,362,276 (-)	NCBI
RGSC_v3.4	1	72,892,399 - 72,899,070 (-)	RGD
Celera	1	60,180,424 - 60,187,048 (-)	RGD

Sequence:

show sequence

GCGGTTGTTCGCAATTCTTGCGGCGCGAGTCTCAGCAGCAAGGGAGGAGGCGGCGCGGGTGGCG
GCGCCGTCGTCTGTAGAGAGGCCGGCAGCCAGCGGCTTGGCCGCATCTCGGCAGCGCCTGGGGC
GCGGCGGGCGTCGGCCCAGGAGACGCGTGGCGGCGCTCGGCCTCGCGGCATCGGCGGCTGCCTG
GCCGTTGGCGGCGAGCGCACTTGCGCCTGCGCAGCGGGCTCGGTGCCCCTCCTCCCCTGGGCGG
CCCCCCCAACCCCCCGGCGGCGTGTGAATGGCGGCCTCGGCGGCGGCGGCGACTGCGGCGGCCT
CGGCCGCGACGGCCGCGTCAGCGGCCTCTGGTAGCCCAGGGTCGGGCGAAGGCTCGGCGGGCGG
TGAGAAGCGCCCCGCTGCCTCTTCAGCCGCGGCGGCCTCGGCCTCCGCGTCGTCCCCTGCGGGG
GGCGGTGGCGAGGCGCAGGAGCTTTTGGAGCACTGCGGCGTGTGTCGCGAGCGCTTGCGGCCTG
AGCGGGATCCTCGGCTGCTGCCCTGTCTGCATTCGGCCTGTAGTGCCTGCCTTGGCCCCGCTAC
ACCCGCCGCAGCTAATAATTCGGGGGATGGCGGCTCGGCGGGCGACGGCGCTATGGTGGATTGT
CCAGTGTGCAAACAACAGTGCTACTCCAAAGACATCGTGGAGAATTACTTTATGCGTGATAGTG
GCAGTAAGGCCTCTTCTGATTCCCAGGATGCTAACCAGTGCTGCACTAGCTGTGAAGATAACGC
CCCAGCCACTAGCTATTGTGTGGAGTGCTCTGAACCACTGTGTGAGACCTGTGTGGAGGCTCAC
CAGCGGGTGAAATACACCAAGGATCACACTGTGCGCTCCACGGGTCCTGCTAAGACTCGAGATG
GAGAACGAACAGTCTATTGTAATGTGCACAAGCATGAACCCCTTGTGCTGTTTTGTGAGAGCTG
TGACACGCTCACTTGCCGGGACTGCCAACTCAATGCTCACAAGGACCACCAGTACCAATTCTTG
GAAGATGCAGTAAGGAACCAACGTAAACTCTTGGCTTCACTGGTGAAACGTCTTGGGGACAAAC
ATGCCACACTGCAGAAAAACACCAAGGAGGTTCGAAGCTCGATCCGCCAGGTGTCTGATGTGCA
GAAGCGAGTGCAGGTTGATGTGAAGATGGCCATTCTGCAGATCATGAAGGAGCTGAATAAACGG
GGACGAGTTCTGGTCAATGATGCCCAGAAGGTGACTGAGGGTCAGCAGGAACGTCTGGAGCGTC
AGCACTGGACCATGACCAAAATCCAGAAGCACCAGGAACACATTTTGCGCTTTGCCTCTTGGGC
TTTGGAGAGTGATAACAATACAGCCCTCTTGCTCTCTAAGAAGCTGATTTATTTCCAGCTGCAT
CGGGCCCTCAAAATGATTGTGGATCCTGTGGAGCCTCATGGTGAGATGAAGTTTCAGTGGGATC
TCAATGCCTGGACCAAGAGTGCTGAAGCCTTTGGTAAGATTGTGGCTGAGCGTCCTGGTACAAA
CTCCACGGGTCCTGGGCCCATGGCTCCTCCAAGAGCCCCAGGCCCCCTAAGCAAGCAAGGTTCT
GGTAGTAGCCAGCCCATGGAAGTACAAGAGGGCTATGGCTTTGGGACAGATGATCCCTACTCAA
GTGCAGAGCCACATGTATCAGGCATGAAGCGGTCCCGCTCTGGTGAGGGAGAAGTAAGTGGCCT
CATGAGGAAGGTGCCACGTGTGAGCCTTGAACGCCTGGATCTGGATCTCACCTCTGATAGCCAG
CCACCAGTCTTCAAGGTCTTTCCTGGAAGCACCACTGAGGACTACAATCTAATTGTTATTGAGC
GTGGTGCTGCTGCAGCAGCCGCTGGCCAGGCTGGGACTGTGCCACCAGGAGCCCCTGGTGCCCC
ACCCCTGCCTGGCATGGCCATTGTCAAGGAAGAAGAGACAGAAGCTGCTATTGGAGCCCCTCCT
GCTGCCCCTGAGGGGCCTGAAACCAAGCCTGTGTTGATGGCTCTGACTGAAGGCCCTGGGGCTG
AGGGACCTCGTCTAGCTTCACCTAGTGGCAGTACCAGCTCAGGCTTGGAGGTGGTAGCTCCTGA
GGTTACCTCAGCCCCAGTAAGTGGGCCAGGTATCCTGGATGACAGTGCCACTATCTGCCGTGTA
TGCCAGAAGCCAGGTGACCTGGTCATGTGCAACCAGTGCGAGTTTTGCTTCCACCTGGATTGTC
ACCTCCCTTCCCTGCAGGATGTTCCAGGGGAGGAATGGAGTTGCTCACTCTGCCACGTGCTCCC
TGATCTAAAGGAGGAAGATGGAAGCCTTAGCTTGGATGGAGCAGATAGCACTGGTGTGGTAGCT
AAACTCTCACCAGCCAACCAGCGGAAATGTGAGCGTGTTCTGCTGGCCCTTTTCTGCCATGAAC
CGTGCCGCCCCTTGCATCAGCTGGCTACCGACTCTACATTCTCCATGGAGCAGCCTGGTGGTAC
CCTAGACCTGACCTTGATTCGTGCTCGCCTCCAAGAGAAGCTGTCACCTCCTTATAGCTCCCCC
CAGGAGTTTGCCCAGGATGTGGGCCGCATGTTCAAACAGTTCAATAAGCTGACTGAGGACAAGG
CAGATGTTCAGTCCATCATCGGCCTCCAGCGCTTCTTTGAGACACGAATGAATGATGCCTTTGG
TGACACCAAGTTTTCTGCTGTGCTGGTAGAACCACCACCACTGAACCTTCCCAGTGCTGGCCTA
AGTTCTCAGGAGCTGTCTGGTCCTGGTGATGGCCCCTGAAGCTGGGGCTCTTGTGGTCAGCCCA
GTCCAGCTCTGGTCTCTGTATTTTCAACCCATACCCTGTCCTTCCTCTGGTGGCCTGACTACCT
GTTCTTGCTGGCCCCATCCCTCAGTCCCTCCTCACAAAATGGTTTTTACTTCTGTGGATTTAAT
AAAAACTTCACTGAGTCAGTCGCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006228108 ⟹ XP_006228170

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	73,652,441 - 73,659,388 (+)	NCBI
Rnor_6.0	1	65,544,369 - 65,551,039 (-)	NCBI
Rnor_5.0	1	66,355,602 - 66,362,276 (-)	NCBI

Sequence:

show sequence

TTGTTCGCAATTCTTGCGGCGCGAGTCTCAGCAGCAAGGGAGGAGGCGGCGCGGGTGGCGGCGC
CGTCGTCTGTAGAGAGGCCGGCAGCCAGCGGCTTGGCCGCATCTCGGCAGCGCCTGGGGCGCGG
CGGGCGTCGGCCCAGGAGACGCGTGGCGGCGCTCGGCCTCGCGGCATCGGCGGCTGCCTGGCCG
TTGGCGGCGAGCGCACTTGCGCCTGCGCAGCGGGCTCGGTGCCCCTCCTCCCCTGGGCGGCCCC
CCCAACCCCCCGGCGGCGTGTGAATGGCGGCCTCGGCGGCGGCGGCGACTGCGGCGGCCTCGGC
CGCGACGGCCGCGTCAGCGGCCTCTGGTAGCCCAGGGTCGGGCGAAGGCTCGGCGGGCGGTGAG
AAGCGCCCCGCTGCCTCTTCAGCCGCGGCGGCCTCGGCCTCCGCGTCGTCCCCTGCGGGGGGCG
GTGGCGAGGCGCAGGAGCTTTTGGAGCACTGCGGCGTGTGTCGCGAGCGCTTGCGGCCTGAGCG
GGATCCTCGGCTGCTGCCCTGTCTGCATTCGGCCTGTAGTGCCTGCCTTGGCCCCGCTACACCC
GCCGCAGCTAATAATTCGGGGGATGGCGGCTCGGCGGGCGACGGCGCTATGGTGGATTGTCCAG
TGTGCAAACAACAGTGCTACTCCAAAGACATCGTGGAGAATTACTTTATGCGTGATAGTGGCAG
TAAGGCCTCTTCTGATTCCCAGGATGCTAACCAGTGCTGCACTAGCTGTGAAGATAACGCCCCA
GCCACTAGCTATTGTGTGGAGTGCTCTGAACCACTGTGTGAGACCTGTGTGGAGGCTCACCAGC
GGGTGAAATACACCAAGGATCACACTGTGCGCTCCACGGGTCCTGCTAAGACTCGAGATGGAGA
ACGAACAGTCTATTGTAATGTGCACAAGCATGAACCCCTTGTGCTGTTTTGTGAGAGCTGTGAC
ACGCTCACTTGCCGGGACTGCCAACTCAATGCTCACAAGGACCACCAGTACCAATTCTTGGAAG
ATGCAGTAAGGAACCAACGTAAACTCTTGGCTTCACTGGTGAAACGTCTTGGGGACAAACATGC
CACACTGCAGAAAAACACCAAGGAGGTTCGAAGCTCGATCCGCCAGGTGTCTGATGTGCAGAAG
CGAGTGCAGGTTGATGTGAAGATGGCCATTCTGCAGATCATGAAGGAGCTGAATAAACGGGGAC
GAGTTCTGGTCAATGATGCCCAGAAGGTGACTGAGGGTCAGCAGGAACGTCTGGAGCGTCAGCA
CTGGACCATGACCAAAATCCAGAAGCACCAGGAACACATTTTGCGCTTTGCCTCTTGGGCTTTG
GAGAGTGATAACAATACAGCCCTCTTGCTCTCTAAGAAGCTGATTTATTTCCAGCTGCATCGGG
CCCTCAAAATGATTGTGGATCCTGTGGAGCCTCATGGTGAGATGAAGTTTCAGTGGGATCTCAA
TGCCTGGACCAAGAGTGCTGAAGCCTTTGGTAAGATTGTGGCTGAGCGTCCTGGTACAAACTCC
ACGGGTCCTGGGCCCATGGCTCCTCCAAGAGCCCCAGGCCCCCTAAGCAAGCAAGGTTCTGGTA
GTAGCCAGCCCATGGAAGTACAAGAGGGCTATGGCTTTGGGACAGATGATCCCTACTCAAGTGC
AGAGCCACATGTATCAGGCATGAAGCGGTCCCGCTCTGGTGAGGGAGAAGTAAGTGGCCTCATG
AGGAAGGTGCCACGTGTGAGCCTTGAACGCCTGGATCTGGATCTCACCTCTGATAGCCAGCCAC
CAGTCTTCAAGGTCTTTCCTGGAAGCACCACTGAGGACTACAATCTAATTGTTATTGAGCGTGG
TGCTGCTGCAGCAGCCGCTGGCCAGGCTGGGACTGTGCCACCAGGAGCCCCTGGTGCCCCACCC
CTGCCTGGCATGGCCATTGTCAAGGAAGAAGAGACAGAAGCTGCTATTGGAGCCCCTCCTGCTG
CCCCTGAGGGGCCTGAAACCAAGCCTGTGTTGATGGCTCTGACTGAAGGCCCTGGGGCTGAGGG
ACCTCGTCTAGCTTCACCTAGTGGCAGTACCAGCTCAGGCTTGGAGGTGGTAGCTCCTGAGGTT
ACCTCAGCCCCAGTAAGTGGGCCAGGTATCCTGGATGACAGTGCCACTATCTGCCGTGTATGCC
AGAAGCCAGGTGACCTGGTCATGTGCAACCAGTGCGAGTTTTGCTTCCACCTGGATTGTCACCT
CCCTTCCCTGCAGGATGTTCCAGGGGAGGAATGGAGTTGCTCACTCTGCCACGTGCTCCCTGAT
CTAAAGGAGGAAGATGGAAGCCTTAGCTTGGATGGAGCAGATAGCACTGGTGTGGTAGCTAAAC
TCTCACCAGCCAACCAGCGGAAATGTGAGCGTGTTCTGCTGGCCCTTTTCTGCCATGAACCGTG
CCGCCCCTTGCATCAGCTGGCTACCGACTCTACATTCTCCATGGTGAGTAGTCCCAGAATAGGA
GAGGTTGCAGGTGTCAAGTTGGTAGCCCCACTCAATGTCTGTTGTCTCTCCCTGCAGGAGCAGC
CTGGTGGTACCCTAGACCTGACCTTGATTCGTGCTCGCCTCCAAGAGAAGCTGTCACCTCCTTA
TAGCTCCCCCCAGGAGTTTGCCCAGGATGTGGGCCGCATGTTCAAACAGTTCAATAAGCTGACT
GAGGACAAGGCAGATGTTCAGTCCATCATCGGCCTCCAGCGCTTCTTTGAGACACGAATGAATG
ATGCCTTTGGTGACACCAAGTTTTCTGCTGTGCTGGTAGAACCACCACCACTGAACCTTCCCAG
TGCTGGCCTAAGTTCTCAGGAGCTGTCTGGTCCTGGTGATGGCCCCTGAAGCTGGGGCTCTTGT
GGTCAGCCCAGTCCAGCTCTGGTCTCTGTATTTTCAACCCATACCCTGTCCTTCCTCTGGTGGC
CTGACTACCTGTTCTTGCTGGCCCCATCCCTCAGTCCCTCCTCACAAAATGGTTTTTACTTCTG
TGGATTTAATAAAAACTTCACTGAGTCAGTCGCTCATTC

hide sequence

Protein Sequences


Protein RefSeqs	NP_446368	(Get FASTA)	NCBI Sequence Viewer
	XP_006228170	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB51518	(Get FASTA)	NCBI Sequence Viewer
	AAI66843	(Get FASTA)	NCBI Sequence Viewer
	O08629	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_446368 ⟸ NM_053916

- UniProtKB:

O08629 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAASAAAATAAASAATAASAASGSPGSGEGSAGGEKRPAASSAAAASASASSPAGGGGEAQELL
EHCGVCRERLRPERDPRLLPCLHSACSACLGPATPAAANNSGDGGSAGDGAMVDCPVCKQQCYS
KDIVENYFMRDSGSKASSDSQDANQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDH
TVRSTGPAKTRDGERTVYCNVHKHEPLVLFCESCDTLTCRDCQLNAHKDHQYQFLEDAVRNQRK
LLASLVKRLGDKHATLQKNTKEVRSSIRQVSDVQKRVQVDVKMAILQIMKELNKRGRVLVNDAQ
KVTEGQQERLERQHWTMTKIQKHQEHILRFASWALESDNNTALLLSKKLIYFQLHRALKMIVDP
VEPHGEMKFQWDLNAWTKSAEAFGKIVAERPGTNSTGPGPMAPPRAPGPLSKQGSGSSQPMEVQ
EGYGFGTDDPYSSAEPHVSGMKRSRSGEGEVSGLMRKVPRVSLERLDLDLTSDSQPPVFKVFPG
STTEDYNLIVIERGAAAAAAGQAGTVPPGAPGAPPLPGMAIVKEEETEAAIGAPPAAPEGPETK
PVLMALTEGPGAEGPRLASPSGSTSSGLEVVAPEVTSAPVSGPGILDDSATICRVCQKPGDLVM
CNQCEFCFHLDCHLPSLQDVPGEEWSCSLCHVLPDLKEEDGSLSLDGADSTGVVAKLSPANQRK
CERVLLALFCHEPCRPLHQLATDSTFSMEQPGGTLDLTLIRARLQEKLSPPYSSPQEFAQDVGR
MFKQFNKLTEDKADVQSIIGLQRFFETRMNDAFGDTKFSAVLVEPPPLNLPSAGLSSQELSGPG
DGP

hide sequence

RefSeq Acc Id:

XP_006228170 ⟸ XM_006228108

- Peptide Label:

isoform X1

- Sequence:

show sequence

MAASAAAATAAASAATAASAASGSPGSGEGSAGGEKRPAASSAAAASASASSPAGGGGEAQELL
EHCGVCRERLRPERDPRLLPCLHSACSACLGPATPAAANNSGDGGSAGDGAMVDCPVCKQQCYS
KDIVENYFMRDSGSKASSDSQDANQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDH
TVRSTGPAKTRDGERTVYCNVHKHEPLVLFCESCDTLTCRDCQLNAHKDHQYQFLEDAVRNQRK
LLASLVKRLGDKHATLQKNTKEVRSSIRQVSDVQKRVQVDVKMAILQIMKELNKRGRVLVNDAQ
KVTEGQQERLERQHWTMTKIQKHQEHILRFASWALESDNNTALLLSKKLIYFQLHRALKMIVDP
VEPHGEMKFQWDLNAWTKSAEAFGKIVAERPGTNSTGPGPMAPPRAPGPLSKQGSGSSQPMEVQ
EGYGFGTDDPYSSAEPHVSGMKRSRSGEGEVSGLMRKVPRVSLERLDLDLTSDSQPPVFKVFPG
STTEDYNLIVIERGAAAAAAGQAGTVPPGAPGAPPLPGMAIVKEEETEAAIGAPPAAPEGPETK
PVLMALTEGPGAEGPRLASPSGSTSSGLEVVAPEVTSAPVSGPGILDDSATICRVCQKPGDLVM
CNQCEFCFHLDCHLPSLQDVPGEEWSCSLCHVLPDLKEEDGSLSLDGADSTGVVAKLSPANQRK
CERVLLALFCHEPCRPLHQLATDSTFSMVSSPRIGEVAGVKLVAPLNVCCLSLQEQPGGTLDLT
LIRARLQEKLSPPYSSPQEFAQDVGRMFKQFNKLTEDKADVQSIIGLQRFFETRMNDAFGDTKF
SAVLVEPPPLNLPSAGLSSQELSGPGDGP

hide sequence

RefSeq Acc Id:

ENSRNOP00000031061 ⟸ ENSRNOT00000029996

RefSeq Acc Id:

ENSRNOP00000090373 ⟸ ENSRNOT00000100960

Protein Domains

Bromo

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-O08629-F1-model_v2	AlphaFold	O08629	1-835	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689671

Promoter ID:

EPDNEW_R196

Type:

initiation region

Name:

Trim28_2

Description:

tripartite motif-containing 28

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_R197

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	65,550,772 - 65,550,832	EPDNEW

RGD ID:

13689672

Promoter ID:

EPDNEW_R197

Type:

initiation region

Name:

Trim28_1

Description:

tripartite motif-containing 28

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_R196

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	65,551,068 - 65,551,128	EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)

ACI/EurMcwi (2019)

Visual

CSV

TAB

Printer

Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (2020)

Visual

CSV

TAB

Printer

Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN-Lx/CubMcwi (2019)

Visual

CSV

TAB

Printer

Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

Visual

CSV

TAB

Printer

Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

Visual

CSV

TAB

Printer

Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

Visual

CSV

TAB

Printer

Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BUF/N (2020)

Visual

CSV

TAB

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

DA/OlaHsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE16/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/FarMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB10/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF10A/StmMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/NRrrcMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MWF/Hsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHR/OlalpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WAG/RijCrl (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
1	72898588	72898589	C	G	snv	SS/JrHsdMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620289	AgrOrtholog
BioCyc Gene	G2FUF-60692	BioCyc
Ensembl Genes	ENSRNOG00000027487	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000031061	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000029996	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	1.20.920.10	UniProtKB/Swiss-Prot
	3.30.40.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:9028761	IMAGE-MGC_LOAD
InterPro	Bbox_C	UniProtKB/Swiss-Prot
	Bromodomain	UniProtKB/Swiss-Prot
	Bromodomain-like_sf	UniProtKB/Swiss-Prot
	KAP1	UniProtKB/Swiss-Prot
	TIF1beta_RING-HC	UniProtKB/Swiss-Prot
	Zinc_finger_PHD-type_CS	UniProtKB/Swiss-Prot
	Znf_B-box	UniProtKB/Swiss-Prot
	Znf_FYVE_PHD	UniProtKB/Swiss-Prot
	Znf_PHD	UniProtKB/Swiss-Prot
	Znf_PHD-finger	UniProtKB/Swiss-Prot
	Znf_RING	UniProtKB/Swiss-Prot
	Znf_RING/FYVE/PHD	UniProtKB/Swiss-Prot
KEGG Report	rno:116698	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:188735	IMAGE-MGC_LOAD
NCBI Gene	116698	ENTREZGENE
PANTHER	PTHR25462:SF274	UniProtKB/Swiss-Prot
Pfam	PHD	UniProtKB/Swiss-Prot
	zf-B_box	UniProtKB/Swiss-Prot
	zf-RING_5	UniProtKB/Swiss-Prot
PhenoGen	Trim28	PhenoGen
PROSITE	ZF_BBOX	UniProtKB/Swiss-Prot
	ZF_PHD_1	UniProtKB/Swiss-Prot
	ZF_PHD_2	UniProtKB/Swiss-Prot
	ZF_RING_2	UniProtKB/Swiss-Prot
SMART	BBC	UniProtKB/Swiss-Prot
	BBOX	UniProtKB/Swiss-Prot
	BROMO	UniProtKB/Swiss-Prot
	PHD	UniProtKB/Swiss-Prot
	RING	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF57903	UniProtKB/Swiss-Prot
UniProt	O08629	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	B2RYN5	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-31	Trim28	tripartite motif-containing 28	Trim28	tripartite motif protein 28	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-02-26	Trim28	tripartite motif protein 28			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Trim28	tripartite motif protein 28			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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - PID (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - PID (archival)