Rnf4 (ring finger protein 4) - Rat Genome Database

Name: Rnf4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Rnf4 (ring finger protein 4) Rattus norvegicus

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Symbol:

Rnf4

Name:

ring finger protein 4

RGD ID:

3583

Description:

Enables several functions, including SUMO polymer binding activity; TBP-class protein binding activity; and nuclear receptor binding activity. Involved in several processes, including cellular response to gamma radiation; cellular response to hydroxyurea; and protein ubiquitination. Located in PML body. Orthologous to human RNF4 (ring finger protein 4); PARTICIPATES IN ataxia telangiectasia-mutated (ATM) signaling pathway; nuclear factor, erythroid 2 like 2 signaling pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

E3 ubiquitin ligase RNF4; E3 ubiquitin-protein ligase RNF4; MGC72476; RING-type E3 ubiquitin transferase RNF4; small nuclear ring finger protein; SNURF

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):	RNF4 (ring finger protein 4)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Rnf4 (ring finger protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Rnf4 (ring finger protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RNF4 (ring finger protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RNF4 (ring finger protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rnf4 (ring finger protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RNF4 (ring finger protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	RNF4 (ring finger protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rnf4 (ring finger protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RNF4 (ring finger protein 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Rnf4 (ring finger protein 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	rnf4 (ring finger protein 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	dgrn	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	rnf4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	80,625,864 - 80,647,138 (-)	NCBI		GRCr8
mRatBN7.2	14	76,401,292 - 76,423,270 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	76,401,299 - 76,422,566 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	80,855,542 - 80,874,657 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	82,096,173 - 82,115,286 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	78,541,415 - 78,560,532 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	81,658,400 - 81,679,756 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	81,660,354 - 81,679,082 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	82,345,311 - 82,366,467 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	82,092,024 - 82,112,036 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	82,093,652 - 82,114,081 (-)	NCBI
Celera	14	75,327,677 - 75,346,979 (-)	NCBI		Celera
Cytogenetic Map	14	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Angelman syndrome (ISO)

cherubism (ISO)

Ellis-Van Creveld syndrome (ISO)

Testicular Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(1->4)-beta-D-glucan (ISO)

17beta-estradiol (EXP)

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

2,4-dinitrotoluene (EXP)

2-ethoxyethanol (EXP)

2-methoxyethanol (EXP)

2-methylcholine (ISO)

3,4-methylenedioxymethamphetamine (ISO)

5-fluorouracil (ISO)

acrolein (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene diol epoxide I (ISO)

beta-lapachone (ISO)

bisphenol A (EXP,ISO)

C60 fullerene (EXP)

cadmium atom (ISO)

caffeine (ISO)

chlorpyrifos (ISO)

choline (ISO)

ciguatoxin CTX1B (ISO)

colforsin daropate hydrochloride (EXP)

crocidolite asbestos (ISO)

cycloheximide (ISO)

cyclosporin A (ISO)

dexamethasone (EXP)

diarsenic trioxide (ISO)

diazinon (ISO)

Dibutyl phosphate (ISO)

diethylstilbestrol (ISO)

dioxygen (ISO)

disodium selenite (ISO)

diuron (EXP)

doxorubicin (ISO)

epoxiconazole (ISO)

ethanol (ISO)

fenpyroximate (ISO)

flavonoids (EXP)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

FR900359 (ISO)

fulvestrant (ISO)

genistein (ISO)

gentamycin (EXP)

hydrogen cyanide (ISO)

hydroxyurea (EXP)

hypochlorous acid (ISO)

L-methionine (ISO)

levofloxacin (EXP)

Methylazoxymethanol acetate (EXP)

Mono-carboxy isooctyl phthalate (ISO)

nefazodone (EXP)

ozone (ISO)

paracetamol (ISO)

perfluorohexanesulfonic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phorbol 13-acetate 12-myristate (EXP)

pirinixic acid (ISO)

potassium cyanide (ISO)

progesterone (EXP)

pyrogallol (ISO)

resveratrol (ISO)

rotenone (ISO)

sodium arsenite (ISO)

testosterone (EXP,ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trimellitic anhydride (ISO)

triptonide (ISO)

triticonazole (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to arsenic-containing substance (IEP)

cellular response to cytokine stimulus (IEP)

cellular response to gamma radiation (IMP)

cellular response to hydroxyurea (IMP)

cellular response to testosterone stimulus (IDA)

male gonad development (IEP)

negative regulation of protein localization to chromatin (IEA,ISO)

positive regulation of DNA-templated transcription (IDA)

positive regulation of transcription by RNA polymerase II (IBA,IDA,IEA,ISO,ISS)

proteasome-mediated ubiquitin-dependent protein catabolic process (IEA,ISO,ISS)

protein autoubiquitination (IDA,IMP)

protein K11-linked ubiquitination (IDA)

protein K48-linked ubiquitination (IDA)

protein K6-linked ubiquitination (IDA)

protein K63-linked ubiquitination (IDA)

protein ubiquitination (IMP)

regulation of kinetochore assembly (IEA,ISO,ISS)

regulation of spindle assembly (IEA,ISO,ISS)

response to arsenic-containing substance (IDA,IEA,ISO)

response to estradiol (IEP)

response to human chorionic gonadotropin (IEP)

spermatogenesis (IEP)

Cellular Component

cytoplasm (IEA,ISO,ISS)

microtubule end (IEA,ISO)

nuclear body (ISO)

nucleoplasm (IDA,ISO)

nucleus (IDA,ISO)

PML body (IBA,IDA,IEA,ISO)

Molecular Function

DNA binding (IDA)

identical protein binding (IEA,IPI,ISO)

nuclear androgen receptor binding (IPI)

nuclear estrogen receptor binding (IPI)

nucleosome binding (IDA)

protein binding (IPI,ISO)

SUMO polymer binding (IDA,IEA,IPI,ISO)

TBP-class protein binding (IDA)

ubiquitin conjugating enzyme binding (IPI)

ubiquitin protein ligase activity (IDA,IEA,ISO)

ubiquitin-protein transferase activity (IDA,IMP)

zinc ion binding (IDA,IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

ataxia telangiectasia-mutated (ATM) signaling pathway (ISO)

nuclear factor, erythroid 2 like 2 signaling pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Differentially expressed genes in L6 rat skeletal muscle myoblasts after incubation with inflammatory cytokines.	Adams V, etal., Cytokine. 2001 Mar 21;13(6):342-8.
2.	Purification and identification of endogenous polySUMO conjugates.	Bruderer R, etal., EMBO Rep. 2011 Feb;12(2):142-8. doi: 10.1038/embor.2010.206. Epub 2011 Jan 21.
3.	Plasma clearance, tissue uptake and expression of pituitary peptide 23/pancreatitis-associated protein in the rat.	Chakraborty C, etal., J Endocrinol. 1995 Jun;145(3):461-9.
4.	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.
5.	Arsenic-induced SUMO-dependent recruitment of RNF4 into PML nuclear bodies.	Geoffroy MC, etal., Mol Biol Cell. 2010 Dec;21(23):4227-39. doi: 10.1091/mbc.E10-05-0449. Epub 2010 Oct 13.
6.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
7.	Transcriptional coregulator SNURF (RNF4) possesses ubiquitin E3 ligase activity.	Hakli M, etal., FEBS Lett. 2004 Feb 27;560(1-3):56-62.
8.	The RING finger protein SNURF is a bifunctional protein possessing DNA binding activity.	Hakli M, etal., J Biol Chem. 2001 Jun 29;276(26):23653-60. Epub 2001 Apr 23.
9.	The Nrf2 regulatory network provides an interface between redox and intermediary metabolism.	Hayes JD and Dinkova-Kostova AT, Trends Biochem Sci. 2014 Apr;39(4):199-218. doi: 10.1016/j.tibs.2014.02.002. Epub 2014 Mar 16.
10.	Small nuclear RING finger protein expression during gonad development: regulation by gonadotropins and estrogen in the postnatal ovary.	Hirvonen-Santti SJ, etal., Endocrinology. 2004 May;145(5):2433-44. Epub 2004 Jan 28.
11.	Down-regulation of estrogen receptor beta and transcriptional coregulator SNURF/RNF4 in testicular germ cell cancer.	Hirvonen-Santti SJ, etal., Eur Urol. 2003 Dec;44(6):742-7; discussion 747.
12.	Identification of RING finger protein 4 (RNF4) as a modulator of DNA demethylation through a functional genomics screen.	Hu XV, etal., Proc Natl Acad Sci U S A. 2010 Aug 24;107(34):15087-92. doi: 10.1073/pnas.1009025107. Epub 2010 Aug 9.
13.	Identification of a novel RING finger protein as a coregulator in steroid receptor-mediated gene transcription.	Moilanen AM, etal., Mol Cell Biol 1998 Sep;18(9):5128-39.
14.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
15.	Push back to respond better: regulatory inhibition of the DNA double-strand break response.	Panier S and Durocher D, Nat Rev Mol Cell Biol. 2013 Oct;14(10):661-72. doi: 10.1038/nrm3659. Epub 2013 Sep 4.
16.	Mechanism of ubiquitylation by dimeric RING ligase RNF4.	Plechanovova A, etal., Nat Struct Mol Biol. 2011 Aug 21;18(9):1052-9. doi: 10.1038/nsmb.2108.
17.	GOA pipeline	RGD automated data pipeline
18.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
19.	SNURF-SNRPN and UBE3A transcript levels in patients with Angelman syndrome.	Runte M, etal., Hum Genet. 2004 May;114(6):553-61. Epub 2004 Mar 10.
20.	RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation.	Tatham MH, etal., Nat Cell Biol. 2008 May;10(5):538-46. doi: 10.1038/ncb1716. Epub 2008 Apr 13.
21.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
22.	Expression of the nuclear RING finger protein SNURF/RNF4 during rat testis development suggests a role in spermatid maturation.	Yan W, etal., Mech Dev. 2002 Oct;118(1-2):247-53.
23.	SUMO-targeted ubiquitin E3 ligase RNF4 is required for the response of human cells to DNA damage.	Yin Y, etal., Genes Dev. 2012 Jun 1;26(11):1196-208. doi: 10.1101/gad.189274.112.

Additional References at PubMed

PMID:10822263	PMID:10849425	PMID:12477932	PMID:12885770	PMID:15489334	PMID:20212317	PMID:21059884	PMID:22842904	PMID:24714598	PMID:24882209	PMID:26148049	PMID:28612051
PMID:31873223

Genomics

Comparative Map Data

Rnf4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	80,625,864 - 80,647,138 (-)	NCBI		GRCr8
mRatBN7.2	14	76,401,292 - 76,423,270 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	76,401,299 - 76,422,566 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	80,855,542 - 80,874,657 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	82,096,173 - 82,115,286 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	78,541,415 - 78,560,532 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	81,658,400 - 81,679,756 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	81,660,354 - 81,679,082 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	82,345,311 - 82,366,467 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	82,092,024 - 82,112,036 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	82,093,652 - 82,114,081 (-)	NCBI
Celera	14	75,327,677 - 75,346,979 (-)	NCBI		Celera
Cytogenetic Map	14	q21	NCBI

RNF4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	2,469,106 - 2,515,857 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	2,462,220 - 2,515,857 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	2,470,833 - 2,517,584 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	2,440,605 - 2,487,382 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	4	2,438,037 - 2,484,812	NCBI
Celera	4	2,381,995 - 2,428,665 (+)	NCBI		Celera
Cytogenetic Map	4	p16.3	NCBI
HuRef	4	2,410,726 - 2,457,392 (+)	NCBI		HuRef
CHM1_1	4	2,468,951 - 2,515,567 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	4	2,467,864 - 2,514,631 (+)	NCBI		T2T-CHM13v2.0

Rnf4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	34,493,594 - 34,510,789 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	34,493,633 - 34,512,973 (+)	Ensembl		GRCm39 Ensembl
GRCm38	5	34,336,250 - 34,353,445 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	34,336,289 - 34,355,629 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	34,679,039 - 34,696,079 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	34,653,247 - 34,670,287 (+)	NCBI		MGSCv36	mm8
Celera	5	31,806,911 - 31,824,034 (+)	NCBI		Celera
Cytogenetic Map	5	B2	NCBI
cM Map	5	17.87	NCBI

Rnf4
(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_004955514	1,511,062 - 1,523,714 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955514	1,501,943 - 1,525,689 (+)	NCBI	ChiLan1.0	ChiLan1.0

RNF4
(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	3	2,806,077 - 2,853,304 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	2,763,804 - 2,789,272 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	2,614,918 - 2,661,785 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	2,518,559 - 2,565,970 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	2,540,612 - 2,563,937 (+)	Ensembl	panpan1.1		panPan2

RNF4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	3	61,721,752 - 61,759,797 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	3	61,723,124 - 61,759,730 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1

Rnf4
(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_024405285	67,323,348 - 67,354,145 (-)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936477	21,025,040 - 21,055,821 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RNF4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	1,353,658 - 1,380,634 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	8	1,353,532 - 1,380,637 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	917,478 - 945,481 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RNF4
(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	27	46,245,786 - 46,290,671 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666051	2,616,728 - 2,662,730 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Rnf4
(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_004624755	25,141,567 - 25,153,942 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624755	25,139,637 - 25,163,586 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Rnf4
163 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	864
Count of miRNA genes:	294
Interacting mature miRNAs:	362
Transcripts:	ENSRNOT00000019555
Prediction methods:	Microtar, Miranda
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
2313089	Bss81	Bone structure and strength QTL 81	3.4	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	14	37669719	82669719	Rat
9590294	Uminl4	Urine mineral level QTL 4	5.66	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	14	55624247	100624247	Rat
1582236	Gluco22	Glucose level QTL 22	3.3	0.0164	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	73415323	92554092	Rat
2300197	Scl59	Serum cholesterol level QTL 59			blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	14	55147478	100147478	Rat
70153	Bp59	Blood pressure QTL 59	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	14	68757796	83368335	Rat
70187	Pancm5	Pancreatic morphology QTL 5	16.7		pancreas mass (VT:0010144)	pancreas weight to body weight ratio (CMO:0000630)	14	30320092	80829842	Rat
631523	Pia13	Pristane induced arthritis QTL 13	3.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	14	40793460	98037301	Rat
1582259	Gluco23	Glucose level QTL 23	3.1	0.0008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	70053989	104886043	Rat
1582197	Gluco27	Glucose level QTL 27	3.4	0.0006	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	73415323	92554092	Rat
2313100	Bss82	Bone structure and strength QTL 82	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	14	37669719	82669719	Rat
634328	Hc5	Hypercalciuria QTL 5	2.3		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	14	58184885	103184885	Rat
1582250	Gluco26	Glucose level QTL 26	3.3	0.0009	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	73415323	95876975	Rat
2317879	Alcrsp27	Alcohol response QTL 27	3.3	0.63	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	14	56631369	101631369	Rat
1641900	Alcrsp11	Alcohol response QTL 11			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	14	70053989	104886043	Rat
631839	Niddm37	Non-insulin dependent diabetes mellitus QTL 37	3.37		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	11030622	95876975	Rat
1582255	Gluco29	Glucose level QTL 29	3.1	0.0025	blood glucose amount (VT:0000188)	absolute change in blood glucose level area under curve (CMO:0002034)	14	73415323	92554092	Rat
9589034	Epfw11	Epididymal fat weight QTL 11	6	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	14	55624247	100624247	Rat
1582209	Gluco20	Glucose level QTL 20	3.8	0.0005	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	73415323	92554092	Rat
2313048	Bss84	Bone structure and strength QTL 84	3.1	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	14	37669719	82669719	Rat
1300136	Rf22	Renal function QTL 22	3.9		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	14	42262529	95023211	Rat
1549834	Scl45	Serum cholesterol level QTL 45	5.8		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	14	50023211	95023211	Rat
738037	Hcas6	Hepatocarcinoma susceptibility QTL 6	2.93		liver integrity trait (VT:0010547)	liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)	14	39057237	83368335	Rat
2313084	Bss83	Bone structure and strength QTL 83	2.9	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	14	37669719	82669719	Rat

Markers in Region

BI277880

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	76,402,837 - 76,402,934 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	81,659,946 - 81,660,042	NCBI	Rnor6.0
Rnor_5.0	14	82,346,857 - 82,346,953	UniSTS	Rnor5.0
RGSC_v3.4	14	82,091,637 - 82,091,733	UniSTS	RGSC3.4
Celera	14	75,327,290 - 75,327,386	UniSTS
Cytogenetic Map	14	q21	UniSTS

Expression

RNA-SEQ Expression

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

Download All Expressed Objects for this Gene

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

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_019182	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017599145	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063272992	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_010057355	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF022081	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY050655	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC062024	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473963	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ211855	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223606	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225378	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000019555 ⟹ ENSRNOP00000019555

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	14	81,660,441 - 81,672,351 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000077799 ⟹ ENSRNOP00000074121

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	14	76,401,303 - 76,413,585 (-)	Ensembl
Rnor_6.0 Ensembl	14	81,660,354 - 81,679,082 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000095762 ⟹ ENSRNOP00000096496

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	14	76,401,299 - 76,422,566 (-)	Ensembl

RefSeq Acc Id:

NM_019182 ⟹ NP_062055

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	80,627,794 - 80,647,138 (-)	NCBI
mRatBN7.2	14	76,403,225 - 76,422,564 (-)	NCBI
Rnor_6.0	14	81,660,333 - 81,679,653 (-)	NCBI
Rnor_5.0	14	82,345,311 - 82,366,467 (-)	NCBI
RGSC_v3.4	14	82,092,024 - 82,112,036 (-)	RGD
Celera	14	75,327,677 - 75,346,979 (-)	RGD

Sequence:

show sequence

AAGTGGGTCTTCGTGAGACGGTGGAGTCTTGCTTGAGCGGGTCTCCTCAGCGGCTGCTGGATTA
GGTGCGTCCTTGCTCGAGCGCGGTGGCCAAGGCGTTTGGCTGATAACACCAACTCCAAAATTTA
GACATTCTGAACATCTAGTTGGCTCCAAATTGTGAACCACAGGATGAGTATTCAGTGGGCATGA
GAGATTGAGAACATTCTACCACACCATAAACCTTGGTGTAGATCACTTCCTATTCTGTGGATTG
AAGCCAGAGAGCACAATGAGTACAAGAAATCCTCAAAGAAAGCGGCGTGGTGGAGCTGTGAATT
CTAGACAAACCCAGAAGCGAACTCGGGAAACAACTTCAACCCCTGAGATTTCCTTGGAAGCAGA
ACCCATAGAACTTGTGGAAACCGTTGGAGATGAAATCGTGGACCTCACCTGTGAATCTTTAGAG
CCTGTGGTTGTGGACCTGACTCACAATGACTCTGTTGTGATTGTTGAAGAAAGGAGAAGGCCAA
GGAGAAATGGGAGGAGGTTGCGCCAAGACCATGCTGACAGCTGTGTGGTGAGCAGTGATGATGA
AGAACTGTCTAAGGACAAAGATGTATACGTGACTACCCATACTCCTCGAAGCACCAAGGATGAA
GGAACTACTGGACTTAGGCCCTCGGGCACCGTCAGTTGTCCGATCTGCATGGATGGATACTCTG
AGATTGTGCAGAATGGGCGTCTCATTGTTTCTACAGAATGTGGCCACGTCTTCTGTAGCCAGTG
CCTCCGTGATTCCCTTAAGAATGCTAACACTTGCCCAACTTGTAGGAAAAAGATCAACCATAAA
CGGTACCATCCCATTTATATATGAAATGTTCACAACTGCTCAGGATAGACCAATGGACAGACAA
CCGGGCTGGCTTTTCTGCATGGTATCTGCCTCCAGTTTCCTGAGCTCAAAAAGACTTTCAAAAA
TCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_063272992 ⟹ XP_063129062

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	80,625,864 - 80,639,968 (-)	NCBI

RefSeq Acc Id:

XR_010057355

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	80,625,864 - 80,639,968 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_062055	(Get FASTA)	NCBI Sequence Viewer
	XP_063129062	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAC35248	(Get FASTA)	NCBI Sequence Viewer
	AAH62024	(Get FASTA)	NCBI Sequence Viewer
	AAL06715	(Get FASTA)	NCBI Sequence Viewer
	EDM00096	(Get FASTA)	NCBI Sequence Viewer
	EDM00097	(Get FASTA)	NCBI Sequence Viewer
	EDM00098	(Get FASTA)	NCBI Sequence Viewer
	EDM00099	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000074121.2
	ENSRNOP00000096496.1
	ENSRNOP00055023237
	ENSRNOP00060022905
	ENSRNOP00065040980
GenBank Protein	O88846	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_062055 ⟸ NM_019182
- UniProtKB:	O88846 (UniProtKB/Swiss-Prot), A6IK32 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSTRNPQRKRRGGAVNSRQTQKRTRETTSTPEISLEAEPIELVETVGDEIVDLTCESLEPVVVD LTHNDSVVIVEERRRPRRNGRRLRQDHADSCVVSSDDEELSKDKDVYVTTHTPRSTKDEGTTGL RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI YI hide sequence

Ensembl Acc Id:

ENSRNOP00000074121 ⟸ ENSRNOT00000077799

Ensembl Acc Id:

ENSRNOP00000019555 ⟸ ENSRNOT00000019555

Ensembl Acc Id:

ENSRNOP00000096496 ⟸ ENSRNOT00000095762

RefSeq Acc Id:	XP_063129062 ⟸ XM_063272992
- Peptide Label:	isoform X1

Protein Domains

RING-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-O88846-F1-model_v2	AlphaFold	O88846	1-194	view protein structure

Transcriptome

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

Promoters

RGD ID:

13699404

Promoter ID:

EPDNEW_R9926

Type:

multiple initiation site

Name:

Rnf4_1

Description:

ring finger protein 4

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	14	81,679,070 - 81,679,130	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3583	AgrOrtholog
BioCyc Gene	G2FUF-15289	BioCyc
Ensembl Genes	ENSRNOG00000013930	Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOG00055016978	UniProtKB/Swiss-Prot
	ENSRNOG00060016549	UniProtKB/Swiss-Prot
	ENSRNOG00065028885	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000077799.2	UniProtKB/TrEMBL
	ENSRNOT00000095762.1	UniProtKB/Swiss-Prot
	ENSRNOT00055028879	UniProtKB/Swiss-Prot
	ENSRNOT00060028458	UniProtKB/Swiss-Prot
	ENSRNOT00065049898	UniProtKB/Swiss-Prot
Gene3D-CATH	3.30.40.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:5623495	IMAGE-MGC_LOAD
InterPro	RING-HC_RNF4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	RNF4-like	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:29274	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72476	IMAGE-MGC_LOAD
NCBI Gene	29274	ENTREZGENE
PANTHER	E3 UBIQUITIN-PROTEIN LIGASE RNF4	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	RING FINGER DOMAIN-CONTAINING	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	zf-RING_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Rnf4	PhenoGen
PROSITE	ZF_RING_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ZF_RING_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000013930	RatGTEx
	ENSRNOG00055016978	RatGTEx
	ENSRNOG00060016549	RatGTEx
	ENSRNOG00065028885	RatGTEx
SMART	RING	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	RING/U-box	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC209613
UniProt	A0A0G2K799_RAT	UniProtKB/TrEMBL
	A6IK32	ENTREZGENE, UniProtKB/TrEMBL
	A6IK33_RAT	UniProtKB/TrEMBL
	O88846	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2002-06-10	Rnf4	ring finger protein 4			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_physical_interaction	displays hormone-dependent binding to the androgen receptor	69969

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

RGD Manual Annotations

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Imported Disease Annotations - ClinVar

RGD Manual Annotations