Rpusd4 (RNA pseudouridine synthase D4)

Gene: Rpusd4 (RNA pseudouridine synthase D4) Rattus norvegicus

Analyze

Symbol:

Rpusd4

Name:

RNA pseudouridine synthase D4

RGD ID:

1311268

Description:

Predicted to enable mitochondrial ribosomal large subunit rRNA binding activity; pseudouridine synthase activity; and tRNA binding activity. Predicted to be involved in mRNA pseudouridine synthesis; mitochondrial tRNA pseudouridine synthesis; and positive regulation of mitochondrial translation. Predicted to be located in mitochondrion; nucleoplasm; and ribonucleoprotein granule. Orthologous to human RPUSD4 (RNA pseudouridine synthase D4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; C60 fullerene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC315550; MGC116175; mitochondrial RNA pseudouridine synthase Rpusd4; pseudouridylate synthase RPUSD4, mitochondrial; RGD1311268; RNA pseudouridylate synthase domain containing 4; RNA pseudouridylate synthase domain-containing protein 4; similar to hypothetical protein FLJ14494

RGD Orthologs

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):	RPUSD4 (RNA pseudouridine synthase D4)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Rpusd4 (RNA pseudouridylate synthase domain containing 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Rpusd4 (RNA pseudouridine synthase D4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RPUSD4 (RNA pseudouridine synthase D4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RPUSD4 (RNA pseudouridine synthase D4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rpusd4 (RNA pseudouridine synthase D4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RPUSD4 (RNA pseudouridine synthase D4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	RPUSD4 (RNA pseudouridine synthase D4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rpusd4 (RNA pseudouridine synthase D4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RPUSD4 (RNA pseudouridine synthase D4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Rpusd4 (RNA pseudouridylate synthase domain containing 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	rpusd4 (RNA pseudouridine synthase D4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ZK287.7	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoInspector\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	PUS5	Alliance	DIOPT (InParanoid\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	rpusd4	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	8	41,875,217 - 41,884,702 (+)	NCBI		GRCr8
mRatBN7.2	8	33,617,384 - 33,626,873 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	33,617,379 - 33,626,873 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	8	37,687,547 - 37,697,027 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	35,970,590 - 35,980,072 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	33,833,432 - 33,842,913 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	36,467,706 - 36,477,190 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	36,467,706 - 36,477,189 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	36,485,875 - 36,495,293 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	35,049,195 - 35,058,741 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	8	35,057,960 - 35,067,504 (+)	NCBI
Celera	8	35,036,893 - 35,046,936 (+)	NCBI		Celera
Cytogenetic Map	8	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

Chromosome 11, Partial Trisomy 11q (ISO)

Dwarfism (ISO)

genetic disease (ISO)

holoprosencephaly 11 (ISO)

Jacobsen Syndrome (ISO)

schizophrenia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

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

2,4-dinitrotoluene (EXP)

acrolein (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

C60 fullerene (EXP)

cadmium atom (ISO)

cadmium dichloride (ISO)

CU-O LINKAGE (ISO)

dimethylarsinous acid (ISO)

diquat (ISO)

doxorubicin (ISO)

methyl methanesulfonate (ISO)

ozone (ISO)

paracetamol (ISO)

perfluorohexanesulfonic acid (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

potassium chromate (ISO)

temozolomide (ISO)

titanium dioxide (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

enzyme-directed rRNA pseudouridine synthesis (IEA)

mitochondrial tRNA pseudouridine synthesis (ISO)

mRNA processing (IEA)

mRNA pseudouridine synthesis (ISO)

positive regulation of mitochondrial translation (ISO,ISS)

RNA splicing (IEA)

Cellular Component

mitochondrial matrix (IEA)

mitochondrion (ISO)

nucleoplasm (IEA,ISO)

ribonucleoprotein granule (ISO)

Molecular Function

mitochondrial ribosomal large subunit rRNA binding (ISO)

protein binding (ISO)

pseudouridine synthase activity (IEA,ISO)

RNA binding (IEA)

tRNA binding (ISO)

tRNA pseudouridine synthase activity (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.	GOA pipeline	RGD automated data pipeline
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
4.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:12477932	PMID:18614015	PMID:22658674	PMID:22681889	PMID:27667664

Genomics

Comparative Map Data

Rpusd4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	8	41,875,217 - 41,884,702 (+)	NCBI		GRCr8
mRatBN7.2	8	33,617,384 - 33,626,873 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	33,617,379 - 33,626,873 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	8	37,687,547 - 37,697,027 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	35,970,590 - 35,980,072 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	33,833,432 - 33,842,913 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	36,467,706 - 36,477,190 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	36,467,706 - 36,477,189 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	36,485,875 - 36,495,293 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	35,049,195 - 35,058,741 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	8	35,057,960 - 35,067,504 (+)	NCBI
Celera	8	35,036,893 - 35,046,936 (+)	NCBI		Celera
Cytogenetic Map	8	q21	NCBI

RPUSD4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	11	126,202,096 - 126,211,650 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	11	126,202,096 - 126,211,692 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	11	126,071,991 - 126,081,545 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	125,577,519 - 125,586,751 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	11	125,577,518 - 125,586,751	NCBI
Celera	11	123,237,291 - 123,246,895 (-)	NCBI		Celera
Cytogenetic Map	11	q24.2	NCBI
HuRef	11	122,013,961 - 122,023,565 (-)	NCBI		HuRef
CHM1_1	11	125,958,497 - 125,968,095 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	11	126,231,624 - 126,241,182 (-)	NCBI		T2T-CHM13v2.0

Rpusd4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	35,179,177 - 35,187,253 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	9	35,179,161 - 35,189,027 (+)	Ensembl		GRCm39 Ensembl
GRCm38	9	35,267,881 - 35,275,957 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	35,267,865 - 35,277,731 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	35,075,466 - 35,083,542 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	9	35,017,552 - 35,025,628 (+)	NCBI		MGSCv36	mm8
Celera	9	32,504,456 - 32,512,514 (+)	NCBI		Celera
Cytogenetic Map	9	A4	NCBI
cM Map	9	20.15	NCBI

Rpusd4
(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_004955412	27,229,492 - 27,239,339 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955412	27,231,371 - 27,239,366 (-)	NCBI	ChiLan1.0	ChiLan1.0

RPUSD4
(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	9	126,867,548 - 126,894,866 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	11	127,976,408 - 128,002,490 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	11	120,997,815 - 121,025,558 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	11	124,926,908 - 124,936,584 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	124,926,910 - 124,936,621 (-)	Ensembl	panpan1.1		panPan2

RPUSD4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	5	8,300,421 - 8,311,193 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	5	8,299,771 - 8,311,210 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	5	8,361,626 - 8,372,396 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	5	8,256,012 - 8,266,783 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	5	8,256,031 - 8,269,068 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	5	8,325,591 - 8,336,354 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	5	8,299,291 - 8,310,070 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	5	8,333,577 - 8,344,368 (+)	NCBI		UU_Cfam_GSD_1.0

Rpusd4
(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_024404947	108,416,888 - 108,436,462 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936572	6,013,582 - 6,026,837 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936572	6,013,920 - 6,027,023 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RPUSD4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	9	53,296,538 - 53,309,180 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	9	53,295,854 - 53,309,192 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	9	59,186,851 - 59,194,507 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RPUSD4
(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	1	117,313,209 - 117,338,728 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	1	117,330,040 - 117,338,682 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666043	8,733,820 - 8,816,405 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Rpusd4
(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_004624812	359,184 - 366,872 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624812	311,912 - 366,427 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Rpusd4
19 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	283
Count of miRNA genes:	184
Interacting mature miRNAs:	211
Transcripts:	ENSRNOT00000015670
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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
12880023	Bw184	Body weight QTL 184		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	8	2097640	47097640	Rat
12880025	Cm102	Cardiac mass QTL 102		0.044	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	8	2097640	47097640	Rat
12880028	Cm103	Cardiac mass QTL 103		0.02	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	8	2097640	47097640	Rat
12880044	Am9	Aortic mass QTL 9		0.007	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	8	2097640	47097640	Rat
2317032	Ginf2	Gastrointestinal inflammation QTL 2	3.21	0.005	liver integrity trait (VT:0010547)	liver granuloma severity score (CMO:0002157)	8	4705810	49705810	Rat
2317036	Livw3	Liver weight QTL 3	2.43	0.01	liver mass (VT:0003402)	liver weight to body weight ratio (CMO:0000633)	8	4705810	49705810	Rat
2317048	Ginf1	Gastrointestinal inflammation QTL 1	3.52	0.005	cecum mucosa thickness (VT:0010234)	enterocolitis severity score (CMO:0002138)	8	4705810	49705810	Rat
2301416	Bp315	Blood pressure QTL 315		0.008	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	7670578	52670578	Rat
1354595	Despr4	Despair related QTL 4	2.16	0.0036	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	8	7688955	52688955	Rat
1354627	Despr14	Despair related QTL 14		0.0056	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	8	7688955	52688955	Rat
1581557	Eae16	Experimental allergic encephalomyelitis QTL 16	3.8		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	8	8462195	110921472	Rat
2317030	Wbc5	White blood cell count QTL 5	3.21	0.005	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	8	8736635	53736635	Rat
2317051	Aia18	Adjuvant induced arthritis QTL 18	2.42		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	8	8736635	53736635	Rat
1598824	Memor4	Memory QTL 4	2.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	8	9712220	53356647	Rat
1357398	Slep3	Serum leptin concentration QTL 3	3.43		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	8	9712463	41866876	Rat
2302367	Slep5	Serum leptin concentration QTL 5	3.43		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	8	9712463	41866876	Rat
631650	Stl6	Serum triglyceride level QTL 6	4	0.0019	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	10378157	112202585	Rat
1558646	Swd5	Spike wave discharge measurement QTL 5	3.45	0.00036	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	8	14906751	59906751	Rat
61373	Mcs4	Mammary carcinoma susceptibility QTL 4	1.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	8	16290444	61290444	Rat
631271	Lecl1	Lens clarity QTL 1		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	8	18984168	84531599	Rat
731182	Uae24	Urinary albumin excretion QTL 24	6.4		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	19331152	93965294	Rat
631842	Inf1	Infertility severity QTL 1	4.1	0.001	seminal gland mass (VT:0010524)	seminal vesicle wet weight (CMO:0001603)	8	22662330	67662330	Rat
2303564	Gluco43	Glucose level QTL 43	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	26130187	71130187	Rat
2303572	Insul13	Insulin level QTL 13	2		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	8	26130187	71130187	Rat
1359021	Bp271	Blood pressure QTL 271	1.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	26644912	46711092	Rat
631648	Stl5	Serum triglyceride level QTL 5	4	0.0003	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	27205715	54998217	Rat
1358892	Kidm26	Kidney mass QTL 26	3.69		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	27205715	99103503	Rat
1358896	Bp262	Blood pressure QTL 262	2.89		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	27205715	99103503	Rat
1358907	Cm40	Cardiac mass QTL 40	1.89		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	27205715	99103503	Rat
1331804	Cm30	Cardiac mass QTL 30	3.77443		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	8	28242912	53961020	Rat
1300146	Rf17	Renal function QTL 17	2.9		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	8	28242912	73242912	Rat
8662823	Vetf5	Vascular elastic tissue fragility QTL 5	1.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	8	28242912	99525068	Rat
2302278	Gluco36	Glucose level QTL 36	4.2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	29502665	50095447	Rat
724514	Uae15	Urinary albumin excretion QTL 15	2.9		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	29502665	70386295	Rat
1549908	Neudeg1	Neurodegradation QTL 1	5.5	0	nervous system integrity trait (VT:0010566)	logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)	8	30188867	94457446	Rat
70206	Alc20	Alcohol consumption QTL 20	2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	8	30848154	40713225	Rat
61337	Bp22	Blood pressure QTL 22	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	30848154	42692818	Rat
1331744	Bp217	Blood pressure QTL 217	3.398		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	30848154	58482492	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	30848154	61290444	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	30848154	61290444	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	30848154	61290444	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	30848154	61290444	Rat
11556286	Cm81	Cardiac mass QTL 81		0.01	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	30848154	61290444	Rat
1359033	Bp273	Blood pressure QTL 273			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	30848154	61290444	Rat
2313046	Bss78	Bone structure and strength QTL 78	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	8	30848154	82460899	Rat
2313057	Bss76	Bone structure and strength QTL 76	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	8	30848154	82460899	Rat
2313067	Bss77	Bone structure and strength QTL 77	3.1	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	8	30848154	82460899	Rat
2313088	Bss75	Bone structure and strength QTL 75	3.1	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	8	30848154	82460899	Rat
1578755	Pur5	Proteinuria QTL 5	3.3	0.0001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	8	30848154	101699754	Rat
1578765	Klgr1	Kidney lesion grade QTL 1	3.3	0.0001	kidney morphology trait (VT:0002135)	organ lesion measurement (CMO:0000677)	8	30848154	101699754	Rat
1578769	Uae31	Urinary albumin excretion QTL 31	3.3	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	30848154	101699754	Rat
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	30848259	105647037	Rat
1298065	Scl16	Serum cholesterol level QTL 16	3.8		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	30856404	75856404	Rat
1582222	Epfw2	Epididymal fat weight QTL 2	3.2	0.0005	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	8	31737729	76737729	Rat

Markers in Region

RH125999

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	8	33,626,661 - 33,626,864 (+)	MAPPER	mRatBN7.2
Rnor_6.0	8	36,476,979 - 36,477,181	NCBI	Rnor6.0
Rnor_5.0	8	36,495,082 - 36,495,284	UniSTS	Rnor5.0
RGSC_v3.4	8	35,058,530 - 35,058,732	UniSTS	RGSC3.4
Celera	8	35,046,725 - 35,046,927	UniSTS
Cytogenetic Map	8	q21	UniSTS

RH131616

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	8	33,626,543 - 33,626,733 (+)	MAPPER	mRatBN7.2
Rnor_6.0	8	36,476,861 - 36,477,050	NCBI	Rnor6.0
Rnor_5.0	8	36,494,964 - 36,495,153	UniSTS	Rnor5.0
RGSC_v3.4	8	35,058,412 - 35,058,601	UniSTS	RGSC3.4
Celera	8	35,046,607 - 35,046,796	UniSTS
RH 3.4 Map	8	289.1	UniSTS
Cytogenetic Map	8	q21	UniSTS

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	33	38	22	19	22		2	61	29	41	11
Low		10	19	19		19	8	9	13	6			8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001025284	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC111781	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC098023	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474007	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000008	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000015670 ⟹ ENSRNOP00000015670

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	8	33,617,379 - 33,626,873 (+)	Ensembl
Rnor_6.0 Ensembl	8	36,467,706 - 36,477,189 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000100792 ⟹ ENSRNOP00000096522

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	8	33,617,379 - 33,624,061 (+)	Ensembl

RefSeq Acc Id:

NM_001025284 ⟹ NP_001020455

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	8	41,875,217 - 41,884,702 (+)	NCBI
mRatBN7.2	8	33,617,384 - 33,626,873 (+)	NCBI
Rnor_6.0	8	36,467,706 - 36,477,190 (+)	NCBI
Rnor_5.0	8	36,485,875 - 36,495,293 (+)	NCBI
RGSC_v3.4	8	35,049,195 - 35,058,741 (+)	RGD
Celera	8	35,036,893 - 35,046,936 (+)	RGD

Sequence:

show sequence

CCGCAAGATGGCCGCGCCCTTGTTGGGTTCCCCTGGTCTCCAGGTCCTGAGTATGAGTTCGCGT
ACCGGGAAATTGTTCACTCCCAGCTCCAGGTCGTTTTGTTCCAGAGCTACTTCCTCCAGGCCCC
TGAATGCTCAGAGACTGGCGGAGAAGCTCCGAGCTCAGAAACAAGAGCAAAAGACGAAGGAAAT
GCGGGTGCCCACCAACCCCGTTCAGCGGCGGGTGCAGGAGCTAGTGAGATTCACACAGCAGCTA
CAGCGTGTTCACCCCAATGTGCTTGCTAAGGAACTGAGCCGAAGGATTCTCCACCAGGACAAAG
ACCTTGTGGTCATTAATAAACCCTATGGTCTCCCTGTCCATGGTGGCCCTGGAGTCCAGCTCTG
CATCAGTGATGTTCTGCCCATCTTGGCAAAGATGCTTCATGGCCACAAGGCAGAACCTTTGCAT
CTGTGCCACCGTCTGGACAAAGAGACCACAGGTGTAATGGTTTTGGCTTGGGAGAAGGACATGG
CACATCAAGTCCAGGAGCTGTTTAGAACCCGCCAGGTGGAAAAGAAGTACTGGGCCATCACTGT
GCGTGTTCCCTTGCCCTCGGCAGGAGTTGTGGATATCCCCATCATGGAGAAGGAAGTGGCTGGG
CAGCAGCAACACCACAAGATGACGCTACGTCCAAGTTACCGCATGGACAATGGGAAAATGGTAA
AGGTACGGGCCAGCCGGGATGCACACGTCGCGGTAACTCAGTACCAGGTGCTGAGCAGCACCCC
GTCCTCCGCCCTTGTGGAGCTGCAGCCTGTCACTGGAATAAAACATCAGCTCCGAGTTCACCTG
GCCTTTGGGTTGGATTGCCCAATCCTCGGTGATCACAAATACTCAGACTGGAATAGGTTGGCCC
CTCAGAAACTTTCTGCTGGCACACTGAAGAAGCTGGGGCTACAACAGTCAAAGGCCCGCTACAT
CCCTCTTCATCTGCATGCCAGGCAGCTCATCCTGCCTGCTCTGGGCTCCAGGACAGAGGAACTC
CTCCTGGCCTGCAAGCTTCCTCACTTCTTTGCACGTTCCCTGCGTCGTCTGGGTTTAGATATGC
CAAATGAGGATCAAAGCAGAAGCCATGAGGCCAGGCATGTGGAAGCACGGTGAAGACTGTTGGG
CAGTTTGGCCCCAGAGCTCTGCTGTATTTATTTCATGGATTCTGCTAACTTCTCACTTAGAACA
GATGACAAGAGCCGGGTGGGGTAAGTTGGAAAAACTTGGCCACTTCAGGACTGTAATGGAGAAC
GAAGTCTTATTTATGGCAGTCGGGCTGTAATGTGGGAAAGCCTGCTGGAGTCTCCTCCATAGGT
CACTTTGTCAAGATGGAGGAGAGCCTAGGAGGCAGCAGACTGAACCAGTAAAGGAGAACCAAAG
GATGGATCTGCTTAGGACTTGTCTTCATCCAACAGGAAGGAAAGCTGAGCTATCAGGAGTGCTC
CGTTGGAAAGATGTCTTGGATAAACATGCATCGAGGGCCCAGGGGTTTTGTCCACTAGAGTGTG
GGTGCTGTACTGCCCCAGCAGTGAGCCTGTGAAAGGGTTGTTGGGGTGAGGTAAGTGACAGGCA
GCTAACATAAGTGAGTGAAGCTGGCAGGGTGGAAGGCAGCGGACAACAGACCAAACTCAAGCTG
TCTAAGGGTTATTAGCACCAGTTGATTGTTGCCCTGTGGGCAAGTTTACTATTTTCTTTTAGAG
AACCAGGAAATCCAGATATTTCTGCGAAATCTCCCAATCTATTGCTATCTAAATAAAAACATTT
TGAAATATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001020455	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH98023	(Get FASTA)	NCBI Sequence Viewer
	EDL83272	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000015670
	ENSRNOP00000015670.4
	ENSRNOP00000096522.1
	ENSRNOP00055012415
	ENSRNOP00060015573
	ENSRNOP00065021569
GenBank Protein	Q4QQT0	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001020455 ⟸ NM_001025284

- UniProtKB:

Q4QQT0 (UniProtKB/Swiss-Prot), A6JYK3 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAAPLLGSPGLQVLSMSSRTGKLFTPSSRSFCSRATSSRPLNAQRLAEKLRAQKQEQKTKEMRV
PTNPVQRRVQELVRFTQQLQRVHPNVLAKELSRRILHQDKDLVVINKPYGLPVHGGPGVQLCIS
DVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKYWAITVRV
PLPSAGVVDIPIMEKEVAGQQQHHKMTLRPSYRMDNGKMVKVRASRDAHVAVTQYQVLSSTPSS
ALVELQPVTGIKHQLRVHLAFGLDCPILGDHKYSDWNRLAPQKLSAGTLKKLGLQQSKARYIPL
HLHARQLILPALGSRTEELLLACKLPHFFARSLRRLGLDMPNEDQSRSHEARHVEAR

hide sequence

RefSeq Acc Id:

ENSRNOP00000015670 ⟸ ENSRNOT00000015670

RefSeq Acc Id:

ENSRNOP00000096522 ⟸ ENSRNOT00000100792

Protein Domains

Pseudouridine synthase RsuA/RluA-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q4QQT0-F1-model_v2	AlphaFold	Q4QQT0	1-377	view protein structure

Transcriptome

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

Promoters

RGD ID:

13695838

Promoter ID:

EPDNEW_R6363

Type:

multiple initiation site

Name:

Rpusd4_1

Description:

RNA pseudouridylate synthase domain containing 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	8	36,467,704 - 36,467,764	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311268	AgrOrtholog
BioCyc Gene	G2FUF-31176	BioCyc
Ensembl Genes	ENSRNOG00000011567	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ENSRNOG00055009160	UniProtKB/Swiss-Prot
	ENSRNOG00060011711	UniProtKB/Swiss-Prot
	ENSRNOG00065016489	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000015670	ENTREZGENE
	ENSRNOT00000015670.7	UniProtKB/Swiss-Prot
	ENSRNOT00000100792.1	UniProtKB/TrEMBL
	ENSRNOT00055015500	UniProtKB/Swiss-Prot
	ENSRNOT00060019827	UniProtKB/Swiss-Prot
	ENSRNOT00065027440	UniProtKB/Swiss-Prot
Gene3D-CATH	Pseudouridine synthase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7455606	IMAGE-MGC_LOAD
InterPro	PsdUridine_synth_cat_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PsdUridine_synth_RluC/D_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PsdUridine_synth_RsuA/RluA	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:315550	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:116175	IMAGE-MGC_LOAD
NCBI Gene	315550	ENTREZGENE
PANTHER	MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PSEUDOURIDYLATE SYNTHASE RPUSD4, MITOCHONDRIAL	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	PseudoU_synth_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Rpusd4	PhenoGen
PROSITE	PSI_RLU	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000011567	RatGTEx
	ENSRNOG00055009160	RatGTEx
	ENSRNOG00060011711	RatGTEx
	ENSRNOG00065016489	RatGTEx
Superfamily-SCOP	SSF55120	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8I6AQL4_RAT	UniProtKB/TrEMBL
	A6JYK3	ENTREZGENE, UniProtKB/TrEMBL
	Q4QQT0	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2018-09-21	Rpusd4	RNA pseudouridine synthase D4	Rpusd4	RNA pseudouridylate synthase domain containing 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Rpusd4	RNA pseudouridylate synthase domain containing 4	RGD1311268	similar to hypothetical protein FLJ14494	Symbol and Name updated	1299863	APPROVED
2005-12-06	RGD1311268	similar to hypothetical protein FLJ14494	RGD1311268_predicted	similar to hypothetical protein FLJ14494 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1311268_predicted	similar to hypothetical protein FLJ14494 (predicted)	LOC315550_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC315550_predicted	similar to hypothetical protein FLJ14494 (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar