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Gene: Rpusd4 (RNA pseudouridine synthase D4) Rattus norvegicus

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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 positive regulation of mitochondrial translation and pseudouridine synthesis. Predicted to be located in mitochondrial matrix 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 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):	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
Rattus rattus (black 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)
Caenorhabditis elegans (roundworm):	ZK287.7	Alliance	DIOPT (Ensembl Compara\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	PUS5	Alliance	DIOPT (InParanoid\|OrthoFinder)
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:

GRCr8 - GRCr8 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	GRCr8		GRCr8
GRCr8 Ensembl	8	41,874,764 - 41,884,699 (+)	Ensembl				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
UTH_Rnor_SHR_Utx	8	37,687,547 - 37,697,027 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	35,970,590 - 35,980,072 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	33,833,432 - 33,842,913 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	36,467,706 - 36,477,190 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	36,467,706 - 36,477,189 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	8	36,485,875 - 36,495,293 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	8	35,049,195 - 35,058,741 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	8	35,036,893 - 35,046,936 (+)	NCBI		Celera
RGSC_v3.1	8	35,057,960 - 35,067,504 (+)	NCBI
Cytogenetic Map	8	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-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)

bis(2-ethylhexyl) phthalate (ISO)

Butylbenzyl phthalate (ISO)

C60 fullerene (EXP)

cadmium atom (ISO)

cadmium dichloride (ISO)

CU-O LINKAGE (ISO)

DDE (ISO)

dimethylarsinous acid (ISO)

diquat (ISO)

doxorubicin (ISO)

methyl methanesulfonate (ISO)

nitrates (ISO)

okadaic acid (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 (IBA)

mitochondrial RNA modification (ISO)

mitochondrial tRNA pseudouridine synthesis (IEA,ISO)

mRNA processing (IEA)

mRNA pseudouridine synthesis (IEA,ISO)

positive regulation of mitochondrial translation (IEA,ISO,ISS)

pseudouridine synthesis (IEA)

RNA modification (IEA)

RNA splicing (IEA)

rRNA processing (IEA)

rRNA pseudouridine synthesis (IEA,ISO)

tRNA processing (IEA)

Cellular Component

cytoplasm (IEA)

mitochondrial matrix (IEA,ISO)

mitochondrion (IEA,ISO)

nucleus (IEA)

ribonucleoprotein granule (IEA,ISO)

Molecular Function

isomerase activity (IEA)

mitochondrial ribosomal large subunit rRNA binding (IEA,ISO)

protein binding (ISO)

pseudouridine synthase activity (IBA,IEA,ISO)

RNA binding (IEA)

tRNA binding (IEA,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	GRCr8		GRCr8
GRCr8 Ensembl	8	41,874,764 - 41,884,699 (+)	Ensembl				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
UTH_Rnor_SHR_Utx	8	37,687,547 - 37,697,027 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	35,970,590 - 35,980,072 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	33,833,432 - 33,842,913 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	36,467,706 - 36,477,190 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	36,467,706 - 36,477,189 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	8	36,485,875 - 36,495,293 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	8	35,049,195 - 35,058,741 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	8	35,036,893 - 35,046,936 (+)	NCBI		Celera
RGSC_v3.1	8	35,057,960 - 35,067,504 (+)	NCBI
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	126,202,095 - 126,211,692 (-)	Ensembl			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	Build 36	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		GRCm39
GRCm38	9	35,267,881 - 35,275,957 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	35,267,865 - 35,277,731 (+)	Ensembl			mm10	GRCm38
MGSCv37	9	35,075,466 - 35,083,542 (+)	NCBI	MGSCv37	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	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			panPan2	panpan1.1

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	CanFam3.1
Dog10K_Boxer_Tasha	5	8,361,626 - 8,372,396 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	5	8,256,012 - 8,266,783 (+)	NCBI	ROS_Cfam_1.0	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	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 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			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 Ensembl	chlSab2	Vervet-AGM
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 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624812	311,912 - 366,427 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Rpusd4
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	8	30,819,271 - 30,826,897 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Rpusd4
73 total Variants

miRNA Target Status (No longer updated)

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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1298065	Scl16	Serum cholesterol level QTL 16	3.8		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	39752803	84752803	Rat
1357398	Slep3	Serum leptin concentration QTL 3	3.43		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	8	17994105	50763951	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	39106258	91341052	Rat
2317030	Wbc5	White blood cell count QTL 5	3.21	0.005	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	8	16994642	61994642	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	39106258	91341052	Rat
1578769	Uae31	Urinary albumin excretion QTL 31	3.3	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	39106363	103375781	Rat
2301416	Bp315	Blood pressure QTL 315		0.008	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	15952279	60952279	Rat
2317032	Ginf2	Gastrointestinal inflammation QTL 2	3.21	0.005	liver integrity trait (VT:0010547)	liver granuloma severity score (CMO:0002157)	8	12964165	57964165	Rat
11556286	Cm81	Cardiac mass QTL 81		0.01	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	39106258	84106258	Rat
2317036	Livw3	Liver weight QTL 3	2.43	0.01	liver mass (VT:0003402)	liver weight to body weight ratio (CMO:0000633)	8	12964165	57964165	Rat
12880023	Bw184	Body weight QTL 184		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	8	10382540	55382540	Rat
1578765	Klgr1	Kidney lesion grade QTL 1	3.3	0.0001	kidney morphology trait (VT:0002135)	organ lesion measurement (CMO:0000677)	8	39106363	103375781	Rat
2317051	Aia18	Adjuvant induced arthritis QTL 18	2.42		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	8	16994642	61994642	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	10382540	55382540	Rat
61337	Bp22	Blood pressure QTL 22	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	39106258	51589833	Rat
1578755	Pur5	Proteinuria QTL 5	3.3	0.0001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	8	39106258	103375958	Rat
2317048	Ginf1	Gastrointestinal inflammation QTL 1	3.52	0.005	cecum mucosa thickness (VT:0010234)	enterocolitis severity score (CMO:0002138)	8	12964165	57964165	Rat
12880025	Cm102	Cardiac mass QTL 102		0.044	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	8	10382540	55382540	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	39106258	91341052	Rat
1358896	Bp262	Blood pressure QTL 262	2.89		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	35464071	107982864	Rat
2302278	Gluco36	Glucose level QTL 36	4.2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	8	37760859	58991895	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	10382540	55382540	Rat
724514	Uae15	Urinary albumin excretion QTL 15	2.9		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	8	37760859	61459705	Rat
631648	Stl5	Serum triglyceride level QTL 5	4	0.0003	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	8	35464071	71842899	Rat
61353	Bp35	Blood pressure QTL 35		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	8	39106258	84106258	Rat
631842	Inf1	Infertility severity QTL 1	4.1	0.001	seminal gland mass (VT:0010524)	seminal vesicle wet weight (CMO:0001603)	8	31543661	76543661	Rat
1359033	Bp273	Blood pressure QTL 273			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	39106258	84106258	Rat
1358907	Cm40	Cardiac mass QTL 40	1.89		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	8	35464071	107982864	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	17993862	62252873	Rat
1331744	Bp217	Blood pressure QTL 217	3.398		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	8	39106258	67378345	Rat
2316950	Scl66	Serum cholesterol level QTL 66	4.1		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	8	39106363	114525825	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	39106258	91341052	Rat
724540	Uae8	Urinary albumin excretion QTL 8	5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	8	39106258	103375958	Rat
1358892	Kidm26	Kidney mass QTL 26	3.69		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	8	35464071	107982864	Rat
1359021	Bp271	Blood pressure QTL 271	1.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	8	34125902	55607752	Rat
2302367	Slep5	Serum leptin concentration QTL 5	3.43		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	8	17994105	50763951	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	39106258	49610361	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

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

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

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

Ensembl Acc Id:

ENSRNOT00000015670 ⟹ ENSRNOP00000015670

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	8	41,874,764 - 41,884,699 (+)	Ensembl
mRatBN7.2 Ensembl	8	33,617,379 - 33,626,873 (+)	Ensembl
Rnor_6.0 Ensembl	8	36,467,706 - 36,477,189 (+)	Ensembl

Ensembl 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
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

Ensembl Acc Id:

ENSRNOP00000015670 ⟸ ENSRNOT00000015670

Ensembl 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
Ensembl Transcript	ENSRNOT00000015670	ENTREZGENE
	ENSRNOT00000015670.7	UniProtKB/Swiss-Prot
Gene3D-CATH	Pseudouridine synthase	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7455606	IMAGE-MGC_LOAD
InterPro	PsdUridine_synth_cat_dom_sf	UniProtKB/Swiss-Prot
	PsdUridine_synth_RluC/D_CS	UniProtKB/Swiss-Prot
	PsdUridine_synth_RsuA/RluA	UniProtKB/Swiss-Prot
	RluA_PseudoU_synthase	UniProtKB/Swiss-Prot
KEGG Report	rno:315550	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:116175	IMAGE-MGC_LOAD
NCBI Gene	315550	ENTREZGENE
PANTHER	MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE	UniProtKB/Swiss-Prot
	PSEUDOURIDYLATE SYNTHASE RPUSD4, MITOCHONDRIAL	UniProtKB/Swiss-Prot
Pfam	PseudoU_synth_2	UniProtKB/Swiss-Prot
PhenoGen	Rpusd4	PhenoGen
PROSITE	PSI_RLU	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000011567	RatGTEx
Superfamily-SCOP	SSF55120	UniProtKB/Swiss-Prot
UniProt	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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