RPUSD4 (RNA pseudouridine synthase D4)

Gene: RPUSD4 (RNA pseudouridine synthase D4) Chlorocebus sabaeus

Analyze

Symbol:

RPUSD4

Name:

RNA pseudouridine synthase D4

RGD ID:

18614054

Description:

ENCODES a protein that exhibits mitochondrial ribosomal large subunit rRNA binding (ortholog); tRNA binding (ortholog); INVOLVED IN mitochondrial tRNA pseudouridine synthesis (ortholog); mRNA pseudouridine synthesis (ortholog); positive regulation of mitochondrial translation (ortholog); ASSOCIATED WITH Chromosome 11, Partial Trisomy 11q (ortholog); Dwarfism (ortholog); genetic disease (ortholog); FOUND IN mitochondrion (ortholog); nucleoplasm (ortholog); ribonucleoprotein granule (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

mitochondrial RNA pseudouridine synthase RPUSD4; RNA pseudouridylate synthase domain containing 4; RNA pseudouridylate synthase domain-containing protein 4

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

ChlSab1.1 - Green Monkey 1.1 Assembly

Position:

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

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 Ontology Annotations Click to see Annotation Detail View

Biological Process

enzyme-directed rRNA pseudouridine synthesis (IEA)

mitochondrial tRNA pseudouridine synthesis (ISO)

mRNA processing (IEA)

mRNA pseudouridine synthesis (ISO)

positive regulation of mitochondrial translation (ISO)

pseudouridine synthesis (IEA)

RNA modification (IEA)

Cellular Component

mitochondrion (ISO)

nucleoplasm (ISO)

ribonucleoprotein granule (ISO)

Molecular Function

mitochondrial ribosomal large subunit rRNA binding (ISO)

protein binding (ISO)

pseudouridine synthase activity (IEA)

RNA binding (IEA)

tRNA binding (ISO)

References

Additional References at PubMed

PMID:22301074

Genomics

Comparative Map Data

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
(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
(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
(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
(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

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

	endocrine system	hemolymphoid system	nervous system
High
Medium	35		36
Low	1	20	24
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_008021429	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008021430	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005242581	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005242582	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000011	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCSAT00000000292 ⟹ ENSCSAP00000015763

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	1	117,330,040 - 117,338,682 (-)	Ensembl

RefSeq Acc Id:

XM_008021429 ⟹ XP_008019620

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	1	117,329,660 - 117,338,728 (-)	NCBI
Vero_WHO_p1.0	NW_023666043	8,733,820 - 8,743,925 (+)	NCBI

Sequence:

show sequence

TGCCGCCCTTCTCCACGTGGTCTTGGCTCGCCCCTCCCTTCCTGGCAAGATGGCGGCGCCCAGG
TGGAGGCCGTCGGGCCTCTGGATCCGGGGAAACAGCCAGGGTTTGGGGAGTCTCTTCAGTCTCG
TCTCAAAGCCATTTTGTGCCGCTGCTGCTGCCTCTACGTCCGTAAATGCCCAGAGATTAGCGGA
GAGGCTCCGAGCCCAGAAACAGGAACAAGACACAAACAAGAAGCCGGTGTCCACAAACCCTGTT
CAGCGGAGAGTGCAAGAAATAGTGCGGTTCACACGGCAGCTGCAGCGAGTCCACCCCAACGTGC
TTGCTAAGGCACTGACCCGAGGAATTCTCCACCAGGACAATAACCTTGTTGTCATCAATAAGCC
CTACGGTCTCCCTGTGCATGGTGGCCCTGGGGTCCAGCTCTGCATCAGTGATGTACTACCTATC
CTGGCAAAGATGCTTCATGGCCACAAGGCAGAGCCCTTGCATCTGTGCCACCGGCTGGACAAGG
AAACCACAGGCGTAATGGTGTTGGCTTGGGACAAGGACATGGCACATCAAGTCCAAGAGTTGTT
TAGAACCCGTCAGGTGGTGAAGAAGTACTGGGCCATCACTGTGCGTGTCCCCATGCCCTCAGCA
GGAGTCGTGGACATCCCCATTGTGGAGAAGGAAGCACAAGGCCAGCAGCAGCACCGCAAGATGA
CATTGTCCCCGAGCTACCGCATGGACAATGGGAAAATGGTGAAAGTGCGGCATAACCGGAATGC
ACAAGTTGCTGTAACTCGGTACCAGGTGCTCAGCAGTACTCTCTCCTCCGCCCTCGTGGAGCTC
CAGCCCATCACAGGAATAAAACATCAGCTTCGAGTTCACTTGTCTTTTGGATTGGATTGTCCAA
TACTTGGTGATCACAAGTACTCAGACTGGAACAGGTTGGCCCCCCAGAAGCTGTCCGTGGGCAC
CCTGAAGAAGCTGGGGCTGGAACAGTCGAAGGCCCGCTACATCCCCCTTCACCTGCATGCCCAG
CAGCTGATCCTGCCTGCCCTGGGGTCCAGGAAGGAGGATCTCAACTTGGTCTGCAAACTTCCTC
GCTTCTTTGTGTGTTCCCTGCGCCGCCTGGGTTTAGAAATGCCAAATCAGGATCAAAATGAGAA
CAACGAAGCCGAACATCTGGGAGCGCAGTGAAGACCGTGGGAGCACCCTGGTACCTGGGAGCGC
AGGTTGGCCTCTGAACTGTTCTTTGTTTACAGGACTCTGCTAACTTCTCACTTGGAACAGACTC
TATAAGACCCAGGTGGGATAAGGTGAAGCAACTCAGCTGCTCCAGGGCTTTTAATGGAGAACAA
AGTCTGTTTACTGATAGTTTGGCTGCACTGTGGAAAAGCCTGCTGGAAGTCTCCCTGCCGTGGG
CTCTCATTGCCAATGTGGAACAGAGCCCAGGGCCAGGCAGACTGGGGCAGTGACTGGAAAAGGA
AAACTAAAGGACAGAATCCAGGATCAGGAACTGTTTTTATCCAGCAGTGAAGCTCTTGAGCTCT
TAGGAAGGTTCCCGTGGTTGGAAAGAA

hide sequence

RefSeq Acc Id:

XR_005242581

Type:

NON-CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
Vero_WHO_p1.0	NW_023666043	8,733,820 - 8,759,417 (+)	NCBI

RefSeq Acc Id:

XR_005242582

Type:

NON-CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
Vero_WHO_p1.0	NW_023666043	8,733,820 - 8,816,405 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_008019620	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000015763.1

RefSeq Acc Id:	XP_008019620 ⟸ XM_008021429
- UniProtKB:	A0A0D9S4H4 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSCSAP00000015763 ⟸ ENSCSAT00000000292

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000002274	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000000292.1	UniProtKB/TrEMBL
Gene3D-CATH	Pseudouridine synthase	UniProtKB/TrEMBL
InterPro	PsdUridine_synth_cat_dom_sf	UniProtKB/TrEMBL
	PsdUridine_synth_RluC/D_CS	UniProtKB/TrEMBL
	PsdUridine_synth_RsuA/RluA	UniProtKB/TrEMBL
KEGG Report	csab:103248785	UniProtKB/TrEMBL
NCBI Gene	RPUSD4	ENTREZGENE
PANTHER	MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE	UniProtKB/TrEMBL
	PSEUDOURIDYLATE SYNTHASE RPUSD4, MITOCHONDRIAL	UniProtKB/TrEMBL
Pfam	PseudoU_synth_2	UniProtKB/TrEMBL
PROSITE	PSI_RLU	UniProtKB/TrEMBL
Superfamily-SCOP	SSF55120	UniProtKB/TrEMBL
UniProt	A0A0D9S4H4	ENTREZGENE, UniProtKB/TrEMBL

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)

Send us a Message

Imported Disease Annotations - ClinVar