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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

RPUSD1 Gene

protein-coding GIFtS: 45
GCID: GC16M000834

RNA pseudouridylate synthase domain containing 1

(Previous name: chromosome 16 open reading frame 40 )
(Previous symbol: C16orf40)

Explore 1 disease affiliated with
RPUSD1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
RNA Pseudouridylate Synthase Domain Containing 1¹ ²		MGC19600¹
C16orf40¹ ² ³		Chromosome 16 Open Reading Frame 40¹
RLUCL¹ ² ³		Ribosomal Large Subunit Pseudouridine Synthase C Like²
Ribosomal Large Subunit Pseudouridine Synthase C-Like Protein² ³		RNA Pseudouridylate Synthase Domain-Containing Protein 1²

External Ids:	HGNC: 14173¹	Entrez Gene: 113000²	Ensembl: ENSG00000007376⁷	UniProtKB: Q9UJJ7³

Export aliases for RPUSD1 gene to outside databases

Previous GC identifers: GC16M000779 GC16M000756

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000016.9 NC_018927.1 NT_010393.16

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the RPUSD1 gene promoter:
Elk-1 MyoD LUN-1 Nkx2-5 LCR-F1 POU2F1 POU2F1a NF-Y CBF(2)
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: RPUSD1 promoter sequence

Search SABiosciences Chromatin IP Primers for RPUSD1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RPUSD1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p13.3 Ensembl cytogenetic band: 16p13.3 HGNC cytogenetic band: 16p13.3

RPUSD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPUSD1 gene location

GeneLoc information about chromosome 16 GeneLoc Exon Structure

GeneLoc location for GC16M000834: view genomic region (about GC identifiers)

Start:	834,974 bp from pter	End:	838,397 bp from pter
Size:	3,424 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RUSD1_HUMAN, Q9UJJ7 (See protein sequence)

Recommended Name: RNA pseudouridylate synthase domain-containing protein 1

Size: 312 amino acids; 34756 Da

Secondary accessions: D3DU66

Explore the universe of human proteins at neXtProt for RPUSD1: NX_Q9UJJ7

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9UJJ7

RPUSD1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_478072.1

ENSEMBL proteins:

ENSP00000455026 ENSP00000007264 ENSP00000457722 ENSP00000455862 ENSP00000454616

ENSP00000456692 ENSP00000457527 ENSP00000458059 ENSP00000456545 ENSP00000456231

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	Uscn Proteins for RPUSD1

Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005575	cellular_component	ND	--

RPUSD1 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

RPUSD1 for domains About GeneDecksing

2 InterPro domains/families:

IPR020103 PsdUridine_synth_cat_dom

IPR006145 PsdUridine_synth_RsuA/RluD

Graphical View of Domain Structure for InterPro Entry Q9UJJ7

ProtoNet protein and cluster: Q9UJJ7

1 Blocks protein family: IPB006224 Pseudouridine synthase

UniProtKB/Swiss-Prot: RUSD1_HUMAN, Q9UJJ7

Similarity: Belongs to the pseudouridine synthase RluA family

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPUSD1

Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003674	molecular_function	ND	--
GO:0003723	RNA binding	IEA	--
GO:0009982	pseudouridine synthase activity	IEA	--

RPUSD1 for ontologies About GeneDecksing

1 GenomeRNAi human phenotype for RPUSD1:

Increased G2M DNA content, inc

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for RPUSD1

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for RPUSD1 (ENSP00000007264⁴) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
FOXJ1	ENSP00000323880⁴	STRING: ENSP00000323880
UBC	ENSP00000344818⁴	STRING: ENSP00000344818

About this table

Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001522	pseudouridine synthesis	IEA	--
GO:0008150	biological_process	ND	--

RPUSD1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for RPUSD1

1 HMDB Compound for RPUSD1 About this table

Compound	Synonyms	CAS #	PubMed Ids
Pseudouridine	5-(b-D-Ribofuranosyl)uracil (see all 12)	1445-07-4	--

Search CenterWatch for drugs/clinical trials and news about RPUSD1 / RUSD1

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for RPUSD1 gene:

NM_058192.2

Unigene Cluster for RPUSD1:

RNA pseudouridylate synthase domain containing 1

Hs.101742 [show with all ESTs]

Unigene Representative Sequence: NM_058192

10 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000561734(uc002cka.3) ENST00000007264(uc002ckb.3) ENST00000565809

ENST00000567114 ENST00000569601 ENST00000565377 ENST00000567283 ENST00000562070

ENST00000565503 ENST00000563560

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Additional cDNA sequence:

BC011783.2 BC012951.2 BC036279.2

11 DOTS entries:

DT.100822833 DT.95179155 DT.91748974 DT.100822841 DT.100822835 DT.311519 DT.100707199 DT.91748990

DT.100719923 DT.100822840 DT.91748976

24/198 AceView cDNA sequences (see all 198):

CR610455 BE385201 CR623234 AW207322 BU182570 BI490085 CR625931 AL520203

CA423712 AA357425 CR610459 BU956473 CR605414 BQ888752 BM821373 BM721153

CB529100 CK903691 CR612793 BE795328 BQ218490 AI827175 BX342363 BM478157

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for RPUSD1 About this scheme

ExUns:	1a	·	1b	^	2a	·	2b	·	2c	^	3a	·	3b	·	3c	^	4	^	5a	·	5b	·	5c	·	5d
SP1:									-						-
SP2:															-
SP3:									-						-
SP4:									-						-
SP5:

ECgene alternative splicing isoforms for RPUSD1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

RPUSD1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CCACAACCTG

About this image
See RPUSD1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for RPUSD1

SOURCE GeneReport for Unigene cluster: Hs.101742

SABiosciences Custom PCR Arrays for RPUSD1

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for RPUSD1 gene from 5/17 species (see all 17) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Rpusd1^{1 , 5}	RNA pseudouridylate synthase domain containing 1^{1, 5}	81.05(n)¹ 83.99(a)¹		17 (12.83 cM)⁵ 106707¹ NM_028009.3¹ NP_082285.1¹ 25727751⁵
chicken (Gallus gallus)	Aves	RPUSD1¹	RNA pseudouridylate synthase domain containing 1	70.64(n) 64.9(a)		771031 XM_003642118.1 XP_003642166.1
lizard (Anolis carolinensis)	Reptilia	RPUSD1⁶	--	65(a)	1 ↔ 1	GL343650.1(342586-350710)
zebrafish (Danio rerio)	Actinopterygii	57061207²	--	75.61(n)		57061207
mosquito (Anopheles gambiae)	Insecta	AgaP_AGAP004401¹	AGAP004401-PA	51.43(n) 44.8(a)		1274545 XM_313685.4 XP_313685.4

ENSEMBL Gene Tree for RPUSD1 (if available)
TreeFam Gene Tree for RPUSD1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 16 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs686180^1,2	C,F,H,	--	834491(+)	`CGGTCC/TGGGCC`	1	--	int¹		11		NA WA CSA EA	373
rs148606943^1,2		--	834530(+)	`CATCTC/TGGCTG`	1	--	int¹		0	--	--	--	--
rs144228444^1,2		--	834591(+)	`GGGGTC/TGTAAC`	1	--	int¹		0	--	--	--	--
rs147377216^1,2		--	834618(+)	`GCCCCA/GGAGCT`	1	--	int¹		0	--	--	--	--
rs116088792^1,2	F,	--	834644(+)	`GGGGCC/TAGGCG`	1	--	int¹		1		WA	118
rs139600107^1,2		--	834714(+)	`CTCTAC/GGAAGA`	1	--	int¹		0	--	--	--	--
rs145136095^1,2		--	834722(+)	`AGATCA/CCTGGC`	1	--	int¹		0	--	--	--	--
rs11861306^1,2	C,F,A,H,	--	834786(+)	`GGGCCG/AGCCCA`	1	--	int¹		2		NA WA	122
rs9934841^1,2	C,F,	--	834865(+)	`CACTGC/TGTCTG`	1	--	int¹		1		WA	118
rs17144436^1,2	C,	--	834965(+)	`CACGTT/CCACGG`	1	--	int¹		3		NA	142

HapMap Linkage Disequilibrium report for RPUSD1 (834974 - 838397 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 7 variations for RPUSD1
7 CNVs: 10493 29986 3987 49763 5329 30732 29983

SABiosciences Cancer Mutation PCR Assays

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

RPUSD1 for disorders About GeneDecksing

1 disease for RPUSD1: About MalaCards

malaria

Export disorders for RPUSD1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for RPUSD1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with RPUSD1)

Utopia: connect your pdf to the dynamic
world of online information

Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. (PubMed id 11157797)^{1, 2} Daniels R.J....Higgs D.R. (2001)
Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)¹ Kim W....Gygi S.P. (2011)
Transcriptome analysis of human gastric cancer. (PubMed id 16341674)¹ Oh J.H....Kim N.S. (2005)
The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)² Martin J.... Pennacchio L.A. (2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)² Gerhard D.S....Malek J. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 113000	HGNC: 14173	AceView: C16orf40	Ensembl:ENSG00000007376	euGenes: HUgn113000
ECgene: RPUSD1	H-InvDB: RPUSD1

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for RPUSD1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for RPUSD1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for RPUSD1 gene:
Search GeneIP for patents involving RPUSD1

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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Advanced Cell Diagnostics
About This Section


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GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes RPUSD1 gene at Home site.

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RPUSD1 Gene

RNA pseudouridylate synthase domain containing 1

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RPUSD1 Gene

RNA pseudouridylate synthase domain containing 1

Aliasesfor RPUSD1 gene

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Genomic Viewsfor RPUSD1 gene

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Protein Domains /Familiesfor RPUSD1 gene

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for RPUSD1 gene

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for RPUSD1 gene

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for RPUSD1 gene

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for RPUSD1 gene

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