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RPS4Y2 Gene

protein-coding GIFtS: 43
GCID: GC0YP022917

Ribosomal Protein S4, Y-Linked 2

(Previous names: ribosomal protein S4, Y-linked 2 pseudogene)
(Previous symbol: RPS4Y2P)

See RPS4Y2-related disease
at

MalaCards

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
About This Section

Aliases
Ribosomal Protein S4, Y-Linked 2¹ ²
RPS4Y2P¹ ² ³
Ribosomal Protein S4, Y-Linked 2 Pseudogene¹ ²
40S Ribosomal Protein S4, Y²
40S Ribosomal Protein S4, Y Isoform 2²

External Ids:	HGNC: 18501¹	Entrez Gene: 140032²	Ensembl: ENSG00000157828⁷	OMIM: 400030⁵	UniProtKB: Q8TD47³

Export aliases for RPS4Y2 gene to outside databases

Previous GC identifers: GC0YP022073 GC0YP021763 GC0YP021256 GC0YP021327 GC0YP016504

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

Entrez Gene summary for RPS4Y2 Gene:

The protein encoded by this gene is a ribosomal protein that is highly similar to RPS4Y1. This gene is located in

the male-specific region of the Y chromosome. (provided by RefSeq, Aug 2012)

GeneCards Summary for RPS4Y2 Gene:

RPS4Y2 (ribosomal protein S4, Y-linked 2) is a protein-coding gene. Diseases associated with RPS4Y2 include y chromosome infertility. GO annotations related to this gene include structural constituent of ribosome and rRNA binding. An important paralog of this gene is RPS4Y1.

(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence at NCBI GenBank:

NC_000024.9 NT_011875.13

Regulatory elements:

Regulatory transcription factor binding sites in the RPS4Y2 gene promoter:
Elk-1 HOXA3 Pax-6 Nkx2-5 RORalpha2 GATA-1 FOXL1 RORalpha1 Ik-1
Other transcription factors

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Search Chromatin IP Primers for RPS4Y2

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPS4Y2

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

Entrez Gene cytogenetic band: Yq11.223 Ensembl cytogenetic band: Yq11.223 HGNC cytogenetic band: Yq11.223

RPS4Y2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPS4Y2 gene location

GeneLoc information about chromosome Y GeneLoc Exon Structure

GeneLoc location for GC0YP022917: view genomic region (about GC identifiers)

Start:	22,917,954 bp from pter	End:	22,942,918 bp from pter
Size:	24,965 bases	Orientation:	plus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, antibodies-online, and/or GeneTex,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
About This Section

UniProtKB/Swiss-Prot: RS4Y2_HUMAN, Q8TD47 (See protein sequence)

Recommended Name: 40S ribosomal protein S4, Y isoform 2

Size: 263 amino acids; 29295 Da

Secondary accessions: A6NIR6

Explore the universe of human proteins at neXtProt for RPS4Y2: NX_Q8TD47

Explore proteomics data for RPS4Y2 at MOPED

Post-translational modifications:

Ubiquitination² at Lys16, Lys22, Lys37, Lys53, Lys62, Lys233

Modification sites at PhosphoSitePlus

See RPS4Y2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001034656.1

ENSEMBL proteins:

ENSP00000288666

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

HGNC Gene Families:

RPS: S ribosomal proteins

Selected InterPro protein domains (see all 6):

IPR013845 Ribosomal_S4e_central_region

IPR002942 S4_RNA-bd

IPR013843 Ribosomal_S4e_N

IPR000876 Ribosomal_S4e

IPR018199 Ribosomal_S4e_N_CS

Graphical View of Domain Structure for InterPro Entry Q8TD47

ProtoNet protein and cluster: Q8TD47

3 Blocks protein domains:

IPB000876 Ribosomal protein S4E

IPB002942 RNA-binding S4

IPB006646 KOW (Kyprides

UniProtKB/Swiss-Prot: RS4Y2_HUMAN, Q8TD47

Similarity: Belongs to the ribosomal protein S4e family

Similarity: Contains 1 S4 RNA-binding domain

Find genes that share domains with RPS4Y2 About GenesLikeMe

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Gene Ontology (GO): 4 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003674	molecular_function	ND	--
GO:0003723	RNA binding	--	--
GO:0003735	structural constituent of ribosome	IEA	--
GO:0019843	rRNA binding	IEA	--

Find genes that share ontologies with RPS4Y2 About GenesLikeMe

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
cytosol	3
mitochondrion	2

About this image

Gene Ontology (GO): 3 cellular component terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005575	cellular_component	ND	--
GO:0005622	intracellular	--	--
GO:0005840	ribosome	IEA	--

Find genes that share ontologies with RPS4Y2 About GenesLikeMe

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GenesLikeMe, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

SuperPaths for RPS4Y2 About

See pathways by source

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by

SuperPath

Contained pathways About

CFTR translational fidelity (class I mutations)

CFTR translational fidelity (class I mutations)

0.60

Pathways by source See SuperPaths
Show all pathways

1 GeneGo (Thomson Reuters) Pathway for RPS4Y2

CFTR translational fidelity (class I mutations)

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Interactions:

Search GeneGlobe Interaction Network for RPS4Y2

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for RPS4Y2 (ENSP00000288666⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 234)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
PDCD11	ENSP00000358812⁴	STRING: ENSP00000358812
RPS13	ENSP00000228140⁴	STRING: ENSP00000228140
RPS3	ENSP00000278572⁴	STRING: ENSP00000278572
RPS14	ENSP00000311028⁴	STRING: ENSP00000311028
RPS16	ENSP00000251453⁴	STRING: ENSP00000251453

About this table

Gene Ontology (GO): 2 biological process terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006412	translation	IEA	--
GO:0008150	biological_process	ND	--

Find genes that share ontologies with RPS4Y2 About GenesLikeMe

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, Sets of similar genes according to GenesLikeMe)
About This Section

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Browse Tocris compounds for RPS4Y2 (RS4Y2)

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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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About This Section

REFSEQ mRNAs for RPS4Y2 gene:

NM_001039567.2

Unigene Cluster for RPS4Y2:

Ribosomal protein S4, Y-linked 2

Hs.367761

Unigene Representative Sequence: NM_001039567

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000288666(uc011nbb.2)

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Additional mRNA sequence: AF497481.2

1 DOTS entry:

DT.120653212

2 AceView cDNA sequences:

NM_138963 AF497481

GeneLoc Exon Structure

(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 GenesLikeMe, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

RPS4Y2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

RPS4Y2 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database


Endothelium (Cardiovascular System)
Human umbilical vein endothelial cells (HUVEC)

RPS4Y2 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

RPS4Y2 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.367761

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In Situ
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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 and fungi.

Orthologs for RPS4Y2 gene from Selected species (see all 11) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
zebrafish (Danio rerio)	Actinopterygii	rps4x⁶	ribosomal protein S4, X-linked	87(a)	1 → many	7(53088995-53094879) ENSDARG00000014690
fruit fly (Drosophila melanogaster)	Insecta	RpS4³	protein biosynthesis structural constituent of more	72(a)		69F6 --
worm (Caenorhabditis elegans)	Secernentea	Y43B11AR.4³	--	61(a)		IV(7083923-7084849) --
baker's yeast (Saccharomyces cerevisiae)	Saccharomycetes	RPS4A⁶ RPS4B⁶	Protein component of the small (40S) ribosomal sub... Protein component of the small (40S) ribosomal sub...	68(a) 68(a)	many ↔ many many ↔ many	X(702027-703068) YJR145C VIII(504476-505530) YHR203C

Species with no ortholog for RPS4Y2

ENSEMBL Gene Tree for RPS4Y2 (if available)
TreeFam Gene Tree for RPS4Y2 (if available)

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

Paralogs for RPS4Y2 gene

RPS4Y1² RPS4X²

2 SIMAP similar genes for RPS4Y2 using alignment to 1 protein entry: RS4Y2_HUMAN:

RPS4Y1 RPS4X

Find genes that share paralogs with RPS4Y2 About GenesLikeMe

1 Pseudogenes.org Pseudogene for RPS4Y2
PGOHUM00000249330

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
About This Section

SNP ID	Valid	Clinical significance	Chr Y pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs35474563^1,2	C	--	22917995(+)	`CACCGC/TAGATT`	1	--	ut5¹		2		MN NA	43
rs16980548^1,2	C,F,H	--	22918577(+)	`ATTACC/TCGTTA`	1	--	int¹		11		NA MN NS EA WA CSA	327
rs13305747^1,2	C	--	22919819(+)	`CAGACA/CTGAGG`	1	--	int¹		0	--	--	--	--
rs13305800^1,2	C	--	22919840(+)	`ATGTGC/ATAAAT`	1	--	int¹		1		NA	2
rs34581739^1,2	C,F	--	22921768(+)	`CCATCG/AACAGG`	2	/S	syn¹		2		MN NA	48
rs34740450^1,2	C,F	--	22922129(+)	`AAGGGG/ATTGGT`	1	--	int¹		2		MN NA	48
rs13304464^1,2	C	--	22924348(+)	`TGTTGT/CGTCTA`	1	--	int¹		1		NA	2
rs13305220^1,2	C,F	--	22927023(+)	`TGGGGC/TCAGAA`	1	--	int¹		2		NA	4
rs34123756^1,2	C	--	22928067(+)	`GCTTTC/TGCTGG`	1	--	int¹		0	--	--	--	--
rs34194308^1,2	C,F,H	--	22928344(+)	`TAAATC/GTAGCA`	1	--	int¹		6		NS EA NA	215

HapMap Linkage Disequilibrium report for RPS4Y2 (22917954 - 22942918 bp)

Structural Variations
Database of Genomic Variants (DGV) 1 variation for RPS4Y2: About this table

Variant ID	Type	Subtype	PubMed ID
nsv10025	CNV	Gain	18304495

Site Specific Mutation Identification with 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, Sets of similar genes according to GenesLikeMe)
About This Section

OMIM gene information: 400030 OMIM disorders: --

1 disease for RPS4Y2:
About MalaCards

y chromosome infertility

Find genes that share disorders with RPS4Y2 About GenesLikeMe

Export disorders for RPS4Y2 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 RPS4Y2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RPS4Y2)

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

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)^{1, 2, 3} Skaletsky H.... Page D.C. (Nature 2003)
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)¹ Udeshi N.D....Carr S.A. (amp 2012)
Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. (PubMed id 22708584)¹ Ye J....Madden T.L. (BMC Bioinformatics 2012)
Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)¹ Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)¹ Kim W....Gygi S.P. (Mol. Cell 2011)
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)¹ Wagner S.A....Choudhary C. (amp 2011)
Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)¹ Emanuele M.J....Elledge S.J. (Cell 2011)
The human RPS4 paralogue on Yq11.223 encodes a structurally conserved ribosomal protein and is preferentially expressed during spermatogenesis. (PubMed id 20459660)¹ Lopes A.M....Affara N.A. (BMC Mol. Biol. 2010)
Y Chromosome Infertility (PubMed id 20301513)¹ Pagon R.A....Stephens K. (1993)

(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: 140032	HGNC: 18501	AceView: RPS4Y2	Ensembl:ENSG00000157828	euGenes: HUgn140032
ECgene: RPS4Y2	H-InvDB: RPS4Y2

(According to HUGE)
About This Section

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

Name	Description
PharmGKB entry for RPS4Y2	Pharmacogenomics, SNPs, Pathways

Intellectual Property for RPS4Y2 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for RPS4Y2 gene:
Search GeneIP for patents involving RPS4Y2

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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, GeneTex, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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About This Section


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RPS4Y2 Gene

Ribosomal Protein S4, Y-Linked 2

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Export list of displayed genes

RPS4Y2 Gene

Ribosomal Protein S4, Y-Linked 2

Aliasesfor RPS4Y2 gene

Summariesfor RPS4Y2 gene

Genomic Viewsfor RPS4Y2 gene

Proteinsfor RPS4Y2 gene

RPS4Y2 Human Recombinant Protein Products:

RPS4Y2 Antibody Products:

RPS4Y2 Assay Products:

Domains /Familiesfor RPS4Y2 gene

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Localizationfor RPS4Y2 gene

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Expression for RPS4Y2 gene

Orthologsfor RPS4Y2 gene

Paralogsfor RPS4Y2 gene

Genomic Variantsfor RPS4Y2 gene

Disorders / Diseasesfor RPS4Y2 gene

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Aliases
for RPS4Y2 gene

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for RPS4Y2 gene

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for RPS4Y2 gene

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for RPS4Y2 gene

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for RPS4Y2 gene

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for RPS4Y2 gene

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for RPS4Y2 gene

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for RPS4Y2 gene

Drugs & Compounds
for RPS4Y2 gene

Transcripts
for RPS4Y2 gene

Expression
for RPS4Y2 gene

Orthologs
for RPS4Y2 gene

Paralogs
for RPS4Y2 gene

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for RPS4Y2 gene

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for RPS4Y2 gene

Publications
for RPS4Y2 gene

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for RPS4Y2 gene

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for RPS4Y2 gene