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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  

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

Browse SwitchGear Promoter luciferase reporter plasmids
   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, and/or antibodies-online,
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.)
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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  

    RPS4Y2 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for RPS4Y2

     
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    antibodies-online proteins for RPS4Y2 

     
    antibodies-online peptides for RPS4Y2

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    antibodies-online antibodies for RPS4Y2 (4 products) 

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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.)
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         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0003723RNA binding ----
    GO:0003735structural constituent of ribosome IEA--
    GO:0019843rRNA binding IEA--
         
    Find genes that share ontologies with RPS4Y2           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RPS4Y2

    miRNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    mitochondrion2

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005622intracellular ----
    GO:0005840ribosome 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 GeneDecks, 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).
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    SuperPaths for RPS4Y2 About    
    See pathways by source

    SuperPathContained pathways About
    1CFTR 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)


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RPS4Y2
    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)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PDCD11ENSP000003588124STRING: ENSP00000358812
    RPS13ENSP000002281404STRING: ENSP00000228140
    RPS3ENSP000002785724STRING: ENSP00000278572
    RPS14ENSP000003110284STRING: ENSP00000311028
    RPS16ENSP000002514534STRING: ENSP00000251453
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006412translation IEA--
    GO:0008150biological_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)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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)
    miRNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat RPS4Y2
      QuantiFast Probe-based Assays in human, mouse, rat RPS4Y2

    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 GeneDecks, 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)
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    RPS4Y2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    RPS4Y2 Expression
    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
        Custom PCR Arrays for RPS4Y2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPS4Y2

    (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)
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    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)
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    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)
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    Selected SNPs for RPS4Y2 (see all 150)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr Y posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs354745631,2
    C--22917995(+) CACCGC/TAGATT 1 -- ut512Minor allele frequency- T:0.02MN NA 43
    rs169805481,2
    C,F,H--22918577(+) ATTACC/TCGTTA 1 -- int111Minor allele frequency- T:0.28NA MN NS EA WA CSA 327
    rs133057471,2
    C--22919819(+) CAGACA/CTGAGG 1 -- int10--------
    rs133058001,2
    C--22919840(+) ATGTGC/ATAAAT 1 -- int11Minor allele frequency- A:0.00NA 2
    rs345817391,2
    C,F--22921768(+) CCATCG/AACAGG 2 /S syn12Minor allele frequency- A:0.04MN NA 48
    rs347404501,2
    C,F--22922129(+) AAGGGG/ATTGGT 1 -- int12Minor allele frequency- A:0.04MN NA 48
    rs133044641,2
    C--22924348(+) TGTTGT/CGTCTA 1 -- int11Minor allele frequency- C:0.00NA 2
    rs133052201,2
    C,F--22927023(+) TGGGGC/TCAGAA 1 -- int12Minor allele frequency- T:0.50NA 4
    rs341237561,2
    C--22928067(+) GCTTTC/TGCTGG 1 -- int10--------
    rs341943081,2
    C,F,H--22928344(+) TAAATC/GTAGCA 1 -- int16Minor allele frequency- G:0.07NS 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 IDTypeSubtypePubMed ID
    nsv10025CNV Gain18304495

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RPS4Y2
    DNA2.0 Custom Variant and Variant Library Synthesis for RPS4Y2

    (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.)
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    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)
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    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

    1. 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)
    2. 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)
    3. 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)
    4. 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)
    5. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    6. 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)
    7. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)
    8. 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)
    9. Y Chromosome Infertility (PubMed id 20301513)1 Pagon R.A....Stephens K. (1993)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    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)
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    Entrez Gene: 140032 HGNC: 18501 AceView: RPS4Y2 Ensembl:ENSG00000157828 euGenes: HUgn140032
    ECgene: RPS4Y2 H-InvDB: RPS4Y2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RPS4Y2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RPS4Y2 gene:
    Search GeneIP for patents involving RPS4Y2

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    (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, 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
    Advanced Cell Diagnostics, Animal models from genOway)
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     Browse OriGene Antibodies   OriGene RNAi products in human, mouse, rat for RPS4Y2  
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     Block miRNA regulation of human, mouse, rat RPS4Y2 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing RPS4Y2
     DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPS4Y2 Predesigned siRNA for gene silencing in human, mouse, rat RPS4Y2
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     Search Tocris compounds for RPS4Y2 (RS4Y2)
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     Browse ESI BIO Cell Lines and PureStem Progenitors for RPS4Y2
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     Browse compounds at ApexBio
     Search Addgene for plasmids for RPS4Y2
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      eBioscience FlowRNA Probe Sets
     genOway: Develop your customized and physiologically relevant rodent model for RPS4Y2
     antibodies-online antibodies for RPS4Y2 (4 products)
      Search antibodies-online for kits for RPS4Y2
     antibodies-online peptides for RPS4Y2
     antibodies-online proteins for RPS4Y2
           
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