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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TSR3 Gene

protein-coding   GIFtS: 40
GCID: GC16M001401

TSR3, 20S rRNA accumulation, homolog (S. cerevisiae)

(Previous name: chromosome 16 open reading frame 42 )
(Previous symbol: C16orf42)
 Explore 1 disease affiliated with
TSR3 via our new
 Human Malady Compendium 
Biological research products
for TSR3
    

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

Aliases
TSR3, 20S RRNA Accumulation, Homolog (S. Cerevisiae)1 2     Probable Ribosome Biogenesis Protein C16orf422
C16orf421 2 3     Ribosome Biogenesis Protein TSR3 Homolog2
MGC243811     UND313L3
Chromosome 16 Open Reading Frame 421     

External Ids:    HGNC: 141751   Entrez Gene: 1159392   Ensembl: ENSG000000075207   UniProtKB: Q9UJK03   

Export aliases for TSR3 gene to outside databases

Previous GC identifer: GC16M001400


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

UniProtKB/Swiss-Prot: TSR3_HUMAN, Q9UJK0
Function: Probable pre-rRNA processing protein involved in ribosome biogenesis (By similarity)

Gene Wiki entry for TSR3 (C16orf42)


(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:
   Search SABiosciences Regulatory transcription factor binding sites for TSR3
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for TSR3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TSR3


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

TSR3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TSR3 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M001401:  view genomic region     (about GC identifiers)

Start:
1,399,241 bp from pter      End:
1,401,912 bp from pter
Size:
2,672 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: TSR3_HUMAN, Q9UJK0 (See protein sequence)
Recommended Name: Ribosome biogenesis protein TSR3 homolog  
Size: 312 amino acids; 33596 Da
Secondary accessions: Q6PJT8

Explore the universe of human proteins at neXtProt for TSR3: NX_Q9UJK0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UJK0

  • TSR3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_001001410.1  
    ENSEMBL proteins: 
     ENSP00000007390   ENSP00000455722  

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

    TSR3 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR022968 Rbsm_biogenesis
     IPR007177 DUF367
     IPR007209 RNaseL-inhib_metal-bd_dom

    Graphical View of Domain Structure for InterPro Entry Q9UJK0

    ProtoNet protein and cluster: Q9UJK0

    2 Blocks protein families:
    IPB007177 Protein of unknown function DUF367
    IPB007209 Possible metal-binding region in RNase L inhibitor


    UniProtKB/Swiss-Prot: TSR3_HUMAN, Q9UJK0
    Similarity: Belongs to the TSR3 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

    Function Summary:

         UniProtKB/Swiss-Prot: TSR3_HUMAN, Q9UJK0
    Function: Probable pre-rRNA processing protein involved in ribosome biogenesis (By similarity)

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    (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 CentralTM Interacting Genes and Proteins Networks for TSR3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

    5/33 Interacting proteins for TSR3 (Q9UJK03 ENSP000000073904) via UniProtKB, MINT, STRING, and/or I2D (see all 33)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ADAT2Q7Z6V53, ENSP000002372834I2D: score=1 STRING: ENSP00000237283
    KARSQ150463, ENSP000003254484I2D: score=1 STRING: ENSP00000325448
    KRR1Q136013, ENSP000002292144I2D: score=1 STRING: ENSP00000229214
    PUS3Q9BZE23, ENSP000002274744I2D: score=1 STRING: ENSP00000227474
    RPL5P467773, ENSP000003593454I2D: score=1 STRING: ENSP00000359345
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006364rRNA processing IEA--


    TSR3 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 TSR3
    Search CenterWatch for drugs/clinical trials and news about TSR3 

    (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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    About This Section

    REFSEQ mRNAs for TSR3 gene: 
    NM_001001410.2  

    Unigene Cluster for TSR3:

    TSR3, 20S rRNA accumulation, homolog (S. cerevisiae)
    Hs.134846  [show with all ESTs]
    Unigene Representative Sequence: BC013943
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000007390(uc002cll.3) ENST00000566296

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    Inhib. RNA
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    Additional cDNA sequence: 

    BC011785.2 BC013943.1 BC016699.1 BC017325.2 

    6 DOTS entries:

    DT.75118306  DT.449556  DT.92435001  DT.97840633  DT.100815748  DT.92434995 

    24/68 AceView cDNA sequences (see all 68):

    AI923651 AW406663 AI659324 AW007556 AI423636 AI264852 BI064315 BC017325 
    AI094880 AI341540 NM_001001410 AI091298 AI560264 AI972013 AI971937 AI813672 
    AI660316 BC013943 AI672681 AI971966 AW007602 BE674893 AW341301 AI925218 

    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™, 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
    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --


    TSR3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BrainHypothalamusBrain
    Neural TubeDiencephalonNeural Tube
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See TSR3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TSR3

    SOURCE GeneReport for Unigene cluster: Hs.134846
        SABiosciences Custom PCR Arrays for TSR3
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    In Situ
    Assay Products:
     

     
    Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for TSR3

    (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 eukaryotes.

    Orthologs for TSR3 gene from 9/32 species (see all 32)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tsr31 , 5 RIKEN cDNA 0610007P22 gene5
    TSR3 20S rRNA accumulation1
    80.04(n)1
    77.67(a)1
      17 (12.53 cM)5
    683271  NM_026676.31  NP_080952.21 
     252401705 
    chicken
    (Gallus gallus)
    Aves C14H16orf421 chromosome 14 open reading frame, human C16orf42 60.83(n)
    61.43(a)
      416590  XM_414890.3  XP_414890.1 
    lizard
    (Anolis carolinensis)
    Reptilia C16orf426
    --
    53(a)
    1 ↔ 1
    GL343612.1(261622-266110)
    zebrafish
    (Danio rerio)
    Actinopterygii tsr31 TSR3, 20S rRNA accumulation, homolog (S. cerevisiae) 59.81(n)
    60.98(a)
      436643  NM_001002370.1  NP_001002370.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG43381 CG4338 55.34(n)
    50.78(a)
      41849  NM_142184.1  NP_650441.1 
    worm
    (Caenorhabditis elegans)
    Secernentea F52C12.21 Protein F52C12.2 47.86(n)
    41.03(a)
      176995  NM_171282.4  NP_741332.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes TSR3(YOR006C)4
    TSR31
    Protein required for correct processing of the 20S more4
    Tsr3p1
    49.37(n)1
    50.48(a)1
      15(338621-337680)4
    8541671, 4  NP_014648.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G100701 RNase L inhibitor protein-like protein 50.97(n)
    51.16(a)
      830871  NM_203032.1  NP_974761.1 
    rice
    (Oryza sativa)
    Liliopsida Os03g01952001 hypothetical protein 50.46(n)
    49.07(a)
      4331931  NM_001055791.1  NP_001049256.1 


    ENSEMBL Gene Tree for TSR3 (if available)
    TreeFam Gene Tree for TSR3 (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
    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

    TSR3 for disorders           About GeneDecksing

    1 disease for TSR3:    About MalaCards
    malaria


    Export disorders for TSR3 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 TSR3 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with TSR3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)1, 2 Martin J.... Pennacchio L.A. (2004)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    4. 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)
    5. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    7. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    8. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (2009)
    9. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 115939 HGNC: 14175 AceView: MGC24381 Ensembl:ENSG00000007520 euGenes: HUgn115939
    ECgene: TSR3 H-InvDB: TSR3

    (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
    NameDescription
    PharmGKB entry for TSR3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for TSR3 gene:
    Search GeneIP for patents involving TSR3

    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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    About This Section

     
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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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    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 


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