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

SURF6 Gene

protein-coding   GIFtS: 48
GCID: GC09M136197

Surfeit 6

  Search for SURF6
at  

(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
Surfeit 61 2
Surfeit Locus Protein 61 2
RRP142
SURF-63

External Ids:    HGNC: 114781   Entrez Gene: 68382   Ensembl: ENSG000001482967   OMIM: 1856425   UniProtKB: O756833   

Export aliases for SURF6 gene to outside databases

Previous GC identifers: GC09M127287 GC09M127754 GC09M129551 GC09M131473 GC09M133227 GC09M135187 GC09M105697


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

Entrez Gene summary for SURF6 Gene:
This gene encodes a conserved protein that is localized to the nucleolus. The encoded protein may function as a
nucleolar-matrix protein with nucleic acid-binding properties. There is a pseudogene for this gene on chromosome
Y. Alternative splicing results in multiple transcript variants. (provided by RefSeq, Jul 2013)

GeneCards Summary for SURF6 Gene: 
SURF6 (surfeit 6) is a protein-coding gene. GO annotations related to this gene include RNA binding and DNA binding.

UniProtKB/Swiss-Prot: SURF6_HUMAN, O75683
Function: Binds to both DNA and RNA in vitro, with a stronger binding capacity for RNA. May represent a nucleolar
constitutive protein involved in ribosomal biosynthesis or assembly (By similarity)

Gene Wiki entry for SURF6 Gene


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NC_018920.2  NT_035014.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SURF6 gene promoter:
         ER-alpha   HTF   Pax-2   Pax-2a   FOXL1   PPAR-gamma1   Pax-2b   Chx10   Sox9   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSURF6 promoter sequence
   Search SABiosciences Chromatin IP Primers for SURF6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SURF6


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

Entrez Gene cytogenetic band: 9q34.2   Ensembl cytogenetic band:  9q34.2   HGNC cytogenetic band: 9q33-q34

SURF6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SURF6 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M136197:  view genomic region     (about GC identifiers)

Start:
136,197,552 bp from pter      End:
136,203,235 bp from pter
Size:
5,684 bases      Orientation:
minus strand

1 alternative location:
Chr9-,NW_003315925 156,810-162,304     

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SURF6_HUMAN, O75683 (See protein sequence)
Recommended Name: Surfeit locus protein 6  
Size: 361 amino acids; 41450 Da
Subcellular location: Nucleus, nucleoplasm (By similarity). Nucleus, nucleolus (By similarity). Note=Granular
component of the nucleolus (By similarity)
Secondary accessions: Q5T8U1 Q9BRK9 Q9BTZ5 Q9UK24

Explore the universe of human proteins at neXtProt for SURF6: NX_O75683

Explore proteomics data for SURF6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O75683

  • SURF6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SURF6 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001265871.1  NP_006744.2  

    ENSEMBL proteins: 
     ENSP00000361092  

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    Cloud-Clone Corp. Proteins for SURF6 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001652granular component ISS--
    GO:0005654nucleoplasm IEA--
    GO:0005730nucleolus TAS10675619
    GO:0044451nucleoplasm part ----

    SURF6 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR007019 Surf6

    Graphical View of Domain Structure for InterPro Entry O75683

    ProtoNet protein and cluster: O75683

    1 Blocks protein domain: IPB007019 Surfeit locus protein 6

    UniProtKB/Swiss-Prot: SURF6_HUMAN, O75683
    Similarity: Belongs to the SURF6 family


    SURF6 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SURF6_HUMAN, O75683
    Function: Binds to both DNA and RNA in vitro, with a stronger binding capacity for RNA. May represent a nucleolar
    constitutive protein involved in ribosomal biosynthesis or assembly (By similarity)

         Genatlas biochemistry entry for SURF6:
    surfeit 6 protein (see SURF@),located in nucleolus,ubiquitously expressed

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ISS--
    GO:0003723RNA binding ISS--
         
    SURF6 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SURF6

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

    5/6 Interacting proteins for SURF6 (O756833 ENSP000003610924) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ESR2Q927313, ENSP000003439254I2D: score=1 STRING: ENSP00000343925
    SMAD2Q157963I2D: score=1 
    SIRT7ENSP000003294664STRING: ENSP00000329466
    SHARPINENSP000003816984STRING: ENSP00000381698
    RPS16ENSP000002514534STRING: ENSP00000251453
    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:0042254ribosome biogenesis IEA--

    SURF6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SURF6

    Search CenterWatch for drugs/clinical trials and news about SURF6

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SURF6 gene (2 alternative transcripts): 
    NM_001278942.1  NM_006753.5  

    Unigene Cluster for SURF6:

    Surfeit 6
    Hs.274430  [show with all ESTs]
    Unigene Representative Sequence: NM_006753
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372022(uc004cdb.4) ENST00000468290
    miRNA
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    Additional mRNA sequence: 

    AK054884.1 BC003001.1 BC006197.2 BC014878.1 

    11 DOTS entries:

    DT.100795328  DT.313301  DT.100795320  DT.100795323  DT.99956444  DT.100759030  DT.100761410  DT.100795321 
    DT.91728468  DT.100795330  DT.121151797 

    24/432 AceView cDNA sequences (see all 432):

    AI421031 CB122347 R50680 BU845334 BC006197 CR617785 BQ070993 AI445134 
    BQ422401 BM911990 BM684392 AI085033 AA459247 BX396541 BQ685121 AA507056 
    CD674663 CR599878 BX444187 CR617587 BE548581 BM848275 AA251344 D80221 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for SURF6    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4
    SP1:                                    
    SP2:        -                           


    ECgene alternative splicing isoforms for SURF6

    (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

    SURF6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGAGTTGGGT
    SURF6 Expression
    About this image


    See SURF6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SURF6

    SOURCE GeneReport for Unigene cluster: Hs.274430
        SABiosciences Custom PCR Arrays for SURF6
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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 eukaryotes.

    Orthologs for SURF6 gene from 9/21 species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Surf61 , 5 surfeit gene 61, 5 77.59(n)1
    74.01(a)1
      2 (19.08 cM)5
    209351  NM_009298.31  NP_033324.11 
     268886285 
    chicken
    (Gallus gallus)
    Aves SURF61 surfeit 6 57.51(n)
    49.58(a)
      417160  NM_001030682.1  NP_001025853.1 
    African clawed frog
    (Xenopus laevis)
    Amphibia surf62 putative SURF6 protein 72.92(n)    AJ276843.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc640082 similar to surfeit gene 6 71.08(n)   394040  BC053193.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Surf61 Surfeit 6 47.79(n)
    26.94(a)
      42370  NM_079684.3  NP_524408.1 
    worm
    (Caenorhabditis elegans)
    Secernentea ZK546.141 Protein ZK546.14 41.69(n)
    29.31(a)
      173854  NM_062506.3  NP_494907.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RRP141 Rrp14p 38.54(n)
    27.43(a)
      853780   NP_012841.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G052101 Surfeit locus protein 6 41(n)
    28.74(a)
      830403  NM_001085062.1  NP_001078531.1 
    rice
    (Oryza sativa)
    Liliopsida Os05g03722001 hypothetical protein 43.78(n)
    25.41(a)
      4338593  NM_001061895.1  NP_001055360.1 


    ENSEMBL Gene Tree for SURF6 (if available)
    TreeFam Gene Tree for SURF6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SURF6 gene

    SURF6 for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for SURF6
    PGOHUM00000249262 PGOHUM00000233969


    (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) 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

    10/272 SNPs in SURF6 are shown (see all 272)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1891701711,2
    --136197067(+) CTGTTC/TCACAA 1 -- ds50010--------
    rs1496359731,2
    --136197099(+) AGACAC/GTCTTG 1 -- ds50010--------
    rs8775601,2
    C,A--136197131(-) CGAGCT/CGCTGC 1 -- ds50011Minor allele frequency- C:0.00NA 2
    rs23536331,2
    C,A--136197135(-) AGATCA/GAGCCG 1 -- ds50011Minor allele frequency- G:0.00NA 2
    rs5511541,2
    C,F--136197278(+) tgttgT/Gccagg 1 -- ds50015Minor allele frequency- G:0.22NA WA CSA 9
    rs5511691,2
    C,F--136197286(+) aggctA/Ggcctt 1 -- ds50014Minor allele frequency- G:0.25NA WA 8
    rs340768031,2
    C--136197427(+) CTAATA/GGCCAT 1 -- ds50013Minor allele frequency- G:0.08NA EA 242
    rs1924354721,2
    --136197456(+) TAGGTA/GATTTA 1 -- ds50010--------
    rs345718541,2
    C,F--136197485(+) TCCAAA/GTATGA 1 -- ds50013Minor allele frequency- G:0.14NA 124
    rs1837661031,2
    --136197522(+) ACAGAA/GCAAGA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for SURF6 (136197552 - 136203235 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for SURF6:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2739138CNV Deletion23290073
    nsv894076CNV Loss21882294
    dgv8325n71CNV Loss21882294
    nsv894079CNV Loss21882294
    nsv894080CNV Loss21882294
    nsv894057CNV Gain21882294

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

    SURF6 for disorders           About MalaCards
    OMIM gene information: 185642    OMIM disorders: --


    SURF6 for disorders           About GeneDecksing


    Export disorders for SURF6 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 SURF6 gene, integrated from 9 sources (see all 26):
    (articles sorted by number of sources associating them with SURF6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and genomic analysis of the human surf-6 gene: a member of the Surfeit locus. (PubMed id 10675619)1, 2, 9 Magoulas C. and Fried M. (2000)
    2. Identification of an evolutionary conserved SURF-6 do main in a family of nucleolar proteins extending from human to yeast. (PubMed id 15629442)1, 3 Polzikov M....Magoulas C. (2005)
    3. 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)
    4. The human homologue of the mouse Surf5 gene encodes multiple alternatively spliced transcripts. (PubMed id 11891058)1, 2 Angiolillo A....Pietropaolo C. (2002)
    5. The human Surfeit locus. (PubMed id 9740673)1, 3 Duhig T.... Fried M. (1998)
    6. Linkage analysis identifies a locus for plasma von Wil lebrand factor undetected by genome-wide association. (PubMed id 23267103)1 Desch K.C....Ginsburg D. (2013)
    7. Development of novel mouse hybridomas producing monocl onal antibodies specific to human and mouse nucleolar protein SURF-6. (PubMed id 22316485)1 Polzikov M.A....Zatsepina O.V. (2012)
    8. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    9. A bead-based approach for large-scale identification o f in vitro kinase substrates. (PubMed id 22113938)1 Zhang M....Zou H. (2011)
    10. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6838 HGNC: 11478 AceView: SURF5andSURF6 Ensembl:ENSG00000148296 euGenes: HUgn6838
    ECgene: SURF6 H-InvDB: SURF6

    (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 SURF6 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 SURF6 gene:
    Search GeneIP for patents involving SURF6

    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, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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, In Situ Hybridization Assays from
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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