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SURF6 Gene

protein-coding   GIFtS: 50
GCID: GC09M136197

Surfeit 6

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(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
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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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.

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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   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 Chromatin IP Primers for SURF6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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: SURF6_HUMAN, O75683 (See protein sequence)
Recommended Name: Surfeit locus protein 6  
Size: 361 amino acids; 41450 Da
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: 

  • Ubiquitination2 at Lys7
  • Modification sites at PhosphoSitePlus

  • See SURF6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000361092  

    SURF6 Human Recombinant Protein Products:

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    antibodies-online proteins for SURF6 (3 products) 

     
    antibodies-online peptides for SURF6

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    antibodies-online antibodies for SURF6 (14 products) 

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    antibodies-online kits for SURF6 (6 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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


    Find genes that share domains with SURF6           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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    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): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ISS--
    GO:0003723RNA binding ISS--
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with SURF6           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SURF6

    miRNA
    Products:
        
    miRTarBase miRNAs that target SURF6:
    hsa-mir-92b-3p (MIRT040736), hsa-mir-92a-3p (MIRT049761), hsa-mir-10b-5p (MIRT047474)

    Block miRNA regulation of human, mouse, rat SURF6 using miScript Target Protectors
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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 UniProtKB/Swiss-Prot
    SURF6_HUMAN, O75683: Nucleus, nucleoplasm (By similarity). Nucleus, nucleolus (By similarity). Note=Granular
    component of the nucleolus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    mitochondrion1

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

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

    Find genes that share ontologies with SURF6           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SURF6
    Interactions:

        Search GeneGlobe Interaction Network for SURF6

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

    Selected Interacting proteins for SURF6 (O756833 ENSP000003610924) via UniProtKB, MINT, STRING, and/or I2D (see all 26)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ESR2Q927313, ENSP000003439254I2D: score=1 STRING: ENSP00000343925
    SMAD2Q157963I2D: score=1 
    NIFKENSP000002858144STRING: ENSP00000285814
    EBNA1BP2ENSP000002360514STRING: ENSP00000236051
    NSA2ENSP000002968024STRING: ENSP00000296802
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042254ribosome biogenesis IEA--

    Find genes that share ontologies with SURF6           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 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,
    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 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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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat SURF6
      QuantiFast Probe-based Assays in human, mouse, rat SURF6

    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 

    Selected AceView cDNA sequences (see all 432):

    AA631627 AA251335 BM681034 BM553348 BM800831 BM817494 CR617292 X85178 
    BX444187 CR617587 CR599878 BQ070993 AI445134 BC006197 BM911990 NM_181491 
    BQ011027 BE548581 BQ212228 T12599 BE906252 CD674663 BE205842 BE783411 

    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™, 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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    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

    SURF6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SURF6 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.274430
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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)
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    This gene was present in the common ancestor of animals.

    Orthologs for SURF6 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Surf61 , 5 surfeit gene 61, 5 77.5(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 56.85(n)
    48.98(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 Surf66
    Surfeit 6
    19(a)
    1 ↔ 1
    3R(15729384-15730589)
    worm
    (Caenorhabditis elegans)
    Secernentea ZK546.146
    Protein ZK546.14, isoform a
    18(a)
    1 ↔ 1
    II(4944040-4945834) WBGene00022765


    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)
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    Paralogs for SURF6 gene

    Find genes that share paralogs with SURF6           About GenesLikeMe


    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), 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 SURF6 (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

    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.)
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    OMIM gene information: 185642    OMIM disorders: --


    Find genes that share disorders with SURF6           About GenesLikeMe


    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)
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    PubMed articles for SURF6 gene, integrated from 10 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. (Gene 2000)
    2. Identification of an evolutionary conserved SURF-6 domain in a family of nucleolar proteins extending from human to yeast. (PubMed id 15629442)1, 3 Polzikov M....Magoulas C. (Biochem. Biophys. Res. Commun. 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. (Genome Res. 2004)
    4. The human homologue of the mouse Surf5 gene encodes multiple alternatively spliced transcripts. (PubMed id 11891058)1, 2 Angiolillo A....Pietropaolo C. (Gene 2002)
    5. The human Surfeit locus. (PubMed id 9740673)1, 3 Duhig T.... Fried M. (Genomics 1998)
    6. Linkage analysis identifies a locus for plasma von Willebrand factor undetected by genome-wide association. (PubMed id 23267103)1 Desch K.C....Ginsburg D. (Proc. Natl. Acad. Sci. U.S.A. 2013)
    7. Development of novel mouse hybridomas producing monoclonal antibodies specific to human and mouse nucleolar protein SURF-6. (PubMed id 22316485)1 Polzikov M.A....Zatsepina O.V. (Hybridoma (Larchmt) 2012)
    8. Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C.... Cristea I.M. (Mol. Cell. Proteomics 2012)
    9. A bead-based approach for large-scale identification of in vitro kinase substrates. (PubMed id 22113938)1 Zhang M....Zou H. (Proteomics 2011)
    10. 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)

    (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: 6838 HGNC: 11478 AceView: SURF5andSURF6 Ensembl:ENSG00000148296 euGenes: HUgn6838
    ECgene: SURF6 H-InvDB: SURF6

    (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 SURF6 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 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



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