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SVIP Gene

protein-coding   GIFtS: 45
GCID: GC11M022799

Small VCP/P97-Interacting Protein

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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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Small VCP/P97-Interacting Protein1 2

External Ids:    HGNC: 252381   Entrez Gene: 2580102   Ensembl: ENSG000001981687   UniProtKB: Q8NHG73   
ORGUL members:         

Export aliases for SVIP gene to outside databases

Previous GC identifer: GC11M022527


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SVIP Gene:
SVIP (small VCP/p97-interacting protein) is a protein-coding 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_000011.9  NC_018922.2  NT_009237.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the SVIP gene promoter:
         Max1   E2F-1   E2F   POU2F1   POU3F1   POU2F1a   E4BP4   c-Myc   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SVIP

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SVIP


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

Entrez Gene cytogenetic band: 11p14.2   Ensembl cytogenetic band:  11p14.3   HGNC cytogenetic band: 11p14.2

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

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M022799:  view genomic region     (about GC identifiers)

Start:
22,835,345 bp from pter      End:
22,851,845 bp from pter
Size:
16,501 bases      Orientation:
minus 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: SVIP_HUMAN, Q8NHG7 (See protein sequence)
Recommended Name: Small VCP/p97-interacting protein  
Size: 77 amino acids; 8443 Da
Subunit: Interacts with VCP (By similarity)

Explore the universe of human proteins at neXtProt for SVIP: NX_Q8NHG7

Explore proteomics data for SVIP at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins: NP_683691.1  
    ENSEMBL proteins: 
     ENSP00000346130  

    SVIP Human Recombinant Protein 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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    ProtoNet protein and cluster: Q8NHG7

    UniProtKB/Swiss-Prot: SVIP_HUMAN, Q8NHG7
    Similarity: Belongs to the SVIP family


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

    miRNA
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    miRTarBase miRNAs that target SVIP:
    hsa-mir-103a-3p (MIRT027071)

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    Selected qRT-PCR Assays for microRNAs that regulate SVIP (see all 14):
    hsa-miR-125a-5p hsa-miR-34c-5p hsa-miR-449b hsa-miR-449a hsa-miR-34a hsa-miR-124 hsa-miR-670 hsa-miR-125b
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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
    SVIP_HUMAN, Q8NHG7: Smooth endoplasmic reticulum membrane; Peripheral membrane protein (By similarity). Golgi
    apparatus membrane; Peripheral membrane protein (By similarity). Cell membrane; Peripheral membrane protein (By
    similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum5
    golgi apparatus5
    plasma membrane5
    nucleus3
    mitochondrion2
    cytosol1
    extracellular1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane IEA--
    GO:0005886plasma membrane IEA--
    GO:0030868smooth endoplasmic reticulum membrane IEA--
    GO:0070062extracellular vesicular exosome IDA--

    Find genes that share ontologies with SVIP           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 SVIP About    
    See pathways by source

    SuperPathContained pathways About
    1Protein processing in endoplasmic reticulum
    Protein processing in endoplasmic reticulum


    Find genes that share SuperPaths with SVIP           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    1 Kegg Pathway  (Kegg details for SVIP):
        Protein processing in endoplasmic reticulum

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SVIP
    Interactions:

        GeneGlobe Interaction Network for SVIP

    STRING Interaction Network Preview (showing 5 interactants - click image to see 14)

    Selected Interacting proteins for SVIP (Q8NHG73 ENSP000003461304) via UniProtKB, MINT, STRING, and/or I2D (see all 14)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    VCPIP1Q96JH73, ENSP000003090314I2D: score=2 STRING: ENSP00000309031
    AMFRQ9UKV53, ENSP000002906494I2D: score=1 STRING: ENSP00000290649
    GOLGA1Q928053, ENSP000003626564I2D: score=1 STRING: ENSP00000362656
    UFD1LQ928903, ENSP000002632024I2D: score=1 STRING: ENSP00000263202
    VCPP550723, ENSP000003517774I2D: score=1 STRING: ENSP00000351777
    About this table

    (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 SVIP



    (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 SVIP gene: 
    NM_148893.1  

    Unigene Cluster for SVIP:

    Small VCP/p97-interacting protein
    Hs.349096  [show with all ESTs]
    Unigene Representative Sequence: AL833119
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000525670 ENST00000354193(uc001mqp.4) ENST00000533774 ENST00000530199
    ENST00000529848
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SVIP (see all 14):
    hsa-miR-125a-5p hsa-miR-34c-5p hsa-miR-449b hsa-miR-449a hsa-miR-34a hsa-miR-124 hsa-miR-670 hsa-miR-125b
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    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SVIP
    Primer
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      QuantiFast Probe-based Assays in human, mouse, rat SVIP

    Additional mRNA sequence: 

    AF527534.1 AK095023.1 AL833119.1 

    10 DOTS entries:

    DT.113615  DT.101963268  DT.95276175  DT.95276178  DT.95276177  DT.91763411  DT.95245265  DT.100815512 
    DT.75138727  DT.95302395 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SVIP    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6
    SP1:        -     -     -                                 
    SP2:                    -                                 
    SP3:                                                      
    SP4:                                            -         


    ECgene alternative splicing isoforms for SVIP

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


    SVIP expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Blood (Cardiovascular System)
             Definitive Hematopoietic Stem Cells Definitive Yolk Sac
     
     Yolk Sac (Extraembryonic Tissues)
             Definitive Hematopoietic Stem Cells Definitive Yolk Sac
    SVIP Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SVIP Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.349096
        Custom PCR Arrays for SVIP
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SVIP

    (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 chordates.

    Orthologs for SVIP gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Svip1 , 5 small VCP/p97-interacting protein1, 5 77.92(n)1
    80.52(a)1
      7 (32.91 cM)5
    757441  NM_001160345.11  NP_001153817.11 
     519971655 
    chicken
    (Gallus gallus)
    Aves SVIP6
    small VCP/p97-interacting protein
    52(a)
    1 ↔ 1
    5(3058775-3063026) ENSGALG00000003648
    zebrafish
    (Danio rerio)
    Actinopterygii SVIP6
    small VCP/p97-interacting protein
    48(a)
    1 ↔ 1
    25(36436052-36447541) ENSDARG00000097236


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (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 SVIP (see all 237)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs7120221,2
    C,F,A,H--22843155(-) AGGAAT/AGATTG 1 -- int134Minor allele frequency- A:0.43MN NS EA NA WA CSA 3357
    rs1923866481,2
    --22843162(+) TCCTTC/TTACTT 1 -- int10--------
    rs1491068461,2
    --22843176(+) GCCTTC/GAAAAA 1 -- int10--------
    rs10192161,2
    C,F,A,H--22843220(-) GAACTA/GTATTT 1 -- int1 ese318Minor allele frequency- G:0.12MN NS EA NA CSA WA 2406
    rs1462340741,2
    C--22843250(+) ATGAAC/GAAAAA 1 -- int10--------
    rs1836694771,2
    --22843341(+) ATAGAA/TAAAAT 1 -- int10--------
    rs1389471661,2
    C--22843445(+) TTTGTC/TGGAGG 1 -- int10--------
    rs1426825811,2
    --22843450(+) TGGAGC/GGGTAG 1 -- int10--------
    rs1880977211,2
    --22843457(+) GTAGAA/TGAAGA 1 -- int10--------
    rs1918030121,2
    --22843498(+) GTGAAC/GTTGGT 1 -- int10--------

    HapMap Linkage Disequilibrium report for SVIP (22835345 - 22851845 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for SVIP:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv523451CNV Loss19592680
    nsv524283CNV Loss19592680

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

    (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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    Find genes that share disorders with SVIP           About GenesLikeMe

    Genetic Association Database (GAD): SVIP

    Export disorders for SVIP 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 SVIP gene, integrated from 10 sources (see all 14):
    (articles sorted by number of sources associating them with SVIP)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. (PubMed id 21546767)1, 4 Murea M....Freedman B.I. (Am. J. Nephrol. 2011)
    2. Regulation of ER-associated degradation via p97/VCP-interacting motif. (PubMed id 18793143)1, 3 Ballar P. and Fang S. (Biochem. Soc. Trans. 2008)
    3. Identification of SVIP as an endogenous inhibitor of endoplasmic reticulum-associated degradation. (PubMed id 17872946)1, 3 Ballar P....Fang S. (J. Biol. Chem. 2007)
    4. SVIP is a novel VCP/p97-interacting protein whose expression causes cell vacuolation. (PubMed id 12529442)1, 3 Nagahama M....Tagaya M. (Mol. Biol. Cell 2003)
    5. Structural and mechanistic insights into the arginine/lysine-rich peptide motifs that interact with P97/VCP. (PubMed id 24100225)1 Liu S....Hu H.Y. (Biochim. Biophys. Acta 2013)
    6. Structure and expression of a novel compact myelin protein - small VCP-interacting protein (SVIP). (PubMed id 24055875)1 Wu J....Li J. (Biochem. Biophys. Res. Commun. 2013)
    7. SVIP induces localization of p97/VCP to the plasma and lysosomal membranes and regulates autophagy. (PubMed id 21909394)1 Wang Y....Fang S. (PLoS ONE 2011)
    8. The structural and functional basis of the p97/valosin-containing protein (VCP)-interacting motif (VIM): mutually exclusive binding of cofactors to the N-terminal domain of p97. (PubMed id 21914798)1 HAonzelmann P. and Schindelin H. (J. Biol. Chem. 2011)
    9. GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. (PubMed id 21658281)4 Aouizerat B.E....Tseng Z.H. (BMC Cardiovasc Disord 2011)
    10. Defining the human deubiquitinating enzyme interaction landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (Cell 2009)

    (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: 258010 HGNC: 25238 Ensembl:ENSG00000198168 euGenes: HUgn258010 ECgene: SVIP Kegg: 258010
    H-InvDB: SVIP

    (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 SVIP 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 SVIP gene:
    Search GeneIP for patents involving SVIP

    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, 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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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