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SLX4IP Gene

protein-coding   GIFtS: 30
GCID: GC20P010415

SLX4 Interacting Protein

(Previous name: chromosome 20 open reading frame 94)
(Previous symbol: C20orf94)
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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
SLX4 Interacting Protein1 2     bA254M13.12
C20orf941 2 3     dJ1099D15.32
SLX4-Interacting Protein2 3     Protein SLX4IP2
Chromosome 20 Open Reading Frame 941     UPF0492 Protein C20orf942
bA204H22.12     

External Ids:    HGNC: 162251   Entrez Gene: 1287102   Ensembl: ENSG000001493467   UniProtKB: Q5VYV73   

Export aliases for SLX4IP gene to outside databases


(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 SLX4IP Gene:
SLX4IP (SLX4 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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Regulatory elements:
   Search for regulatory transcription factor binding sites for SLX4IP
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SLX4IP

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLX4IP


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

Entrez Gene cytogenetic band: 20p12.2   Ensembl cytogenetic band:  20p12.2   HGNC cytogenetic band: 20p12

SLX4IP Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLX4IP gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P010415:  view genomic region     (about GC identifiers)

Start:
10,415,951 bp from pter      End:
10,617,477 bp from pter
Size:
201,527 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, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SLX4I_HUMAN, Q5VYV7 (See protein sequence)
Recommended Name: Protein SLX4IP  
Size: 408 amino acids; 45552 Da
Subunit: Interacts with SLX4/BTBD12; subunit of different structure-specific endonucleases
Sequence caution: Sequence=AAH20787.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential
poly-A sequence; Sequence=AAH26094.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential
poly-A sequence;
Secondary accessions: Q05CG2 Q05CT9

Explore the universe of human proteins at neXtProt for SLX4IP: NX_Q5VYV7

Explore proteomics data for SLX4IP at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SLX4IP Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001009608.1  
    ENSEMBL proteins: 
     ENSP00000335557   ENSP00000432784  

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    antibodies-online peptides for SLX4IP

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    antibodies-online antibodies for SLX4IP (12 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: Q5VYV7

    UniProtKB/Swiss-Prot: SLX4I_HUMAN, Q5VYV7
    Similarity: Belongs to the SLX4IP family


    (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,
    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): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19596235
         
    Find genes that share ontologies with SLX4IP           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SLX4IP:
     Increased G2M DNA content 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SLX4IP
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    miRTarBase miRNAs that target SLX4IP:
    hsa-mir-335-5p (MIRT019191)

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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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    (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 SLX4IP
    Interactions:

        Search GeneGlobe Interaction Network for SLX4IP

    STRING Interaction Network Preview (showing 5 interactants - click image to see 23)

    Selected Interacting proteins for SLX4IP (Q5VYV71, 3 ENSP000003355574) via UniProtKB, MINT, STRING, and/or I2D (see all 24)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SLX4Q8IY921, 3, ENSP000002940084EBI-2370881,EBI-2370740 I2D: score=2 STRING: ENSP00000294008
    SLX1AQ9BQ833, ENSP000002513034I2D: score=2 STRING: ENSP00000251303
    SLX1BQ9BQ833, ENSP000003289404I2D: score=2 STRING: ENSP00000328940
    CUL1Q136163, ENSP000003268044I2D: score=2 STRING: ENSP00000326804
    ERCC4Q928893, ENSP000003105204I2D: score=2 STRING: ENSP00000310520
    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 SLX4IP (SLX4I)



    (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 SLX4IP gene: 
    NM_001009608.1  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000334534(uc010zre.2) ENST00000488816
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat SLX4IP

    Selected AceView cDNA sequences (see all 61):

    AA953742 BC020787 AI457817 AW005530 AW950573 AW027259 AI689906 AI801974 
    AI620428 CB178597 BF196123 BX089224 AI380777 BE218083 BF110549 AI299862 
    BF111044 BQ001289 AA985554 AI703159 BG771223 BE327279 BC026094 AA834451 

    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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    SLX4IP expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SLX4IP Expression
    About this image

    SLX4IP Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLX4IP Protein Expression
        Custom PCR Arrays for SLX4IP
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLX4IP

    (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 SLX4IP gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slx4ip1 , 5 RIKEN cDNA 2210009G21 gene5
    SLX4 interacting protein1
    82.18(n)1
    70.79(a)1
      2 (67.65 cM)5
    742431  NM_028834.21  NP_083110.11 
     1368915015 
    chicken
    (Gallus gallus)
    Aves C3H20ORF941 chromosome 3 open reading frame, human C20orf94 60.84(n)
    45.5(a)
      416738  NM_001199412.1  NP_001186341.1 
    lizard
    (Anolis carolinensis)
    Reptilia SLX4IP6
    SLX4 interacting protein
    54(a)
    1 ↔ 1
    1(134170553-134218296)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia slx4ip1 SLX4 interacting protein 55.4(n)
    44.25(a)
      100038267  NM_001097385.1  NP_001090854.1 
    zebrafish
    (Danio rerio)
    Actinopterygii slx4ip6
    SLX4 interacting protein
    21(a)
    1 ↔ 1
    13(35613201-35694123) ENSDARG00000039069


    ENSEMBL Gene Tree for SLX4IP (if available)
    TreeFam Gene Tree for SLX4IP (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 SLX4IP (see all 3734)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1119330451,2
    C--10414281(+) CTGTC-/A/AA  
            
    AAAAA
    1 -- int11CSA 2
    rs1472956141,2
    C--10416902(+) TTCAT-/GACTC 
    TCACCCCA
    GAGCT
    1 -- int10--------
    rs1839676641,2
    --10416996(+) GATACA/TGCCCT 1 -- int10--------
    rs562044081,2
    C--10417013(+) CTTTCT/-TTTTT 1 -- int11Minor allele frequency- -:0.50CSA 2
    rs1399856241,2
    --10417067(+) TGGCGC/TGATCT 1 -- int10--------
    rs1453979061,2
    C--10417166(+) CCCCCA/GGCTAA 1 -- int10--------
    rs1889187881,2
    --10417324(+) CAACCC/TGTGCT 1 -- int10--------
    rs60328781,2
    C,F,H--10417445(+) CAATTT/CAGCTT 1 -- int123Minor allele frequency- C:0.11NS EA NA WA 2900
    rs23272941,2
    C,F,A,H--10417492(+) TACTTA/TTATGT 1 -- int116Minor allele frequency- T:0.27NS EA NA WA CSA 788
    rs1510485371,2
    --10417494(+) CTTATA/GTGTAA 1 -- int10--------

    HapMap Linkage Disequilibrium report for SLX4IP (10415951 - 10617477 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SLX4IP: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SLX4IP
    DNA2.0 Custom Variant and Variant Library Synthesis for SLX4IP

    (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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    (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 SLX4IP gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SLX4IP)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. (PubMed id 19596235)1, 2, 3 Svendsen J.M.... Harper J.W. (Cell 2009)
    2. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    3. Proliferating cell nuclear antigen (PCNA)-binding protein C1orf124 is a regulator of translesion synthesis. (PubMed id 22902628)1 Ghosal G.... Chen J. (J. Biol. Chem. 2012)
    4. The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. (PubMed id 21555518)1 Warnatz H.J....Yaspo M.L. (J. Biol. Chem. 2011)
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    6. Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific repression by the LSD1/CoREST1/HDAC complex. (PubMed id 19394292)1 Ouyang J....Gill G. (Mol. Cell 2009)
    7. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. (PubMed id 18691976)2 Daub H.... Mann M. (Mol. Cell 2008)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    10. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)2 Deloukas P....Rogers J. (Nature 2001)

    (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: 128710 HGNC: 16225 AceView: LOC128710 Ensembl:ENSG00000149346 euGenes: HUgn128710
    ECgene: SLX4IP H-InvDB: SLX4IP

    (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 SLX4IP 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 SLX4IP gene:
    Search GeneIP for patents involving SLX4IP

    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, LSBio, 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 inGenious Targeting Laboratory, 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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