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

SUSD4 Gene

protein-coding   GIFtS: 48
GCID: GC01M223394

sushi domain containing 4

 Explore 3 diseases affiliated with
SUSD4 via our new
 Human Malady Compendium 
Biological research products
for SUSD4
    

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

Aliases
Sushi Domain Containing 41 2
FLJ100521
PRO2222
YHGM1962
Sushi Domain-Containing Protein 42

External Ids:    HGNC: 254701   Entrez Gene: 550612   Ensembl: ENSG000001435027   UniProtKB: Q5VX713   

Export aliases for SUSD4 gene to outside databases

Previous GC identifers: GC01M219767 GC01M221460 GC01M194069


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

  --

(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_000001.10  NC_018912.1  NT_167186.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SUSD4 gene promoter:
         SRF   STAT1   AML1a   GATA-3   SRF (504 AA)   STAT1beta   STAT1alpha   GATA-1   GATA-2   Msx-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSUSD4 promoter sequence
   Search SABiosciences Chromatin IP Primers for SUSD4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SUSD4


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

Entrez Gene cytogenetic band: 1q41   Ensembl cytogenetic band:  1q41   HGNC cytogenetic band: 1q41

SUSD4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SUSD4 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M223394:  view genomic region     (about GC identifiers)

Start:
223,394,161 bp from pter      End:
223,537,544 bp from pter
Size:
143,384 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: SUSD4_HUMAN, Q5VX71 (See protein sequence)
Recommended Name: Sushi domain-containing protein 4 precursor  
Size: 490 amino acids; 53778 Da
Subcellular location: Membrane; Single-pass type I membrane protein (Potential)
Secondary accessions: D3DTB9 Q6UX62 Q9BSR0 Q9NWG0
Alternative splicing: 4 isoforms:  Q5VX71-1   Q5VX71-2   Q5VX71-3   Q5VX71-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SUSD4: NX_Q5VX71

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5VX71

  • SUSD4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001032252.1  NP_060452.3  

    ENSEMBL proteins: 
     ENSP00000344219   ENSP00000339926   ENSP00000340917   ENSP00000355843   ENSP00000399288  
     ENSP00000355842  

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    Novus Biologicals SUSD4 Protein
    Novus Biologicals SUSD4 Lysates
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for SUSD4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--


    SUSD4 for ontologies           About GeneDecksing



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

    SUSD4 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR000436 Sushi_SCR_CCP

    Graphical View of Domain Structure for InterPro Entry Q5VX71

    ProtoNet protein and cluster: Q5VX71

    1 Blocks protein family: IPB000436 Sushi domain/SCR domain/CCP module

    UniProtKB/Swiss-Prot: SUSD4_HUMAN, Q5VX71
    Similarity: Contains 4 Sushi (CCP/SCR) domains


    (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

    miRNA
    Products:
        
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SUSD4
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    hsa-miR-622 hsa-miR-590-3p
    SwitchGear 3'UTR luciferase reporter plasmidSUSD4 3' UTR sequence
    Inhib. RNA
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SUSD4 

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SUSD4

    1 GenomeRNAi human phenotype for SUSD4:
     Elongated cells 

    Animal Models:
         Mouse knock-out Susd4tm1Lex for SUSD4
         1 MGI phenotypic allele for Susd4 (no phenotypes)

    SUSD4 for phenotypes           About GeneDecksing


    (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 SUSD4

    5/6 Interacting proteins for SUSD4 (Q5VX712, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MAPK6Q166592, 3MINT-8277455 I2D: score=1 
    COPS6Q7L5N13I2D: score=1 
    HLA-DRB3P794833I2D: score=1 
    NAT6Q930153I2D: score=1 
    RPL3P390233I2D: score=1 
    About this table

    (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 SUSD4
    Search CenterWatch for drugs/clinical trials and news about SUSD4 

    (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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SUSD4 gene (2 alternative transcripts): 
    NM_001037175.2  NM_017982.3  

    Unigene Cluster for SUSD4:

    Sushi domain containing 4
    Hs.497841  [show with all ESTs]
    Unigene Representative Sequence: AK096265
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000343846(uc001hnx.3) ENST00000494793 ENST00000478605 ENST00000483818
    ENST00000484503 ENST00000470249 ENST00000484758 ENST00000344029(uc001hnz.2)
    ENST00000497669 ENST00000342943 ENST00000366878(uc001hny.4 uc010puw.2 uc010pux.1)
    ENST00000454695 ENST00000366877

    miRNA
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    2 QIAGEN miScript miRNA Assays for microRNAs that regulate SUSD4:
    hsa-miR-622 hsa-miR-590-3p
    SwitchGear 3'UTR luciferase reporter plasmidSUSD4 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SUSD4 (see all 7)
    OriGene shRNA RFP: SUSD4
    OriGene siRNA: SUSD4
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SUSD4
    Clone
    Products:
         
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SUSD4 (see all 4)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SUSD4 (see all 4)
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector (see all 2): SUSD4 (NM_017982)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SUSD4 
    Primer
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    OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SUSD4
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SUSD4
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SUSD4

    Additional cDNA sequence: 

    AK000914.1 AK096265.1 AK295553.1 AK296923.1 AY358495.1 BC004888.2 EF560748.1 

    12 DOTS entries:

    DT.100749746  DT.40127876  DT.411506  DT.40127212  DT.100675234  DT.91713619  DT.91888592  DT.97796827 
    DT.121337348  DT.91661507  DT.92051348  DT.99933510 

    24/99 AceView cDNA sequences (see all 99):

    BM311465 AI628101 BE671439 AK000914 AA335726 AA988038 AA418002 BF447665 
    BC004888 AI538781 BE744704 BQ045203 AI417581 BM849437 BP360736 AW204351 
    AI984400 AI090524 BQ128216 CA942864 AI701529 BE503579 BE644888 F12032 

    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

    SUSD4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTGATCTGTG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    SUSD4 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    3 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    LiverLiver LobulePerivenous HepatocytesLiver
    OvaryPrimary FollicleGranulosa CellsOvary
    TestisSeminiferous TubulesSertoli cellsTestis
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SUSD4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SUSD4

    SOURCE GeneReport for Unigene cluster: Hs.497841
        SABiosciences Custom PCR Arrays for SUSD4
    Primer
    Products:
    OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for SUSD4
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SUSD4
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SUSD4

    (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 chordates.

    Orthologs for SUSD4 gene from 3/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves SUSD41 sushi domain containing 4 73.32(n)
    73.7(a)
      770442  XM_001233776.2  XP_001233777.2 
    lizard
    (Anolis carolinensis)
    Reptilia SUSD46
    --
    75(a)
    1 ↔ 1
    1(244767376-244773161)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5603041 sushi domain-containing protein 4-like 63.3(n)
    58.92(a)
      560304  XM_683701.2  XP_688793.1 


    ENSEMBL Gene Tree for SUSD4 (if available)
    TreeFam Gene Tree for SUSD4 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SUSD4 gene
    KIAA02472  
    1 SIMAP similar gene for SUSD4 using alignment to 4 protein entries:     SUSD4_HUMAN (see all proteins):
    KIAA0247

    SUSD4 for paralogs           About GeneDecksing



    (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

    10/2131 NCBI SNPs in SUSD4 are shown (see all 2131    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1843349861,2
    --223393694(+) AAACAC/TCCTAA 1 -- int10--------
    rs1510715141,2
    --223393804(+) GATATG/TCTATA 1 -- int10--------
    rs8511531,2
    C,F,H,--223393826(-) tcttaG/Ctccac 1 -- int117Minor allele frequency- C:0.03NS EA NA WA 2016
    rs1409230011,2
    --223393861(+) TGCTGC/TGGGCT 1 -- int10--------
    rs1159478951,2
    --223393870(+) CTGGAG/TAGGCA 1 -- int11Minor allele frequency- T:0.01NA 120
    rs1889239281,2
    --223393891(+) TGGTCC/TGCCAG 1 -- int10--------
    rs8511521,2
    C,F,H,--223394018(-) TGGAGG/ATTGTC 1 -- int123Minor allele frequency- A:0.02NS EA NA WA 2230
    rs1820084271,2
    --223394068(+) TCTCTA/TGTTCT 1 -- int10--------
    rs1147375941,2
    F,--223394119(+) CACCCC/TACTCC 1 -- int11Minor allele frequency- T:0.02WA 118
    rs798359641,2
    --223394134(+) CACCCG/AACTCT 1 -- int11Minor allele frequency- A:0.01WA 118

    HapMap Linkage Disequilibrium report for SUSD4 (223394161 - 223537544 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for SUSD4
         1 Indel: 48247

    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

    SUSD4 for disorders           About GeneDecksing

    3 diseases for SUSD4:    About MalaCards
    fryns syndrome    hepatitis b    hepatitis

    Human Genome Epidemiology (HuGE) Navigator: SUSD4 (1 document)

    Export disorders for SUSD4 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 SUSD4 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SUSD4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    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. New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)1 Davila S....Seielstad M. (2010)
    5. Tissue distribution and functional analysis of Sushi domain-containing protein 4. (PubMed id 20348246)1 Tu Z....Lin F. (2010)
    6. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    7. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (2006)
    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. (2004)

    (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: 55061 HGNC: 25470 AceView: FLJ10052 Ensembl:ENSG00000143502 euGenes: HUgn55061
    ECgene: SUSD4 H-InvDB: SUSD4

    (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 SUSD4 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 SUSD4 gene:
    Search GeneIP for patents involving SUSD4

    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),
    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
    About This Section

     
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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    Category
    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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