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SUSD3 Gene

protein-coding   GIFtS: 45
GCID: GC09P095820

Sushi Domain Containing 3

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disease database 

(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
Sushi Domain Containing 31 2
Sushi Domain-Containing Protein 32

External Ids:    HGNC: 283911   Entrez Gene: 2033282   Ensembl: ENSG000001573037   UniProtKB: Q96L083   

Export aliases for SUSD3 gene to outside databases

Previous GC identifers: GC09P091162 GC09P092900 GC09P094860 GC09P065497


(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 SUSD3 Gene:
SUSD3 (sushi domain containing 3) 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_000009.11  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SUSD3 gene promoter:
         STAT1   Pax-5   STAT4   STAT1beta   STAT5A   STAT1alpha   HNF-1A   HNF-1   STAT2   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSUSD3 promoter sequence
   Search Chromatin IP Primers for SUSD3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SUSD3


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

Entrez Gene cytogenetic band: 9q22.31   Ensembl cytogenetic band:  9q22.31   HGNC cytogenetic band: 9q22.32

SUSD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SUSD3 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P095820:  view genomic region     (about GC identifiers)

Start:
95,820,989 bp from pter      End:
95,847,420 bp from pter
Size:
26,432 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SUSD3_HUMAN, Q96L08 (See protein sequence)
Recommended Name: Sushi domain-containing protein 3  
Size: 255 amino acids; 27119 Da
Secondary accessions: Q49AA6 Q6UXV7
Alternative splicing: 3 isoforms:  Q96L08-1   Q96L08-2   Q96L08-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SUSD3: NX_Q96L08

Explore proteomics data for SUSD3 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn27
  • Modification sites at PhosphoSitePlus

  • See SUSD3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_001273934.1  NP_001273935.1  NP_001273936.1  NP_001273937.1  NP_659443.1  

    ENSEMBL proteins: 
     ENSP00000364621   ENSP00000475051   ENSP00000474695   ENSP00000364618  

    SUSD3 Human Recombinant Protein Products:

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    Search eBioscience for ELISAs for SUSD3 


    (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:
     IPR000436 Sushi_SCR_CCP

    Graphical View of Domain Structure for InterPro Entry Q96L08

    ProtoNet protein and cluster: Q96L08

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

    UniProtKB/Swiss-Prot: SUSD3_HUMAN, Q96L08
    Similarity: Contains 1 Sushi (CCP/SCR) domain


    Find genes that share domains with SUSD3           About GenesLikeMe


    (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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SUSD3
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SUSD3

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SUSD3
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    miRTarBase miRNAs that target SUSD3:
    hsa-mir-335-5p (MIRT017039)

    Block miRNA regulation of human, mouse, rat SUSD3 using miScript Target Protectors
    4 qRT-PCR Assays for microRNAs that regulate SUSD3:
    hsa-miR-137 hsa-miR-1323 hsa-miR-708* hsa-miR-548o
    SwitchGear 3'UTR luciferase reporter plasmidSUSD3 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector: SUSD3 (NM_145006)
    Sino Biological Human cDNA Clone for SUSD3
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SUSD3

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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
    SUSD3_HUMAN, Q96L08: Membrane; Single-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane2
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with SUSD3           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 SUSD3
    Interactions:

        Search GeneGlobe Interaction Network for SUSD3

    (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 SUSD3



    (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 SUSD3 gene (5 alternative transcripts): 
    NM_001287005.1  NM_001287006.1  NM_001287007.1  NM_001287008.1  NM_145006.3  

    Unigene Cluster for SUSD3:

    Sushi domain containing 3
    Hs.88417  [show with all ESTs]
    Unigene Representative Sequence: AK128289
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000375472(uc004atb.3 uc004atc.3) ENST00000465709 ENST00000471462
    ENST00000375469
    miRNA
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    4 qRT-PCR Assays for microRNAs that regulate SUSD3:
    hsa-miR-137 hsa-miR-1323 hsa-miR-708* hsa-miR-548o
    SwitchGear 3'UTR luciferase reporter plasmidSUSD3 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for SUSD3
    Predesigned siRNA for gene silencing in human, mouse, rat SUSD3
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    GenScript: all cDNA clones in your preferred vector: SUSD3 (NM_145006)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SUSD3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SUSD3
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SUSD3
      QuantiTect SYBR Green Assays in human, mouse, rat SUSD3
      QuantiFast Probe-based Assays in human, mouse, rat SUSD3

    Additional mRNA sequence: 

    AK128289.1 AK128453.1 AL137623.1 AY358190.1 BC014601.2 BC041834.1 

    10 DOTS entries:

    DT.456084  DT.101959046  DT.101981230  DT.100674322  DT.75101910  DT.92048102  DT.121162377  DT.121162385 
    DT.97772950  DT.430383 

    Selected AceView cDNA sequences (see all 92):

    AI802088 BC041834 BE857970 AI684361 AI972041 AA714720 BM458621 AW027022 
    AI801840 AY358190 AA404586 AI760200 AA916701 BI910862 AA490088 AK128453 
    AI373233 CD366701 AA383827 AI452970 AA626321 AA810774 AW300436 BI463984 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SUSD3    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b
    SP1:                    -           -           -                           
    SP2:                    -     -     -           -                           
    SP3:                    -     -     -           -           -               
    SP4:                                                                        
    SP5:                                                                        


    ECgene alternative splicing isoforms for SUSD3

    (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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    SUSD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CGCCCAGCTC
    SUSD3 Expression
    About this image


    SUSD3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Kidney (Urinary System)    fully expand to see all 5 entries
             Loop of Henle Cells Loop of Henle
             Proximal Tubule
     
     Epithelial Cells
             Loop of Henle Cells Loop of Henle
     
     Testis (Reproductive System)
    SUSD3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SUSD3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.88417
        Custom PCR Arrays for SUSD3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SUSD3

    (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 SUSD3 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Susd31 , 5 sushi domain containing 31, 5 75.4(n)1
    69.76(a)1
      13 (25.16 cM)5
    663291  NM_025491.31  NP_079767.21 
     492306905 
    chicken
    (Gallus gallus)
    Aves SUSD36
    sushi domain containing 3
    39(a)
    1 ↔ 1
    12(6644909-6670629)
    lizard
    (Anolis carolinensis)
    Reptilia SUSD36
    sushi domain containing 3
    37(a)
    1 ↔ 1
    GL343225.1(1941305-2006190)
    zebrafish
    (Danio rerio)
    Actinopterygii SUSD36
    sushi domain containing 3
    27(a)
    1 ↔ 1
    25(1476126-1483765) ENSDARG00000077995


    ENSEMBL Gene Tree for SUSD3 (if available)
    TreeFam Gene Tree for SUSD3 (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 SUSD3 (see all 648)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0356634
    A breast cancer sample4--see VAR_0356632 S T mis40--------
    rs1401230001,2
    C--95819004(+) CTGGTC/TGCAAA 1 -- us2k10--------
    rs1919777891,2
    --95819078(+) CTGAGC/TCTGGC 1 -- us2k10--------
    rs1139627231,2
    C,F--95819081(+) AGCCTG/AGCCGG 1 -- us2k12Minor allele frequency- A:0.03NA 122
    rs1161549701,2
    F--95819289(+) TGGAGT/GTTTTG 1 -- us2k11Minor allele frequency- G:0.01WA 118
    rs1439325041,2
    --95819339(+) CTGGCC/TTCCTG 1 -- us2k10--------
    rs1468697561,2
    --95819471(+) CCTGGA/GTCACA 1 -- us2k10--------
    rs1851602431,2
    --95819513(+) GGTGTC/TTTCCA 1 -- us2k10--------
    rs1405284941,2
    --95819655(+) GGCCTG/TAGAGG 1 -- us2k10--------
    rs1503922621,2
    C--95819808(+) CGTGTC/GTGACC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SUSD3 (95820989 - 95847420 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for SUSD3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2738780CNV Deletion23290073
    esv2659260CNV Deletion23128226
    dgv8260n71CNV Loss21882294
    nsv893575CNV Loss21882294
    nsv526296CNV Loss19592680
    nsv893576CNV Gain21882294
    esv32996CNV Gain17666407

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SUSD3
    DNA2.0 Custom Variant and Variant Library Synthesis for SUSD3

    (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 SUSD3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SUSD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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, 3 Clark H.F.... Gray A.M. (Genome Res. 2003)
    2. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
    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. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    5. Identification of genes related to Parkinson's disease using expressed sequence tags. (PubMed id 17213182)1 Kim J.M.... Kim N.S. (DNA Res. 2006)
    6. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
    7. 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)

    (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: 203328 HGNC: 28391 AceView: SUSD3 Ensembl:ENSG00000157303 euGenes: HUgn203328
    ECgene: SUSD3 H-InvDB: SUSD3

    (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 SUSD3 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 SUSD3 gene:
    Search GeneIP for patents involving SUSD3

    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, 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

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