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SFT2D3 Gene

protein-coding   GIFtS: 43
GCID: GC02P128458

SFT2 Domain Containing 3

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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
SFT2 Domain Containing 31 2
SFT2 Domain-Containing Protein 32 3
Vesicle Transport Protein SFT2C2

External Ids:    HGNC: 287671   Entrez Gene: 848262   Ensembl: ENSG000001733497   UniProtKB: Q587I93   

Export aliases for SFT2D3 gene to outside databases

Previous GC identifers: GC02P128175 GC02P120764


(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 SFT2D3 Gene:
SFT2D3 (SFT2 domain containing 3) is a protein-coding gene.

UniProtKB/Swiss-Prot: SFT2C_HUMAN, Q587I9
Function: May be involved in fusion of retrograde transport vesicles derived from an endocytic compartment with
the Golgi complex (By similarity)




(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_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the SFT2D3 gene promoter:
         AML1a   MAZR   Pax-5   MIF-1   Nkx5-1   POU3F2   YY1   HNF-4alpha1   CP2   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SFT2D3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SFT2D3


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

Entrez Gene cytogenetic band: 2q14.3   Ensembl cytogenetic band:  2q14.3   HGNC cytogenetic band: 2q14.3

SFT2D3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SFT2D3 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P128458:  view genomic region     (about GC identifiers)

Start:
128,458,597 bp from pter      End:
128,461,407 bp from pter
Size:
2,811 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: SFT2C_HUMAN, Q587I9 (See protein sequence)
Recommended Name: Vesicle transport protein SFT2C  
Size: 215 amino acids; 21790 Da
Secondary accessions: Q8N2P9

Explore the universe of human proteins at neXtProt for SFT2D3: NX_Q587I9

Explore proteomics data for SFT2D3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SFT2D3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_116129.3  
    ENSEMBL proteins: 
     ENSP00000310803  

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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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    2 InterPro protein domains:
     IPR007305 Vesicle_transpt_Got1/SFT2
     IPR011691 Vesicle_transpt_SFT2

    Graphical View of Domain Structure for InterPro Entry Q587I9

    ProtoNet protein and cluster: Q587I9

    UniProtKB/Swiss-Prot: SFT2C_HUMAN, Q587I9
    Similarity: Belongs to the SFT2 family


    Find genes that share domains with SFT2D3           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SFT2C_HUMAN, Q587I9
    Function: May be involved in fusion of retrograde transport vesicles derived from an endocytic compartment with
    the Golgi complex (By similarity)

    Animal Models:

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    SwitchGear 3'UTR luciferase reporter plasmidSFT2D3 3' UTR sequence
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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
    SFT2C_HUMAN, Q587I9: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    peroxisome1

    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 SFT2D3           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 SFT2D3
    Interactions:

        Search GeneGlobe Interaction Network for SFT2D3

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for SFT2D3 (ENSP000003108034) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015031protein transport IEA--
    GO:0016192vesicle-mediated transport IEA--

    Find genes that share ontologies with SFT2D3           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 SFT2D3 (SFT2C)



    (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 SFT2D3 gene: 
    NM_032740.3  

    Unigene Cluster for SFT2D3:

    SFT2 domain containing 3
    Hs.345849  [show with all ESTs]
    Unigene Representative Sequence: NM_032740
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000310981(uc002tpf.3)
    miRNA
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    hsa-miR-3128 hsa-miR-539 hsa-let-7d hsa-let-7c hsa-miR-888* hsa-miR-378b hsa-miR-3167 hsa-let-7g
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      QuantiFast Probe-based Assays in human, mouse, rat SFT2D3

    Additional mRNA sequence: 

    AK074549.1 BC006808.1 BC063637.1 BC110324.1 BC133675.1 

    5 DOTS entries:

    DT.114076  DT.120966434  DT.409300  DT.85105571  DT.100774516 

    Selected AceView cDNA sequences (see all 298):

    BM560256 F12417 AA773744 BM675133 CR591938 AI418601 BF931513 BQ640405 
    CB243802 CA450493 AK002156 BF515130 Z41772 AA235688 BM994732 BF063402 
    BQ277834 AU138991 BC013990 AA339047 AA410628 BE747336 AW407659 AA284061 

    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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    SFT2D3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GATTTCTACA
    SFT2D3 Expression
    About this image

    SFT2D3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SFT2D3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.345849
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    In Situ
    Assay Products:
     

     
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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 and fungi.

    Orthologs for SFT2D3 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sft2d31 , 5 SFT2 domain containing 31, 5 79.4(n)1
    78.77(a)1
      18 (17.88 cM)5
    671581  NM_026006.11  NP_080282.11 
     319090945 
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.298302 Xenopus laevis transcribed sequence with weak similarity more 76.3(n)    CD329880.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sft2d31 SFT2 domain containing 3 56.96(n)
    52.53(a)
      407688  NM_001163995.1  NP_001157467.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG336351 CG33635 46.39(n)
    44.06(a)
      3772540  NM_001032044.2  NP_001027215.1 
    worm
    (Caenorhabditis elegans)
    Secernentea C18E9.101 C18E9.10 43.2(n)
    41.84(a)
      174427  NM_063504.3  NP_495905.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SFT26
    Non-essential tetra-spanning membrane protein foun...
    23(a)
    1 ↔ 1
    II(24098-24745) YBL102W


    ENSEMBL Gene Tree for SFT2D3 (if available)
    TreeFam Gene Tree for SFT2D3 (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 SFT2D3 (see all 91)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1467318231,2
    --128456665(+) TGCACA/GCAGAG 1 -- us2k10--------
    rs1149028451,2
    C,F--128456685(+) AACACG/AGGCTG 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs1844147991,2
    --128456686(+) ACACGA/GGCTGG 1 -- us2k10--------
    rs729689291,2
    C,F--128456705(+) GTGCCG/AAGAGA 1 -- us2k15Minor allele frequency- A:0.11WA CSA EA 244
    rs747107231,2
    C,F--128456806(+) AGGGCC/TGAAAC 1 -- us2k12Minor allele frequency- T:0.03NA EA 240
    rs1403218461,2
    --128456904(+) AGGGAG/TACAGG 1 -- us2k10--------
    rs1454332241,2
    --128456942(+) GAGTTC/TTGCTG 1 -- us2k10--------
    rs1883729861,2
    --128457068(+) AATGGA/GAAGCC 1 -- us2k10--------
    rs1812405841,2
    --128457132(+) GTAGGG/TGACCT 1 -- us2k10--------
    rs133889601,2
    C,F--128457218(+) ctataC/Tggtag 1 -- us2k11Minor allele frequency- T:0.03WA 118

    HapMap Linkage Disequilibrium report for SFT2D3 (128458597 - 128461407 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for SFT2D3:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv4301n71CNV Loss21882294
    nsv875030CNV Loss21882294
    nsv470482CNV Loss18288195
    nsv875015CNV Loss21882294
    nsv875033CNV Loss21882294
    dgv4299n71CNV Loss21882294

    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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    (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 SFT2D3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SFT2D3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1, 2 Otsuki T....Isogai T. (DNA Res. 2005)
    2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W.... Wilson R.K. (Nature 2005)
    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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    5. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

    (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: 84826 HGNC: 28767 AceView: WDR33 Ensembl:ENSG00000173349 euGenes: HUgn84826
    ECgene: SFT2D3 H-InvDB: SFT2D3

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for SFT2D3 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 SFT2D3 gene:
    Search GeneIP for patents involving SFT2D3

    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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