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SCFD2 Gene

protein-coding   GIFtS: 46
GCID: GC04M053739

Sec1 Family Domain Containing 2

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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
Sec1 Family Domain Containing 21 2
Syntaxin-Binding Protein 1-Like 12 3
STXBP1L12 3
Sec1 Family Domain-Containing Protein 22
Syntaxin Binding Protein 1-Like 12

External Ids:    HGNC: 306761   Entrez Gene: 1525792   Ensembl: ENSG000001841787   UniProtKB: Q8WU763   

Export aliases for SCFD2 gene to outside databases

Previous GC identifers: GC04M053655 GC04M053654 GC04M053580 GC04M053433 GC04M049683


(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 SCFD2 Gene:
SCFD2 (sec1 family domain containing 2) is a protein-coding gene.

UniProtKB/Swiss-Prot: SCFD2_HUMAN, Q8WU76
Function: May be involved in protein transport




(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_000004.11  NC_018915.2  NT_022853.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the SCFD2 gene promoter:
         AML1a   AP-1   MZF-1   AREB6   MEF-2A   POU2F1   POU2F1a   aMEF-2   TGIF   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCFD2 promoter sequence
   Search Chromatin IP Primers for SCFD2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCFD2


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

Entrez Gene cytogenetic band: 4q12   Ensembl cytogenetic band:  4q12   HGNC cytogenetic band: 4q12

SCFD2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCFD2 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M053739:  view genomic region     (about GC identifiers)

Start:
53,739,149 bp from pter      End:
54,232,242 bp from pter
Size:
493,094 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., 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: SCFD2_HUMAN, Q8WU76 (See protein sequence)
Recommended Name: Sec1 family domain-containing protein 2  
Size: 684 amino acids; 75127 Da
Secondary accessions: Q8N5F3 Q8N8H0 Q96ED3
Alternative splicing: 2 isoforms:  Q8WU76-1   Q8WU76-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SCFD2: NX_Q8WU76

Explore proteomics data for SCFD2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys196, Lys424, Lys664
  • Modification sites at PhosphoSitePlus

  • See SCFD2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689753.2  
    ENSEMBL proteins: 
     ENSP00000384182   ENSP00000373592   ENSP00000427202  

    SCFD2 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SCFD2

     
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    Search eBioscience for ELISAs for SCFD2 


    (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:
     IPR001619 Sec1-like
     IPR027482 Sec-1-like_dom2

    Graphical View of Domain Structure for InterPro Entry Q8WU76

    ProtoNet protein and cluster: Q8WU76

    1 Blocks protein domain: IPB001619 Sec1-like protein

    UniProtKB/Swiss-Prot: SCFD2_HUMAN, Q8WU76
    Similarity: Belongs to the STXBP/unc-18/SEC1 family


    Find genes that share domains with SCFD2           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: SCFD2_HUMAN, Q8WU76
    Function: May be involved in protein transport

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    Find genes that share ontologies with SCFD2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SCFD2:
     Synthetic lethal with Ras 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SCFD2
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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 COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane2
    endoplasmic reticulum1
    mitochondrion1
    nucleus1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--

    Find genes that share ontologies with SCFD2           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 SCFD2
    Interactions:

        Search GeneGlobe Interaction Network for SCFD2

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

    1 Interacting protein for SCFD2 (ENSP000003841824) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006904vesicle docking involved in exocytosis IEA--
    GO:0008150biological_process ND--
    GO:0015031protein transport IEA--
    GO:0016192vesicle-mediated transport ----

    Find genes that share ontologies with SCFD2           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 SCFD2



    (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 SCFD2 gene: 
    NM_152540.3  

    Unigene Cluster for SCFD2:

    Sec1 family domain containing 2
    Hs.302287  [show with all ESTs]
    Unigene Representative Sequence: AY299407
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000401642(uc003gzu.3 uc010igm.3) ENST00000388940 ENST00000503450

    miRNA
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    Inhib. RNA
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SCFD2 (NM_152540)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SCFD2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SCFD2
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat SCFD2
      QuantiFast Probe-based Assays in human, mouse, rat SCFD2

    Additional mRNA sequence: 

    AB074276.1 AK024713.1 AK096833.1 AY299407.1 BC012458.1 BC021137.1 BC032453.1 

    6 DOTS entries:

    DT.455853  DT.75102857  DT.100780198  DT.97789775  DT.91668726  DT.86849775 

    Selected AceView cDNA sequences (see all 83):

    AI612830 BX096206 BI870212 CA434983 BE220738 AA971592 AI609833 BE552186 
    AW770810 AI640397 BQ003799 AK024713 BU623093 AW084139 AA974688 AI360898 
    AW770802 AW770391 AA599803 AA708986 AI094692 BM683445 N79222 CN480424 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for SCFD2    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
    SP1:                                                            
    SP2:                                            -               


    ECgene alternative splicing isoforms for SCFD2

    (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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    SCFD2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGGTAATAA
    SCFD2 Expression
    About this image

    SCFD2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SCFD2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.302287
        Custom PCR Arrays for SCFD2
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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 eukaryotes.

    Orthologs for SCFD2 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scfd21 , 5 Sec1 family domain containing 21, 5 84.75(n)1
    83.48(a)1
      5 (39.44 cM)5
    2129861  NM_001114660.21  NP_001108132.11 
     742048165 
    chicken
    (Gallus gallus)
    Aves SCFD21 sec1 family domain containing 2 67.52(n)
    65.62(a)
      770088  XM_001233405.3  XP_001233406.3 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    --
    68(a)
    66(a)
    many → 1
    many → 1
    5(103391406-103433008)
    GL343293.1(1575895-1604451)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia scfd21 sec1 family domain containing 2 62.45(n)
    55.17(a)
      394663  NM_203735.1  NP_989066.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BQ605480.12   -- 76.3(n)    BQ605480.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G427001 AT2G42700 43.41(n)
    30.22(a)
      818870  NM_129831.4  NP_181798.2 
    rice
    (Oryza sativa)
    Liliopsida Os11g01691001 Os11g0169100 41.86(n)
    28.88(a)
      4349884  NM_001072381.1  NP_001065849.1 


    ENSEMBL Gene Tree for SCFD2 (if available)
    TreeFam Gene Tree for SCFD2 (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 SCFD2 (see all 9210)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs719685061,2
    C--49944101(+) TCTCA-/AAAAAA 1 -- int10--------
    rs339300571,2
    C--50011989(+) TTTAT-/TTTAA 
            
    TTTAA
    1 -- int10--------
    rs1458473531,2
    --53738709(+) CAGAAC/TCTAGC 1 -- int10--------
    rs1141312101,2
    C,F--53738784(+) TTTGAG/ATCACG 1 -- int12Minor allele frequency- A:0.03WA NA 238
    rs1896907251,2
    --53738787(+) GAGTCA/GCGTAA 1 -- int10--------
    rs1490153431,2
    --53738804(+) ACTTTA/CCAATT 1 -- int10--------
    rs1812899441,2
    --53738850(+) TCTTAC/TGGATG 1 -- int10--------
    rs1436424791,2
    --53738862(+) CTACCA/GTTAAC 1 -- int10--------
    rs1858837741,2
    --53738921(+) CCTGCA/GGTCTC 1 -- int10--------
    rs1902194851,2
    --53739056(+) AAAAAC/TGACAG 1 -- int10--------

    HapMap Linkage Disequilibrium report for SCFD2 (53739149 - 53989149 bp, first 250kb of SCFD2)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SCFD2 (see all 23):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2019878CNV Deletion18987734
    esv2727605CNV Deletion23290073
    esv2727608CNV Deletion23290073
    esv2421791CNV Deletion20811451
    esv2727604CNV Deletion23290073
    esv2664238CNV Deletion23128226
    esv2727603CNV Deletion23290073
    esv2670287CNV Deletion23128226
    esv2727606CNV Deletion23290073
    esv272915CNV Insertion20981092

    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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    Find genes that share disorders with SCFD2           About GenesLikeMe

    Genetic Association Database (GAD): SCFD2
    Human Genome Epidemiology (HuGE) Navigator: SCFD2 (1 document)

    Export disorders for SCFD2 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 SCFD2 gene, integrated from 10 sources (see all 14):
    (articles sorted by number of sources associating them with SCFD2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. (PubMed id 20395239)1, 4 Macgregor S....Mackey D.A. (Hum. Mol. Genet. 2010)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. 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)
    6. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (J. Cell. Sci. 2012)
    7. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    9. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    10. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)

    (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: 152579 HGNC: 30676 AceView: SCFD2 Ensembl:ENSG00000184178 euGenes: HUgn152579
    ECgene: SCFD2 H-InvDB: SCFD2

    (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 SCFD2 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 SCFD2 gene:
    Search GeneIP for patents involving SCFD2

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    (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)
    About This Section

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