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

SCFD2 Gene

protein-coding   GIFtS: 45
GCID: GC04M053739

Sec1 Family Domain Containing 2

  Search for SCFD2
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

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

GeneCards Summary for SCFD2 Gene: 
SCFD2 (sec1 family domain containing 2) is a protein-coding gene. GO annotations related to this gene include molecular_function.

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NT_022853.15  NC_018915.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for SCFD2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8WU76

  • SCFD2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SCFD2 Protein Expression
    REFSEQ proteins: NP_689753.2  
    ENSEMBL proteins: 
     ENSP00000384182   ENSP00000373592   ENSP00000427202  

    Human Recombinant Protein Products for SCFD2: 
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    Novus Biologicals SCFD2 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SCFD2 

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

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

    SCFD2 for ontologies           About GeneDecksing



    SCFD2 Antibody Products: 
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    Cloud-Clone Corp. CLIAs for SCFD2


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


    SCFD2 for domains           About GeneDecksing


    (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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

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

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    SCFD2 for ontologies           About GeneDecksing


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

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for SCFD2 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for SCFD2

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SCFD2 
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    miRNA
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    Inhib. RNA
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    Gene Editing
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCFD2


    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks 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 (GO ID links to tree view):    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 ----

    SCFD2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SCFD2

    Search CenterWatch for drugs/clinical trials and news about 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,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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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    Search QIAGEN for miScript miRNA Assays for microRNAs that regulate SCFD2
    SwitchGear 3'UTR luciferase reporter plasmidSCFD2 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for SCFD2
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SCFD2
    Clone
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    OriGene clones in human, mouse for SCFD2 (see all 8)
    OriGene ORF clones in mouse, rat for SCFD2
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    GenScript: all cDNA clones in your preferred vector: SCFD2 (NM_152540)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SCFD2
    Sirion Biotech Customized lentivirus for stable overexpression of SCFD2 
                         Customized lentivirus expression plasmids for stable overexpression of SCFD2 
    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SCFD2
      QIAGEN 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 

    24/83 AceView cDNA sequences (see all 83):

    AI609833 BE552186 AW770810 AI640397 BQ003799 AK024713 BU623093 AW084139 
    AA974688 AI360898 AW770802 AW770391 AA599803 AI612830 BX096206 BI870212 
    CA434983 BE220738 AA971592 AW299799 AI580218 BM663856 BF740075 BM991288 

    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™, 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

    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


    See SCFD2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SCFD2

    SOURCE GeneReport for Unigene cluster: Hs.302287
        SABiosciences Custom PCR Arrays for SCFD2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCFD2

    (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 eukaryotes.

    Orthologs for SCFD2 gene from 6/14 species (see all 14)    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_001114660.11  NP_001108132.11 
     742048165 
    chicken
    (Gallus gallus)
    Aves SCFD21 sec1 family domain containing 2 67.32(n)
    65.5(a)
      770088  XM_001233405.2  XP_001233406.2 
    lizard
    (Anolis carolinensis)
    Reptilia SCFD26
    --
    Uncharacterized protein
    65(a)
    64(a)
    1 ↔ 1
    possible ortholog
    5(103391406-103433008)
    GL343293.1(1575895-1604451)
    zebrafish
    (Danio rerio)
    Actinopterygii BQ605480.12   -- 76.3(n)    BQ605480.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G427001 hypothetical protein 44.2(n)
    30.9(a)
      818870  NM_001202805.1  NP_001189734.1 
    rice
    (Oryza sativa)
    Liliopsida Os11g01691001 hypothetical protein 42.11(n)
    28.7(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)
    About This Section
      --

    (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) 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

    10/9210 SNPs in SCFD2 are shown (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) 10/23 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

    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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SCFD2 for disorders           About MalaCards

    SCFD2 for disorders           About GeneDecksing

    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)
    About This Section

    PubMed articles for SCFD2 gene, integrated from 9 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 g ene determining human optic disc size. (PubMed id 20395239)1, 4 Macgregor S....Mackey D.A. (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. (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. (2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (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. (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. (2012)
    7. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    9. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    10. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)

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

    (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 SCFD2 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 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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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