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Aliases for SCFD2 Gene

Aliases for SCFD2 Gene

  • Sec1 Family Domain Containing 2 2 3 5
  • STXBP1L1 3 4
  • Sec1 Family Domain-Containing Protein 2 3
  • Syntaxin Binding Protein 1-Like 1 3
  • Syntaxin-Binding Protein 1-Like 1 4

External Ids for SCFD2 Gene

Previous GeneCards Identifiers for SCFD2 Gene

  • GC04M053655
  • GC04M053654
  • GC04M053580
  • GC04M053433
  • GC04M049683
  • GC04M053739

Summaries for SCFD2 Gene

GeneCards Summary for SCFD2 Gene

SCFD2 (Sec1 Family Domain Containing 2) is a Protein Coding gene.

UniProtKB/Swiss-Prot for SCFD2 Gene

  • May be involved in protein transport.

Additional gene information for SCFD2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCFD2 Gene

Genomics for SCFD2 Gene

GeneHancer (GH) Regulatory Elements for SCFD2 Gene

Promoters and enhancers for SCFD2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I053363 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 556.8 +0.7 723 3.2 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B SCFD2 ENSG00000272650 FIP1L1 CHIC2 GC04M053266 RNU6-310P
GH04I053195 Enhancer 1.3 VISTA Ensembl ENCODE 10.9 +168.9 168901 3.8 MEIS2 CTCF FEZF1 RAD21 ZNF335 ZNF664 ZSCAN5C ZNF143 SMC3 NFE2 SCFD2 FIP1L1 GC04P053179 PIR49160
GH04I053376 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 5.9 -11.9 -11934 2.3 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A DMAP1 ZNF48 YY1 ETS1 FIP1L1 LOC105377654 ENSG00000282278 ENSG00000272650 CHIC2 SCFD2 GC04M053405
GH04I053319 Enhancer 1 Ensembl ENCODE 11.4 +45.1 45144 2.9 INSM2 FEZF1 ZEB1 ZNF213 CAVIN1 CEBPB ZEB2 TSHZ1 HDAC8 ZNF843 SCFD2 RNU6-310P GC04M053266
GH04I053188 Enhancer 0.9 ENCODE 10.9 +177.2 177207 2 FOXA2 ARID4B RAD21 RARA ETS1 YY1 CREM MIXL1 HMG20B RXRA SCFD2 GC04P053179 PIR49160
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCFD2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCFD2 gene promoter:

Genomic Locations for SCFD2 Gene

Genomic Locations for SCFD2 Gene
chr4:52,872,982-53,366,111
(GRCh38/hg38)
Size:
493,130 bases
Orientation:
Minus strand
chr4:53,739,149-54,232,242
(GRCh37/hg19)

Genomic View for SCFD2 Gene

Genes around SCFD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCFD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCFD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCFD2 Gene

Proteins for SCFD2 Gene

  • Protein details for SCFD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WU76-SCFD2_HUMAN
    Recommended name:
    Sec1 family domain-containing protein 2
    Protein Accession:
    Q8WU76
    Secondary Accessions:
    • Q8N5F3
    • Q8N8H0
    • Q96ED3

    Protein attributes for SCFD2 Gene

    Size:
    684 amino acids
    Molecular mass:
    75127 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SCFD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCFD2 Gene

Post-translational modifications for SCFD2 Gene

  • Ubiquitination at isoforms=2196, posLast=424424, and posLast=664664

No data available for DME Specific Peptides for SCFD2 Gene

Domains & Families for SCFD2 Gene

Gene Families for SCFD2 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SCFD2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SCFD2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8WU76

UniProtKB/Swiss-Prot:

SCFD2_HUMAN :
  • Belongs to the STXBP/unc-18/SEC1 family.
Family:
  • Belongs to the STXBP/unc-18/SEC1 family.
genes like me logo Genes that share domains with SCFD2: view

Function for SCFD2 Gene

Molecular function for SCFD2 Gene

UniProtKB/Swiss-Prot Function:
May be involved in protein transport.

Phenotypes From GWAS Catalog for SCFD2 Gene

Gene Ontology (GO) - Molecular Function for SCFD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with SCFD2: view
genes like me logo Genes that share phenotypes with SCFD2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCFD2 Gene

Localization for SCFD2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCFD2 gene
Compartment Confidence
plasma membrane 2
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SCFD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
genes like me logo Genes that share ontologies with SCFD2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SCFD2 Gene

Pathways & Interactions for SCFD2 Gene

SuperPathways for SCFD2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCFD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006904 vesicle docking involved in exocytosis IEA --
GO:0008150 biological_process ND --
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IEA --
genes like me logo Genes that share ontologies with SCFD2: view

No data available for Pathways by source and SIGNOR curated interactions for SCFD2 Gene

Drugs & Compounds for SCFD2 Gene

No Compound Related Data Available

Transcripts for SCFD2 Gene

Unigene Clusters for SCFD2 Gene

Sec1 family domain containing 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCFD2 Gene

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

Relevant External Links for SCFD2 Gene

GeneLoc Exon Structure for
SCFD2
ECgene alternative splicing isoforms for
SCFD2

Expression for SCFD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCFD2 Gene

Protein differential expression in normal tissues from HIPED for SCFD2 Gene

This gene is overexpressed in Bone (16.5) and Peripheral blood mononuclear cells (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SCFD2 Gene



Protein tissue co-expression partners for SCFD2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCFD2 Gene:

SCFD2

SOURCE GeneReport for Unigene cluster for SCFD2 Gene:

Hs.302287

Evidence on tissue expression from TISSUES for SCFD2 Gene

  • Nervous system(4.7)
  • Heart(4.2)
  • Intestine(4.2)
  • Lung(4.1)
genes like me logo Genes that share expression patterns with SCFD2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCFD2 Gene

Orthologs for SCFD2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SCFD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCFD2 33 34
  • 99.32 (n)
cow
(Bos Taurus)
Mammalia SCFD2 33 34
  • 88.11 (n)
dog
(Canis familiaris)
Mammalia SCFD2 33 34
  • 87.36 (n)
mouse
(Mus musculus)
Mammalia Scfd2 33 16 34
  • 84.75 (n)
rat
(Rattus norvegicus)
Mammalia Scfd2 33
  • 84.5 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 80 (a)
OneToMany
-- 34
  • 78 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SCFD2 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCFD2 33 34
  • 67.52 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 68 (a)
OneToMany
-- 34
  • 66 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia scfd2 33
  • 62.45 (n)
zebrafish
(Danio rerio)
Actinopterygii SCFD2 (2 of 2) 34
  • 69 (a)
OneToMany
scfd2 33 34
  • 58.06 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G42700 33
  • 43.41 (n)
rice
(Oryza sativa)
Liliopsida Os11g0169100 33
  • 41.86 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 30 (a)
OneToOne
Species where no ortholog for SCFD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCFD2 Gene

ENSEMBL:
Gene Tree for SCFD2 (if available)
TreeFam:
Gene Tree for SCFD2 (if available)

Paralogs for SCFD2 Gene

No data available for Paralogs for SCFD2 Gene

Variants for SCFD2 Gene

Sequence variations from dbSNP and Humsavar for SCFD2 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000012456 -- 53,231,073(-) G/A intron_variant
rs1000017896 -- 52,905,169(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000020813 -- 53,236,673(-) T/C intron_variant
rs1000032656 -- 53,263,421(-) T/G intron_variant
rs1000061590 -- 53,023,631(-) G/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SCFD2 Gene

Variant ID Type Subtype PubMed ID
esv1439510 CNV insertion 17803354
esv2019878 CNV deletion 18987734
esv2421791 CNV deletion 20811451
esv24249 CNV loss 19812545
esv2664238 CNV deletion 23128226
esv2670287 CNV deletion 23128226
esv2727603 CNV deletion 23290073
esv2727604 CNV deletion 23290073
esv2727605 CNV deletion 23290073
esv2727606 CNV deletion 23290073
esv2727608 CNV deletion 23290073
esv2762432 CNV loss 21179565
esv2763360 CNV loss 21179565
esv3307040 CNV mobile element insertion 20981092
esv3327964 CNV insertion 20981092
esv3421850 CNV insertion 20981092
esv3429621 CNV insertion 20981092
esv3569417 CNV loss 25503493
esv3569418 CNV loss 25503493
esv3569419 CNV loss 25503493
esv3575701 CNV gain 25503493
esv3600513 CNV loss 21293372
esv3600517 CNV gain 21293372
esv3600518 CNV loss 21293372
esv3600519 CNV gain 21293372
esv3600521 CNV loss 21293372
esv3893922 CNV loss 25118596
nsv1008593 CNV loss 25217958
nsv1161084 CNV deletion 26073780
nsv292479 CNV deletion 16902084
nsv4339 CNV insertion 18451855
nsv441876 CNV loss 18776908
nsv471810 CNV loss 16327809
nsv473249 CNV novel sequence insertion 20440878
nsv476079 CNV novel sequence insertion 20440878
nsv507167 OTHER sequence alteration 20534489
nsv508280 CNV deletion 20534489
nsv514213 CNV gain+loss 21397061
nsv525346 CNV loss 19592680
nsv997614 CNV loss 25217958

Variation tolerance for SCFD2 Gene

Residual Variation Intolerance Score: 25.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.92; 89.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCFD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCFD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCFD2 Gene

Disorders for SCFD2 Gene

Additional Disease Information for SCFD2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SCFD2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCFD2 Gene

Publications for SCFD2 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  2. Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. (PMID: 20395239) Macgregor S … Mackey DA (Human molecular genetics 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58

Products for SCFD2 Gene

Sources for SCFD2 Gene

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