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Aliases for SCFD1 Gene

Aliases for SCFD1 Gene

  • Sec1 Family Domain Containing 1 2 3 5
  • Syntaxin-Binding Protein 1-Like 2 3 4
  • C14orf163 3 4
  • STXBP1L2 3 4
  • Sec1 Family Domain-Containing Protein 1 3
  • Chromosome 14 Open Reading Frame 163 2
  • Vesicle Transport-Related Protein 3
  • SLY1 Homolog 4
  • KIAA0917 4
  • RA410 3
  • SLY1P 3
  • Sly1p 4
  • SLY1 3

External Ids for SCFD1 Gene

Previous HGNC Symbols for SCFD1 Gene

  • C14orf163

Previous GeneCards Identifiers for SCFD1 Gene

  • GC14P029082
  • GC14P029083
  • GC14P030161
  • GC14P031091
  • GC14P011209

Summaries for SCFD1 Gene

GeneCards Summary for SCFD1 Gene

SCFD1 (Sec1 Family Domain Containing 1) is a Protein Coding gene. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include protein N-terminus binding and syntaxin binding.

UniProtKB/Swiss-Prot for SCFD1 Gene

  • Plays a role in SNARE-pin assembly and Golgi-to-ER retrograde transport via its interaction with COG4. Involved in vesicular transport between the endoplasmic reticulum and the Golgi (By similarity).

Gene Wiki entry for SCFD1 Gene

Additional gene information for SCFD1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCFD1 Gene

Genomics for SCFD1 Gene

GeneHancer (GH) Regulatory Elements for SCFD1 Gene

Promoters and enhancers for SCFD1 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
GH14J030620 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 688.5 +0.1 138 3.5 PKNOX1 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 SCFD1 RPL21P5 G2E3 GC14M030683
GH14J030621 Enhancer 0.6 ENCODE 650.7 -1.8 -1762 0.2 PKNOX1 ZNF189 JUNB EBF1 DPF2 BATF ATF2 FOSL1 JUND BCL11A SCFD1 G2E3-AS1
GH14J030558 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 22.1 -62.6 -62573 2.7 SMAD1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 G2E3 SCFD1 LOC101927124 G2E3-AS1
GH14J031204 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 20.3 +585.2 585179 5.1 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 HECTD1 RPL21P5 G2E3 SCFD1 ARHGAP5 HEATR5A DTD2 RNU6-541P
GH14J031228 Enhancer 1.6 FANTOM5 Ensembl ENCODE 19.6 +607.3 607344 2.6 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 NFYC PPARGC1A MEF2D HECTD1 SCFD1 RPL21P5 G2E3 ENSG00000203546 STRN3 GC14P031245
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCFD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCFD1 gene promoter:
  • LCR-F1
  • RSRFC4
  • POU2F1a
  • POU2F1
  • MEF-2A
  • aMEF-2
  • AREB6
  • C/EBPalpha
  • USF-1
  • USF1

Genomic Locations for SCFD1 Gene

Genomic Locations for SCFD1 Gene
chr14:30,622,112-30,735,828
(GRCh38/hg38)
Size:
113,717 bases
Orientation:
Plus strand
chr14:31,091,318-31,205,018
(GRCh37/hg19)
Size:
113,701 bases
Orientation:
Plus strand

Genomic View for SCFD1 Gene

Genes around SCFD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCFD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCFD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCFD1 Gene

Proteins for SCFD1 Gene

  • Protein details for SCFD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WVM8-SCFD1_HUMAN
    Recommended name:
    Sec1 family domain-containing protein 1
    Protein Accession:
    Q8WVM8
    Secondary Accessions:
    • A8K2Z5
    • B7Z4U7
    • B7Z594
    • O60754
    • O94990
    • Q7Z529
    • Q9BZI3
    • Q9UNL3
    • Q9Y6A8

    Protein attributes for SCFD1 Gene

    Size:
    642 amino acids
    Molecular mass:
    72380 Da
    Quaternary structure:
    • Interacts with STX17. Interacts with STX5A. Interacts with the COG complex via COG4 (By similarity).
    SequenceCaution:
    • Sequence=AAD40381.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=AAD48586.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=AAP97146.1; Type=Frameshift; Positions=5; Evidence={ECO:0000305}; Sequence=BAA74940.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SCFD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCFD1 Gene

Post-translational modifications for SCFD1 Gene

  • Ubiquitination at posLast=501501, posLast=494494, posLast=324324, and posLast=6363
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SCFD1 Gene

Domains & Families for SCFD1 Gene

Gene Families for SCFD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SCFD1 Gene

Graphical View of Domain Structure for InterPro Entry

Q8WVM8

UniProtKB/Swiss-Prot:

SCFD1_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 SCFD1: view

Function for SCFD1 Gene

Molecular function for SCFD1 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in SNARE-pin assembly and Golgi-to-ER retrograde transport via its interaction with COG4. Involved in vesicular transport between the endoplasmic reticulum and the Golgi (By similarity).

Phenotypes From GWAS Catalog for SCFD1 Gene

Gene Ontology (GO) - Molecular Function for SCFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19536132
GO:0019905 syntaxin binding ISS --
GO:0047485 protein N-terminus binding IEA --
genes like me logo Genes that share ontologies with SCFD1: view
genes like me logo Genes that share phenotypes with SCFD1: view

Animal Model Products

CRISPR Products

miRNA for SCFD1 Gene

miRTarBase miRNAs that target SCFD1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCFD1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCFD1 Gene

Localization for SCFD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCFD1 Gene

Cytoplasm. Endoplasmic reticulum membrane; Peripheral membrane protein. Golgi apparatus, Golgi stack membrane; Peripheral membrane protein.

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 SCFD1 gene
Compartment Confidence
plasma membrane 5
cytosol 5
golgi apparatus 5
endoplasmic reticulum 4
nucleus 2
mitochondrion 1
peroxisome 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005798 Golgi-associated vesicle ISS --
genes like me logo Genes that share ontologies with SCFD1: view

Pathways & Interactions for SCFD1 Gene

genes like me logo Genes that share pathways with SCFD1: view

Gene Ontology (GO) - Biological Process for SCFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis ISS --
GO:0001666 response to hypoxia IEA --
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER ISS --
GO:0006892 post-Golgi vesicle-mediated transport ISS --
GO:0006904 vesicle docking involved in exocytosis IEA --
genes like me logo Genes that share ontologies with SCFD1: view

No data available for SIGNOR curated interactions for SCFD1 Gene

Drugs & Compounds for SCFD1 Gene

No Compound Related Data Available

Transcripts for SCFD1 Gene

Unigene Clusters for SCFD1 Gene

Sec1 family domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCFD1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCFD1 Gene

No ASD Table

Relevant External Links for SCFD1 Gene

GeneLoc Exon Structure for
SCFD1
ECgene alternative splicing isoforms for
SCFD1

Expression for SCFD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCFD1 Gene

Protein differential expression in normal tissues from HIPED for SCFD1 Gene

This gene is overexpressed in Salivary gland (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SCFD1 Gene



Protein tissue co-expression partners for SCFD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SCFD1 Gene:

SCFD1

SOURCE GeneReport for Unigene cluster for SCFD1 Gene:

Hs.369168

Evidence on tissue expression from TISSUES for SCFD1 Gene

  • Nervous system(4.8)
  • Heart(4.3)
  • Liver(4.3)
  • Blood(4.2)
genes like me logo Genes that share expression patterns with SCFD1: view

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 SCFD1 Gene

Orthologs for SCFD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SCFD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCFD1 34 33
  • 99.95 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SCFD1 34
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SCFD1 34 33
  • 94.85 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SCFD1 34 33
  • 93.9 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Scfd1 16 34 33
  • 91.1 (n)
rat
(Rattus norvegicus)
Mammalia Scfd1 33
  • 90.57 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCFD1 34
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCFD1 34 33
  • 84.87 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 90 (a)
OneToMany
-- 34
  • 84 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia scfd1 33
  • 77.11 (n)
Str.11932 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8397 33
zebrafish
(Danio rerio)
Actinopterygii sly1 34 33 33
  • 74.83 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Slh 34 33
  • 56.69 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011358 33
  • 51.27 (n)
worm
(Caenorhabditis elegans)
Secernentea F43D9.3 34 33
  • 56.17 (n)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGL120W 33
  • 48.14 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SLY1 36 34 33
  • 47.69 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D18480g 33
  • 46.38 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons ATSLY1 33
  • 49.34 (n)
rice
(Oryza sativa)
Liliopsida Os03g0620800 33
  • 47.02 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7199 34
  • 58 (a)
OneToOne
Cin.14654 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sly1 33
  • 51.34 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU04252 33
  • 48.94 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14654 33
Species where no ortholog for SCFD1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)

Evolution for SCFD1 Gene

ENSEMBL:
Gene Tree for SCFD1 (if available)
TreeFam:
Gene Tree for SCFD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCFD1: view image

Paralogs for SCFD1 Gene

(1) SIMAP similar genes for SCFD1 Gene using alignment to 14 proteins:

  • SCFD1_HUMAN
  • B7Z5N7_HUMAN
  • B7Z738_HUMAN
  • G3V2M8_HUMAN
  • G3V363_HUMAN
  • G3V3K9_HUMAN
  • G3V4I1_HUMAN
  • G3V551_HUMAN
  • G3V5E2_HUMAN
  • G3V5F3_HUMAN
  • H0YIZ7_HUMAN
  • H0YJS6_HUMAN
  • H0YJY1_HUMAN
  • J3KNG4_HUMAN
genes like me logo Genes that share paralogs with SCFD1: view

No data available for Paralogs for SCFD1 Gene

Variants for SCFD1 Gene

Sequence variations from dbSNP and Humsavar for SCFD1 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1000002913 -- 30,652,118(+) A/C intron_variant
rs1000018690 -- 30,712,977(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000070975 -- 30,713,357(+) AAAAA/AAAAAA genic_downstream_transcript_variant, intron_variant
rs1000072306 -- 30,734,472(+) G/T genic_downstream_transcript_variant, intron_variant
rs1000123477 -- 30,637,476(+) G/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SCFD1 Gene

Variant ID Type Subtype PubMed ID
esv1928439 CNV deletion 18987734
esv3305404 CNV mobile element insertion 20981092
esv33189 CNV loss 17666407
esv3327410 CNV insertion 20981092
esv3413675 CNV insertion 20981092
esv3581098 CNV loss 25503493
nsv1230 CNV insertion 18451855
nsv472436 CNV novel sequence insertion 20440878
nsv509529 CNV insertion 20534489
nsv526536 CNV gain 19592680
nsv564169 CNV gain 21841781
nsv564171 CNV loss 21841781
nsv564172 CNV loss 21841781
nsv84475 CNV insertion 16902084
nsv84774 CNV insertion 16902084

Variation tolerance for SCFD1 Gene

Residual Variation Intolerance Score: 30.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.86; 48.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCFD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCFD1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCFD1 Gene

Disorders for SCFD1 Gene

Additional Disease Information for SCFD1

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

No disorders were found for SCFD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCFD1 Gene

Publications for SCFD1 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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. 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
  4. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. (PMID: 12665801) Gevaert K … Vandekerckhove J (Nature biotechnology 2003) 3 4 58
  5. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10048485) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4 58

Products for SCFD1 Gene

Sources for SCFD1 Gene

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