Human Gene SCFD1 (ENST00000458591.7_10) from GENCODE V47lift37
  Description: sec1 family domain containing 1, transcript variant 1 (from RefSeq NM_016106.4)
Gencode Transcript: ENST00000458591.7_10
Gencode Gene: ENSG00000092108.22_22
Transcript (Including UTRs)
   Position: hg19 chr14:31,091,525-31,205,056 Size: 113,532 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr14:31,091,545-31,204,815 Size: 113,271 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:31,091,525-31,205,056)mRNA (may differ from genome)Protein (642 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SCFD1_HUMAN
DESCRIPTION: RecName: Full=Sec1 family domain-containing protein 1; AltName: Full=SLY1 homolog; Short=Sly1p; AltName: Full=Syntaxin-binding protein 1-like 2;
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).
SUBUNIT: Binds STX5A. Interacts with the COG complex via COG4 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Endoplasmic reticulum membrane; Peripheral membrane protein (By similarity). Golgi apparatus, Golgi stack membrane; Peripheral membrane protein (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the STXBP/unc-18/SEC1 family.
SEQUENCE CAUTION: Sequence=AAD40381.1; Type=Frameshift; Positions=Several; Sequence=AAD48586.1; Type=Frameshift; Positions=Several; Sequence=AAP97146.1; Type=Frameshift; Positions=5; Sequence=BAA74940.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.80 RPKM in Pituitary
Total median expression: 562.49 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -10.4020-0.520 Picture PostScript Text
3' UTR -32.00241-0.133 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001619 - Sec1-like

Pfam Domains:
PF00995 - Sec1 family

SCOP Domains:
56815 - Sec1/munc18-like (SM) proteins

ModBase Predicted Comparative 3D Structure on Q8WVM8
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019905 syntaxin binding
GO:0047485 protein N-terminus binding

Biological Process:
GO:0000902 cell morphogenesis
GO:0001666 response to hypoxia
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0006892 post-Golgi vesicle-mediated transport
GO:0006904 vesicle docking involved in exocytosis
GO:0009636 response to toxic substance
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0048208 COPII vesicle coating
GO:0051223 regulation of protein transport
GO:0060628 regulation of ER to Golgi vesicle-mediated transport
GO:1901998 toxin transport
GO:1902902 negative regulation of autophagosome assembly

Cellular Component:
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005798 Golgi-associated vesicle
GO:0005801 cis-Golgi network
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0017119 Golgi transport complex
GO:0032580 Golgi cisterna membrane


-  Descriptions from all associated GenBank mRNAs
  AF319958 - Homo sapiens vesicle transport-related protein (FKSG23) mRNA, complete cds.
HV325274 - JP 2011505850-A/40: SM-PROTEIN BASED SECRETION ENGINEERING.
AK301406 - Homo sapiens cDNA FLJ57213 complete cds, highly similar to Sec1 family domain-containing protein 1.
AK297873 - Homo sapiens cDNA FLJ61324 complete cds, highly similar to Sec1 family domain-containing protein 1.
AK307960 - Homo sapiens cDNA, FLJ97908.
AB020724 - Homo sapiens KIAA0917 mRNA for KIAA0917 protein.
AK290410 - Homo sapiens cDNA FLJ75633 complete cds, highly similar to Homo sapiens sec1 family domain containing 1 (SCFD1), transcript variant 1, mRNA.
AK316212 - Homo sapiens cDNA, FLJ79111 complete cds, highly similar to Sec1 family domain-containing protein 1.
AK299222 - Homo sapiens cDNA FLJ58612 complete cds, highly similar to Sec1 family domain-containing protein 1.
AK298622 - Homo sapiens cDNA FLJ58209 complete cds, highly similar to Sec1 family domain-containing protein 1.
AK222820 - Homo sapiens mRNA for vesicle transport-related protein isoform a variant, clone: HEP04812.
AB463243 - Synthetic construct DNA, clone: pF1KA0917, Homo sapiens SCFD1 gene for sec1 family domain containing 1, without stop codon, in Flexi system.
BC017734 - Homo sapiens sec1 family domain containing 1, mRNA (cDNA clone MGC:21568 IMAGE:4420306), complete cds.
AF092139 - Homo sapiens vesicle transport-related protein mRNA, complete cds.
AF086916 - Homo sapiens sly1p mRNA, complete cds.
AF110646 - Homo sapiens vesicle transport-related protein mRNA, complete cds.
AF067205 - Homo sapiens vesicle transport related protein mRNA, partial cds.
AK308587 - Homo sapiens cDNA, FLJ98628.
CU676040 - Synthetic construct Homo sapiens gateway clone IMAGE:100020753 5' read SCFD1 mRNA.
JD027013 - Sequence 8037 from Patent EP1572962.
JD032762 - Sequence 13786 from Patent EP1572962.
JD064770 - Sequence 45794 from Patent EP1572962.
JD290405 - Sequence 271429 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8WVM8 (Reactome details) participates in the following event(s):

R-HSA-5694425 NSF ATPase activity dissociates cis-SNARE
R-HSA-5694446 BET1:GOSR2:STX5 bind v-SNARES on tethered vesicle
R-HSA-5694423 NSF and SNAPs bind cis-SNARE complex
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8K2Z5, B7Z4U7, B7Z594, C14orf163, ENST00000458591.1, ENST00000458591.2, ENST00000458591.3, ENST00000458591.4, ENST00000458591.5, ENST00000458591.6, FKSG23, KIAA0917, NM_016106, O60754, O94990, Q7Z529, Q8WVM8, Q9BZI3, Q9UNL3, Q9Y6A8, SCFD1_HUMAN, STXBP1L2, uc320zjq.1, uc320zjq.2
UCSC ID: ENST00000458591.7_10
RefSeq Accession: NM_016106.4
Protein: Q8WVM8 (aka SCFD1_HUMAN or SFD1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SCFD1:
als-overview (Amyotrophic Lateral Sclerosis Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.