Human Gene SCFD2 (uc003gzu.3) Description and Page Index
  Description: Homo sapiens sec1 family domain containing 2 (SCFD2), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:53,739,151-54,232,242 Size: 493,092 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr4:53,740,136-54,232,108 Size: 491,973 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:53,739,151-54,232,242)mRNA (may differ from genome)Protein (684 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SCFD2_HUMAN
DESCRIPTION: RecName: Full=Sec1 family domain-containing protein 2; AltName: Full=Syntaxin-binding protein 1-like 1;
FUNCTION: May be involved in protein transport.
SIMILARITY: Belongs to the STXBP/unc-18/SEC1 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SCFD2
CDC HuGE Published Literature: SCFD2
Positive Disease Associations: Body Fat Distribution , Body Mass Index , Body Weight , Cholesterol, LDL , Eye , Waist-Hip Ratio
Related Studies:
  1. Body Fat Distribution
    , , . [PubMed 0]
  2. Body Fat Distribution
    , , . [PubMed 0]
  3. Body Mass Index
    , , . [PubMed 0]
           more ... click here to view the complete list

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.57 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 191.74 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -42.40134-0.316 Picture PostScript Text
3' UTR -281.80985-0.286 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 Q8WU76
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function

Biological Process:
GO:0006904 vesicle docking involved in exocytosis
GO:0008150 biological_process
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport

Cellular Component:
GO:0005575 cellular_component


-  Descriptions from all associated GenBank mRNAs
  BC021137 - Homo sapiens sec1 family domain containing 2, mRNA (cDNA clone MGC:32058 IMAGE:4866354), complete cds.
AY299407 - Homo sapiens syntaxin binding protein 1-like 1 (STXBP1L1) mRNA, complete cds.
JD071808 - Sequence 52832 from Patent EP1572962.
BC012458 - Homo sapiens sec1 family domain containing 2, mRNA (cDNA clone IMAGE:3860908), partial cds.
AB074276 - Homo sapiens primary neuroblastoma cDNA, clone:Nbla10988, full insert sequence.
BC032453 - Homo sapiens sec1 family domain containing 2, mRNA (cDNA clone MGC:40484 IMAGE:5176029), complete cds.
AK096833 - Homo sapiens cDNA FLJ39514 fis, clone PUAEN1000085.
GQ129375 - Synthetic construct Homo sapiens clone HAIB:100068600; DKFZo008E1135 sec1 family domain containing 2 protein (SCFD2) gene, complete cds.
KJ900294 - Synthetic construct Homo sapiens clone ccsbBroadEn_09688 SCFD2 gene, encodes complete protein.
GQ129374 - Synthetic construct Homo sapiens clone HAIB:100068697; DKFZo004E1136 sec1 family domain containing 2 protein (SCFD2) gene, partial cds.
AK024713 - Homo sapiens cDNA: FLJ21060 fis, clone CAS00963.
JD161018 - Sequence 142042 from Patent EP1572962.
CU689380 - Synthetic construct Homo sapiens gateway clone IMAGE:100020013 5' read SCFD2 mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_152540, NP_689753, Q8N5F3, Q8N8H0, Q8WU76, Q96ED3, SCFD2_HUMAN, STXBP1L1
UCSC ID: uc003gzu.3
RefSeq Accession: NM_152540
Protein: Q8WU76 (aka SCFD2_HUMAN or SFD2_HUMAN)
CCDS: CCDS33984.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_152540.3
exon count: 9CDS single in 3' UTR: no RNA size: 3204
ORF size: 2055CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4310.00frame shift in genome: no % Coverage: 99.06
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.