Human Gene SCG3 (ENST00000220478.8_4) from GENCODE V47lift37
  Description: secretogranin III, transcript variant 1 (from RefSeq NM_013243.4)
Gencode Transcript: ENST00000220478.8_4
Gencode Gene: ENSG00000104112.9_9
Transcript (Including UTRs)
   Position: hg19 chr15:51,973,700-52,013,223 Size: 39,524 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr15:51,973,953-52,011,723 Size: 37,771 Coding Exon Count: 12 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:51,973,700-52,013,223)mRNA (may differ from genome)Protein (468 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SCG3_HUMAN
DESCRIPTION: RecName: Full=Secretogranin-3; AltName: Full=Secretogranin III; Short=SgIII; Flags: Precursor;
SUBUNIT: Interacts with CHGA (By similarity).
SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle lumen (By similarity). Cytoplasmic vesicle, secretory vesicle membrane; Peripheral membrane protein (By similarity). Secreted. Note=Associated with the secretory granule membrane through direct binding to cholesterol-enriched lipid rafts in intragranular conditions (By similarity). Neuroendocrine and endocrine secretory granules.
TISSUE SPECIFICITY: Expressed in brain, heart, kidney, liver and skeletal muscle.
POLYMORPHISM: Polymorphisms in the 5'-flanking region and in intron 1 may have an effect on transcriptional activity and be associated with an increase in subcutaneous, but not visceral, fat area. Hence, may influence the risk of obesity.

-  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: 80.08 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 619.63 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 -64.70253-0.256 Picture PostScript Text
3' UTR -370.101500-0.247 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
IPR026197 - SCG3

Pfam Domains:
PF15467 - Secretogranin-3

SCOP Domains:
52518 - Thiamin diphosphate-binding fold (THDP-binding)

ModBase Predicted Comparative 3D Structure on Q8WXD2
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 orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding

Biological Process:
GO:0002576 platelet degranulation
GO:0043687 post-translational protein modification
GO:0044267 cellular protein metabolic process

Cellular Component:
GO:0005576 extracellular region
GO:0005788 endoplasmic reticulum lumen
GO:0016020 membrane
GO:0030658 transport vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0034774 secretory granule lumen


-  Descriptions from all associated GenBank mRNAs
  AF453583 - Homo sapiens secretogranin III mRNA, complete cds.
AF078851 - Homo sapiens secretogranin III mRNA, complete cds.
AY359093 - Homo sapiens clone DNA96042 secretogranin (UNQ2502) mRNA, complete cds.
AK075314 - Homo sapiens cDNA FLJ90833 fis, clone Y79AA1001803, highly similar to Secretogranin-3 precursor.
AK296466 - Homo sapiens cDNA FLJ50788 complete cds, highly similar to Secretogranin-3 precursor.
AK290175 - Homo sapiens cDNA FLJ77891 complete cds, highly similar to Homo sapiens secretogranin III mRNA, complete cds.
JD232367 - Sequence 213391 from Patent EP1572962.
JD394937 - Sequence 375961 from Patent EP1572962.
JD518918 - Sequence 499942 from Patent EP1572962.
JD123156 - Sequence 104180 from Patent EP1572962.
JD097531 - Sequence 78555 from Patent EP1572962.
JD315979 - Sequence 297003 from Patent EP1572962.
JD196937 - Sequence 177961 from Patent EP1572962.
BC014539 - Homo sapiens secretogranin III, mRNA (cDNA clone MGC:13448 IMAGE:4283082), complete cds.
JD548912 - Sequence 529936 from Patent EP1572962.
KJ898720 - Synthetic construct Homo sapiens clone ccsbBroadEn_08114 SCG3 gene, encodes complete protein.
BC009511 - Homo sapiens secretogranin III, mRNA (cDNA clone IMAGE:3537207), partial cds.
JD309170 - Sequence 290194 from Patent EP1572962.
JD094057 - Sequence 75081 from Patent EP1572962.
JD227472 - Sequence 208496 from Patent EP1572962.
JD096724 - Sequence 77748 from Patent EP1572962.
JD498982 - Sequence 480006 from Patent EP1572962.
JD283657 - Sequence 264681 from Patent EP1572962.
JD281138 - Sequence 262162 from Patent EP1572962.
JD244487 - Sequence 225511 from Patent EP1572962.
JD115793 - Sequence 96817 from Patent EP1572962.
JD394481 - Sequence 375505 from Patent EP1572962.

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

Protein Q8WXD2 (Reactome details) participates in the following event(s):

R-HSA-482770 Release of platelet secretory granule components
R-HSA-8952289 FAM20C phosphorylates FAM20C substrates
R-HSA-114608 Platelet degranulation
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-HSA-8957275 Post-translational protein phosphorylation
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: A8K2B0, B3KQP6, B4DK99, ENST00000220478.1, ENST00000220478.2, ENST00000220478.3, ENST00000220478.4, ENST00000220478.5, ENST00000220478.6, ENST00000220478.7, F5H3R8, NM_013243, Q8WXD2, Q96C83, Q96GE8, Q9Y6G7, SCG3_HUMAN, uc317cyx.1, uc317cyx.2, UNQ2502/PRO5990
UCSC ID: ENST00000220478.8_4
RefSeq Accession: NM_013243.4
Protein: Q8WXD2 (aka SCG3_HUMAN or SG3_HUMAN)

-  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.