Human Gene SCG2 (ENST00000305409.3_7) from GENCODE V47lift37
  Description: secretogranin II (from RefSeq NM_003469.5)
Gencode Transcript: ENST00000305409.3_7
Gencode Gene: ENSG00000171951.5_12
Transcript (Including UTRs)
   Position: hg19 chr2:224,461,658-224,467,079 Size: 5,422 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr2:224,462,147-224,464,000 Size: 1,854 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:224,461,658-224,467,079)mRNA (may differ from genome)Protein (617 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SCG2_HUMAN
DESCRIPTION: RecName: Full=Secretogranin-2; AltName: Full=Chromogranin-C; AltName: Full=Secretogranin II; Short=SgII; Contains: RecName: Full=Secretoneurin; Short=SN; Flags: Precursor;
FUNCTION: Secretogranin-2 is a neuroendocrine secretory granule protein, which is the precursor for biologically active peptides.
SUBCELLULAR LOCATION: Secreted. Note=Neuroendocrine and endocrine secretory granules.
MISCELLANEOUS: Binds calcium with a low-affinity.
SIMILARITY: Belongs to the chromogranin/secretogranin protein family.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SCG2
Diseases sorted by gene-association score: intracranial primitive neuroectodermal tumor (16), lymph node cancer (16), neuroendocrine tumor (9), collagenous colitis (9), pick disease (5), pheochromocytoma (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 246.12 RPKM in Pituitary
Total median expression: 1051.35 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 -26.4091-0.290 Picture PostScript Text
3' UTR -101.10489-0.207 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
IPR018054 - Chromogranin_CS
IPR001990 - Granin

Pfam Domains:
PF01271 - Granin (chromogranin or secretogranin)

ModBase Predicted Comparative 3D Structure on P13521
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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005515 protein binding
GO:0042056 chemoattractant activity

Biological Process:
GO:0000165 MAPK cascade
GO:0001525 angiogenesis
GO:0001937 negative regulation of endothelial cell proliferation
GO:0001938 positive regulation of endothelial cell proliferation
GO:0006954 inflammatory response
GO:0009306 protein secretion
GO:0010469 regulation of receptor activity
GO:0035556 intracellular signal transduction
GO:0043542 endothelial cell migration
GO:0043687 post-translational protein modification
GO:0044267 cellular protein metabolic process
GO:0048245 eosinophil chemotaxis
GO:0050918 positive chemotaxis
GO:0050930 induction of positive chemotaxis
GO:2000352 negative regulation of endothelial cell apoptotic process
GO:2001237 negative regulation of extrinsic apoptotic signaling pathway

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005788 endoplasmic reticulum lumen
GO:0030141 secretory granule
GO:0031045 dense core granule
GO:0098992 neuronal dense core vesicle


-  Descriptions from all associated GenBank mRNAs
  BC022509 - Homo sapiens secretogranin II (chromogranin C), mRNA (cDNA clone MGC:26541 IMAGE:4820104), complete cds.
M25756 - Human secretogranin II gene, complete cds.
AK298828 - Homo sapiens cDNA FLJ51276 complete cds, highly similar to Secretogranin-2 precursor.
JD320002 - Sequence 301026 from Patent EP1572962.
JD186570 - Sequence 167594 from Patent EP1572962.
JD239845 - Sequence 220869 from Patent EP1572962.
JD410634 - Sequence 391658 from Patent EP1572962.
AK312452 - Homo sapiens cDNA, FLJ92807, highly similar to Homo sapiens secretogranin II (chromogranin C) (SCG2), mRNA.
KJ897788 - Synthetic construct Homo sapiens clone ccsbBroadEn_07182 SCG2 gene, encodes complete protein.
JD303666 - Sequence 284690 from Patent EP1572962.
JD338128 - Sequence 319152 from Patent EP1572962.
JD171384 - Sequence 152408 from Patent EP1572962.

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

Protein P13521 (Reactome details) participates in the following event(s):

R-HSA-8952289 FAM20C phosphorylates FAM20C substrates
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-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification

-  Other Names for This Gene
  Alternate Gene Symbols: B2R662, CHGC, ENST00000305409.1, ENST00000305409.2, NM_003469, P13521, Q53T11, Q8TBH3, SCG2_HUMAN, uc317npx.1, uc317npx.2
UCSC ID: ENST00000305409.3_7
RefSeq Accession: NM_003469.5
Protein: P13521 (aka SCG2_HUMAN or SG2_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.