Human Gene SCGN (ENST00000377961.3) from GENCODE V44
  Description: Homo sapiens secretagogin, EF-hand calcium binding protein (SCGN), mRNA. (from RefSeq NM_006998)
RefSeq Summary (NM_006998): The encoded protein is a secreted calcium-binding protein which is found in the cytoplasm. It is related to calbindin D-28K and calretinin. This protein is thought to be involved in KCL-stimulated calcium flux and cell proliferation. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000377961.3
Gencode Gene: ENSG00000079689.15
Transcript (Including UTRs)
   Position: hg38 chr6:25,652,215-25,701,783 Size: 49,569 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg38 chr6:25,652,404-25,701,335 Size: 48,932 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr6:25,652,215-25,701,783)mRNA (may differ from genome)Protein (276 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Secretagogin;
SUBCELLULAR LOCATION: Cytoplasm. Secreted (By similarity). Cytoplasmic vesicle, secretory vesicle membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Note=Predominantly cytoplasmic. A small proportion is associated with secretory granules and membrane fractions (By similarity). Detectable in human serum after ischemic neuronal damage.
TISSUE SPECIFICITY: Expressed at high levels in the pancreatic islets of Langerhans and to a much lesser extent in the gastrointestinal tract (stomach, small intestine and colon), the adrenal medulla and cortex and the thyroid C-cells. In the brain, the expression is restricted to distinct subtypes of neurons with highest expression in the molecular layer of the cerebellum (stellate and basket cells), in the anterior part of the pituitary gland, in the thalamus, in the hypothalamus and in a subgroup of neocortical neurons.
SIMILARITY: Contains 6 EF-hand domains.

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 27.34 RPKM in Pituitary
Total median expression: 140.32 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 -54.00189-0.286 Picture PostScript Text
3' UTR -141.70448-0.316 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
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd

Pfam Domains:
PF13202 - EF hand

ModBase Predicted Comparative 3D Structure on O76038
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0008150 biological_process
GO:0051480 regulation of cytosolic calcium ion concentration

Cellular Component:
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0030658 transport vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0043005 neuron projection
GO:0045202 synapse

-  Descriptions from all associated GenBank mRNAs
  AK289477 - Homo sapiens cDNA FLJ75349 complete cds, highly similar to Homo sapiens secretagogin, EF-hand calcium binding protein (SCGN),mRNA.
BC000336 - Homo sapiens secretagogin, EF-hand calcium binding protein, mRNA (cDNA clone MGC:8532 IMAGE:2822613), complete cds.
BC003036 - Homo sapiens secretagogin, EF-hand calcium binding protein, mRNA (cDNA clone MGC:4356 IMAGE:2822613), complete cds.
Y16752 - Homo sapiens mRNA for secretagogin, complete CDS.
KJ893085 - Synthetic construct Homo sapiens clone ccsbBroadEn_02479 SCGN gene, encodes complete protein.
AF420280 - Homo sapiens setagin mRNA, complete cds, alternatively spliced.
JD151895 - Sequence 132919 from Patent EP1572962.
JD347895 - Sequence 328919 from Patent EP1572962.
AK094387 - Homo sapiens cDNA FLJ37068 fis, clone BRACE2015270.
JD302744 - Sequence 283768 from Patent EP1572962.
JD183221 - Sequence 164245 from Patent EP1572962.
JD037299 - Sequence 18323 from Patent EP1572962.
JD136582 - Sequence 117606 from Patent EP1572962.
JD310207 - Sequence 291231 from Patent EP1572962.
JD218721 - Sequence 199745 from Patent EP1572962.
JD137022 - Sequence 118046 from Patent EP1572962.
JD356068 - Sequence 337092 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K0B2, ENST00000377961.1, ENST00000377961.2, NM_006998, O76038, Q5VV44, Q96QV7, Q9UJF6, SECRET, SEGN_HUMAN, uc003nfb.1, uc003nfb.2, uc003nfb.3, uc003nfb.4, uc003nfb.5
UCSC ID: ENST00000377961.3
RefSeq Accession: NM_006998
Protein: O76038 (aka SEGN_HUMAN)
CCDS: CCDS4561.1

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