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Aliases for SCGN Gene

Aliases for SCGN Gene

  • Secretagogin, EF-Hand Calcium Binding Protein 2 3 5
  • SECRET 3 4
  • Calbindin-Like 2
  • Secretagogin 3
  • DJ501N12.8 3
  • Setagin 3
  • CALBL 3
  • SEGN 3

External Ids for SCGN Gene

Previous GeneCards Identifiers for SCGN Gene

  • GC06P025709
  • GC06P025760

Summaries for SCGN Gene

Entrez Gene Summary for SCGN Gene

  • 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]

GeneCards Summary for SCGN Gene

SCGN (Secretagogin, EF-Hand Calcium Binding Protein) is a Protein Coding gene. Among its related pathways are Ca, cAMP and Lipid Signaling and Neuroscience. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CALB2.

Gene Wiki entry for SCGN Gene

Additional gene information for SCGN Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCGN Gene

Genomics for SCGN Gene

GeneHancer (GH) Regulatory Elements for SCGN Gene

Promoters and enhancers for SCGN Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J025652 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 665.9 +0.1 118 0.3 MLX ZFP64 ARID4B SIN3A ZNF48 SLC30A9 ZNF766 ZNF143 NFKBIZ NCOA1 SCGN GC06P025671
GH06J025660 Enhancer 1.1 Ensembl ENCODE 16.6 +8.4 8377 1 FOXA2 SIN3A RAD21 ZNF48 ZSCAN9 RARA GLIS2 EGR1 SCRT2 FOS SCGN RPL21P68 GC06P025671
GH06J025604 Enhancer 0.7 dbSUPER 23.4 -45.5 -45469 5.2 HDAC1 TEAD4 TAL1 EBF1 TCF12 CTBP1 ZNF316 POLR2A CBFA2T2 MAFK SCGN RPL21P68 CMAHP LOC100533655 CARMIL1 HIST1H3E BTN3A2 GC06M025592 GC06M025617
GH06J025641 Enhancer 1 ENCODE dbSUPER 14.2 -10.0 -9963 1.3 ELF3 FOXA2 RARA SLC30A9 ZNF614 CREM THAP11 MIXL1 MIER2 REST SCGN SLC17A4 CARMIL1 ENSG00000272462 GC06M025617
GH06J025635 Enhancer 1.1 ENCODE dbSUPER 12.1 -15.9 -15923 1.9 FOXA2 MLX ARID4B NFKBIZ ZHX2 MIER2 PPARG KAT8 NFIL3 MIER3 SCGN RPL21P68 CARMIL1 HCG11 GC06M025617
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCGN on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCGN gene promoter:
  • NRSF form 2
  • NRSF form 1
  • S8
  • E47
  • Tal-1
  • HNF-1
  • HNF-1A
  • FOXO3b

Genomic Locations for SCGN Gene

Genomic Locations for SCGN Gene
chr6:25,652,201-25,701,783
(GRCh38/hg38)
Size:
49,583 bases
Orientation:
Plus strand
chr6:25,652,429-25,702,011
(GRCh37/hg19)
Size:
49,583 bases
Orientation:
Plus strand

Genomic View for SCGN Gene

Genes around SCGN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCGN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCGN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCGN Gene

Proteins for SCGN Gene

  • Protein details for SCGN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O76038-SEGN_HUMAN
    Recommended name:
    Secretagogin
    Protein Accession:
    O76038
    Secondary Accessions:
    • A8K0B2
    • Q5VV44
    • Q96QV7
    • Q9UJF6

    Protein attributes for SCGN Gene

    Size:
    276 amino acids
    Molecular mass:
    32040 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SCGN Gene

Post-translational modifications for SCGN Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SCGN Gene

Antibody Products

  • Abcam antibodies for SCGN
  • Santa Cruz Biotechnology (SCBT) Antibodies for SCGN

No data available for DME Specific Peptides for SCGN Gene

Domains & Families for SCGN Gene

Gene Families for SCGN Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SCGN Gene

Suggested Antigen Peptide Sequences for SCGN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCGN: view

No data available for UniProtKB/Swiss-Prot for SCGN Gene

Function for SCGN Gene

Phenotypes From GWAS Catalog for SCGN Gene

Gene Ontology (GO) - Molecular Function for SCGN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding NAS 10811645
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SCGN: view
genes like me logo Genes that share phenotypes with SCGN: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCGN

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SCGN Gene

Localization for SCGN Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCGN Gene

Cytoplasm. Secreted. Cytoplasmic vesicle, secretory vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Note=Predominantly cytoplasmic. A small proportion is associated with secretory granules and membrane fractions (By similarity). Detectable in human serum after ischemic neuronal damage. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCGN gene
Compartment Confidence
cytosol 5
nucleus 4
extracellular 3
plasma membrane 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SCGN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm NAS 10811645
GO:0005829 cytosol IBA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SCGN: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCGN Gene

Pathways & Interactions for SCGN Gene

genes like me logo Genes that share pathways with SCGN: view

Pathways by source for SCGN Gene

2 Cell Signaling Technology pathways for SCGN Gene

Gene Ontology (GO) - Biological Process for SCGN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
GO:0051480 regulation of cytosolic calcium ion concentration IBA --
GO:0099509 regulation of presynaptic cytosolic calcium ion concentration IBA --
GO:1900271 regulation of long-term synaptic potentiation IBA --
genes like me logo Genes that share ontologies with SCGN: view

No data available for SIGNOR curated interactions for SCGN Gene

Drugs & Compounds for SCGN Gene

(1) Drugs for SCGN Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SCGN: view

Transcripts for SCGN Gene

mRNA/cDNA for SCGN Gene

Unigene Clusters for SCGN Gene

Secretagogin, EF-hand calcium binding protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCGN

Alternative Splicing Database (ASD) splice patterns (SP) for SCGN Gene

No ASD Table

Relevant External Links for SCGN Gene

GeneLoc Exon Structure for
SCGN
ECgene alternative splicing isoforms for
SCGN

Expression for SCGN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCGN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCGN Gene

This gene is overexpressed in Brain - Hypothalamus (x12.1), Pituitary (x7.5), Pancreas (x7.1), Brain - Cerebellum (x5.7), and Brain - Cerebellar Hemisphere (x5.0).

Protein differential expression in normal tissues from HIPED for SCGN Gene

This gene is overexpressed in Islet of Langerhans (37.1) and Pancreas (19.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SCGN Gene



NURSA nuclear receptor signaling pathways regulating expression of SCGN Gene:

SCGN

SOURCE GeneReport for Unigene cluster for SCGN Gene:

Hs.116428

mRNA Expression by UniProt/SwissProt for SCGN Gene:

O76038-SEGN_HUMAN
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.

Evidence on tissue expression from TISSUES for SCGN Gene

  • Pancreas(4.7)
  • Nervous system(4.5)
  • Lung(4.3)
genes like me logo Genes that share expression patterns with SCGN: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCGN Gene

Orthologs for SCGN Gene

This gene was present in the common ancestor of animals.

Orthologs for SCGN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCGN 34 33
  • 99.52 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SCGN 34 33
  • 90.46 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SCGN 34 33
  • 88.16 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Scgn 33
  • 83.33 (n)
mouse
(Mus musculus)
Mammalia Scgn 16 34 33
  • 82.97 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCGN 34
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SCGN 34
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCGN 34 33
  • 75.56 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCGN 34
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scgn 33
  • 72.96 (n)
zebrafish
(Danio rerio)
Actinopterygii scgn 34 33
  • 70.96 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4518 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012179 33
  • 54.41 (n)
fruit fly
(Drosophila melanogaster)
Insecta Cbp53E 34 35 33
  • 53.04 (n)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 51 (a)
OneToOne
Cin.13086 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13086 33
Species where no ortholog for SCGN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCGN Gene

ENSEMBL:
Gene Tree for SCGN (if available)
TreeFam:
Gene Tree for SCGN (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCGN: view image

Paralogs for SCGN Gene

Paralogs for SCGN Gene

(2) SIMAP similar genes for SCGN Gene using alignment to 2 proteins:

  • SEGN_HUMAN
  • Q96P10_HUMAN
genes like me logo Genes that share paralogs with SCGN: view

Variants for SCGN Gene

Sequence variations from dbSNP and Humsavar for SCGN Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000164684 -- 25,671,174(+) T/C intron_variant
rs1000230399 -- 25,679,859(+) C/A/T intron_variant
rs1000237550 -- 25,654,401(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000321046 -- 25,700,169(+) C/T intron_variant
rs1000365096 -- 25,661,724(+) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SCGN Gene

Variant ID Type Subtype PubMed ID
esv3608389 CNV gain 21293372

Variation tolerance for SCGN Gene

Residual Variation Intolerance Score: 74.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.31; 53.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCGN Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCGN

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCGN Gene

Disorders for SCGN Gene

Additional Disease Information for SCGN

No disorders were found for SCGN Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SCGN Gene

Publications for SCGN Gene

  1. Cloning and expression of secretagogin, a novel neuroendocrine- and pancreatic islet of Langerhans-specific Ca2+-binding protein. (PMID: 10811645) Wagner L … Pasternack MS (The Journal of biological chemistry 2000) 2 3 4 22 58
  2. Cerebral expression and serum detectability of secretagogin, a recently cloned EF-hand Ca(2+)-binding protein. (PMID: 11709487) Gartner W … Wagner L (Cerebral cortex (New York, N.Y. : 1991) 2001) 3 4 22 58
  3. Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels. (PMID: 19084217) Benyamin B … Visscher PM (American journal of human genetics 2009) 3 44 58
  4. Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations. (PMID: 19503597) Kolz M … Gieger C (PLoS genetics 2009) 3 44 58
  5. Identification and characterization of secretagogin promoter activity. (PMID: 17083620) Skovhus KV … Pociot F (Scandinavian journal of immunology 2006) 3 22 58

Products for SCGN Gene

Sources for SCGN Gene

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