Human Gene CHGA (ENST00000216492.10_7) from GENCODE V47lift37
  Description: chromogranin A, transcript variant 1 (from RefSeq NM_001275.4)
Gencode Transcript: ENST00000216492.10_7
Gencode Gene: ENSG00000100604.13_9
Transcript (Including UTRs)
   Position: hg19 chr14:93,389,495-93,401,630 Size: 12,136 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr14:93,389,705-93,401,229 Size: 11,525 Coding Exon Count: 8 

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 (chr14:93,389,495-93,401,630)mRNA (may differ from genome)Protein (457 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CMGA_HUMAN
DESCRIPTION: RecName: Full=Chromogranin-A; Short=CgA; AltName: Full=Pituitary secretory protein I; Short=SP-I; Contains: RecName: Full=Vasostatin-1; AltName: Full=Vasostatin I; Contains: RecName: Full=Vasostatin-2; AltName: Full=Vasostatin II; Contains: RecName: Full=EA-92; Contains: RecName: Full=ES-43; Contains: RecName: Full=Pancreastatin; Contains: RecName: Full=SS-18; Contains: RecName: Full=WA-8; Contains: RecName: Full=WE-14; Contains: RecName: Full=LF-19; Contains: RecName: Full=AL-11; Contains: RecName: Full=GV-19; Contains: RecName: Full=GR-44; Contains: RecName: Full=ER-37; Flags: Precursor;
FUNCTION: Pancreastatin strongly inhibits glucose induced insulin release from the pancreas.
SUBUNIT: Interacts with SCG3 (By similarity).
SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle lumen (By similarity). Cytoplasmic vesicle, secretory vesicle membrane (By similarity). Secreted. Note=Associated with the secretory granule membrane through direct interaction to SCG3 that in turn binds to cholesterol-enriched lipid rafts in intragranular conditions (By similarity).
PTM: Sulfated on tyrosine residues and/or contains sulfated glycans.
PTM: O-glycosylated with core 1 or possibly core 8 glycans.
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: CHGA
Diseases sorted by gene-association score: neuroendocrine tumor (58), atrophic gastritis (32), acinar cell carcinoma (31), tubular adenocarcinoma (30), mixed ductal-endocrine carcinoma (24), lymphocytic colitis (22), somatostatinoma (21), glucagonoma (19), islet cell tumor (19), large cell carcinoma (18), large cell neuroendocrine carcinoma (18), vipoma (18), autoimmune atrophic gastritis (18), small cell carcinoma of the bladder (18), primary hepatic neuroendocrine carcinoma (18), carcinoid syndrome (18), small cell neuroendocrine carcinoma (17), gastrinoma (17), gastric small cell carcinoma (16), clear cell meningioma (16), liver leiomyosarcoma (15), auditory system cancer (15), merkel cell carcinoma (15), epithelioid malignant peripheral nerve sheath tumor (15), endocrine gland cancer (15), ureter small cell carcinoma (15), zollinger-ellison syndrome (15), female urethral cancer (15), urinary bladder small cell neuroendocrine carcinoma (15), ovarian large-cell neuroendocrine carcinoma (15), atypical follicular adenoma (14), paraganglioma (14), adrenal cortical carcinoma (13), small cell carcinoma (13), pulmonary large cell neuroendocrine carcinoma (13), goblet cell carcinoid (13), chordoid meningioma (13), ganglioglioma (12), pituitary carcinoma (12), sclerosing hemangioma (12), prostate adenocarcinoma (12), pulmonary sclerosing hemangioma (12), small cell cancer of the lung, somatic (12), pancreatoblastoma (11), gastritis (11), dermoid cyst (11), non-functioning pancreatic endocrine tumor (11), carcinoid tumors, intestinal (11), adult teratoma (10), pancreatic serous cystadenoma (10), gastric tubular adenocarcinoma (10), acinar cell cystadenocarcinoma (10), olfactory neuroblastoma (10), intracranial primitive neuroectodermal tumor (10), parathyroid adenoma (10), gastrointestinal neuroendocrine benign tumor (10), gastric neuroendocrine neoplasm (10), chronic myocardial ischemia (10), gallbladder small cell carcinoma (10), phaeochromocytoma (10), gastric adenocarcinoma (10), collagenous colitis (10), ureter cancer (9), binswanger's disease (9), central neurocytoma (9), subependymoma (9), medullary thyroid carcinoma, familial (9), gastrointestinal neuroendocrine tumor (8), diarrhea 4, malabsorptive, congenital (8), cellular ependymoma (8), peritoneal serous adenocarcinoma (8), sclerosing hepatic carcinoma (8), multiple endocrine neoplasia (8), ganglioneuroma (8), pulmonary blastoma (8), pheochromocytoma (8), serotonin syndrome (8), pleomorphic xanthoastrocytoma (7), cervix small cell carcinoma (7), basaloid squamous cell carcinoma (7), von hippel-lindau syndrome (7), insulinoma (7), multiple endocrine neoplasia 1 (7), cranial nerve malignant neoplasm (7), primary pigmented nodular adrenocortical disease (7), lung cancer (7), lung benign neoplasm (7), nodular ganglioneuroblastoma (7), chief cell adenoma (7), pick disease (7), hemangioma of lung (7), cystadenoma (7), signet ring cell adenocarcinoma (7), vaginal benign neoplasm (7), vaginal adenoma (7), vaginal tubulovillous adenoma (7), pancreatic acinar cell adenocarcinoma (7), irritable bowel syndrome (6), olfactory groove meningioma (6), anterior cranial fossa meningioma (6), pancreatic cystadenocarcinoma (6), hyperparathyroidism (6), endodermal sinus tumor (6), pineocytoma (6), cauda equina neoplasm (6), syndrome of inappropriate antidiuretic hormone (6), glycogen storage disease vi (6), sensory organ benign neoplasm (6), urethral benign neoplasm (6), acute thyroiditis (6), conventional angiosarcoma (6), liver sarcoma (6), horseshoe kidney (6), respiratory system benign neoplasm (5), olfactory nerve neoplasm (5), granulosa cell tumor of the ovary (5), gastric leiomyoma (5), hyperparathyroidism, familial primary (5), cecal disease (5), gastric squamous cell carcinoma (5), breast papillary carcinoma (5), pancreatic gastrinoma (5), prostate cancer (5), auditory neuropathy (5), diffuse pulmonary fibrosis (5), cecum adenocarcinoma (5), spinal canal and spinal cord meningioma (5), desmoplastic small round cell tumor (5), spinal meningioma (4), papillary ependymoma (4), tanycytic ependymoma (4), malignant skin fibrous histiocytoma (4), malignant dermis tumor (4), cowden disease (4), cerebellar liponeurocytoma (4), meninges hemangiopericytoma (3), pancreatic cancer (3), ewing sarcoma (2), male reproductive organ cancer (1), cell type benign neoplasm (1), cell type cancer (1), thyroid cancer, nonmedullary, 2 (1)

-  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: 343.70 RPKM in Pituitary
Total median expression: 1091.61 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 -85.00210-0.405 Picture PostScript Text
3' UTR -132.70401-0.331 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
IPR001819 - Chromogranin_AB
IPR018054 - Chromogranin_CS
IPR001990 - Granin

Pfam Domains:
PF01271 - Granin (chromogranin or secretogranin)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1LV4 - NMR


ModBase Predicted Comparative 3D Structure on P10645
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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
  Biological Process:
GO:0002026 regulation of the force of heart contraction
GO:0002551 mast cell chemotaxis
GO:0006996 organelle organization
GO:0008217 regulation of blood pressure
GO:0019730 antimicrobial humoral response
GO:0030816 positive regulation of cAMP metabolic process
GO:0031640 killing of cells of other organism
GO:0032762 mast cell cytokine production
GO:0033604 negative regulation of catecholamine secretion
GO:0042742 defense response to bacterium
GO:0043303 mast cell degranulation
GO:0045087 innate immune response
GO:0045576 mast cell activation
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0050832 defense response to fungus
GO:0060452 positive regulation of cardiac muscle contraction
GO:0086030 adrenergic receptor signaling pathway involved in cardiac muscle relaxation
GO:1900738 positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway
GO:1901215 negative regulation of neuron death
GO:1901899 positive regulation of relaxation of cardiac muscle
GO:2000707 positive regulation of dense core granule biogenesis

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0016020 membrane
GO:0030133 transport vesicle
GO:0030141 secretory granule
GO:0030658 transport vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0042583 chromaffin granule
GO:0042629 mast cell granule
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  LF209629 - JP 2014500723-A/17132: Polycomb-Associated Non-Coding RNAs.
AK313757 - Homo sapiens cDNA, FLJ94358, highly similar to Homo sapiens chromogranin A (parathyroid secretory protein 1) (CHGA), mRNA.
AK223381 - Homo sapiens mRNA for chromogranin A variant, clone: FCC106D09.
JD255080 - Sequence 236104 from Patent EP1572962.
BC006459 - Homo sapiens chromogranin A (parathyroid secretory protein 1), mRNA (cDNA clone MGC:1781 IMAGE:3503641), complete cds.
BX248263 - human full-length cDNA clone CS0DN001YP04 of Adult brain of Homo sapiens (human).
JD462887 - Sequence 443911 from Patent EP1572962.
JD128440 - Sequence 109464 from Patent EP1572962.
J03483 - Human chromogranin A mRNA, complete cds.
JD455698 - Sequence 436722 from Patent EP1572962.
BC001059 - Homo sapiens chromogranin A (parathyroid secretory protein 1), mRNA (cDNA clone MGC:2080 IMAGE:3509603), complete cds.
J03915 - Human chromogranin A mRNA, complete cds.
DQ891820 - Synthetic construct clone IMAGE:100004450; FLH180269.01X; RZPDo839A05134D chromogranin A (parathyroid secretory protein 1) (CHGA) gene, encodes complete protein.
DQ895007 - Synthetic construct Homo sapiens clone IMAGE:100009467; FLH180265.01L; RZPDo839A05133D chromogranin A (parathyroid secretory protein 1) (CHGA) gene, encodes complete protein.
CU674536 - Synthetic construct Homo sapiens gateway clone IMAGE:100023443 5' read CHGA mRNA.
KJ896596 - Synthetic construct Homo sapiens clone ccsbBroadEn_05990 CHGA gene, encodes complete protein.
KR709826 - Synthetic construct Homo sapiens clone CCSBHm_00006427 CHGA (CHGA) mRNA, encodes complete protein.
KR709827 - Synthetic construct Homo sapiens clone CCSBHm_00006428 CHGA (CHGA) mRNA, encodes complete protein.
BT006869 - Homo sapiens chromogranin A (parathyroid secretory protein 1) mRNA, complete cds.
BC009384 - Homo sapiens chromogranin A (parathyroid secretory protein 1), mRNA (cDNA clone IMAGE:4127895), partial cds.
BC012755 - Homo sapiens chromogranin A (parathyroid secretory protein 1), mRNA (cDNA clone IMAGE:3627785), partial cds.
LF330250 - JP 2014500723-A/137753: Polycomb-Associated Non-Coding RNAs.
BC106953 - Homo sapiens cDNA clone IMAGE:40035584, **** WARNING: chimeric clone ****.
LF330251 - JP 2014500723-A/137754: Polycomb-Associated Non-Coding RNAs.
JD343547 - Sequence 324571 from Patent EP1572962.
JD162677 - Sequence 143701 from Patent EP1572962.
JD401327 - Sequence 382351 from Patent EP1572962.
JD242085 - Sequence 223109 from Patent EP1572962.
JD039580 - Sequence 20604 from Patent EP1572962.
JD402435 - Sequence 383459 from Patent EP1572962.
JD534063 - Sequence 515087 from Patent EP1572962.
JD199210 - Sequence 180234 from Patent EP1572962.
MA565827 - JP 2018138019-A/137753: Polycomb-Associated Non-Coding RNAs.
MA565828 - JP 2018138019-A/137754: Polycomb-Associated Non-Coding RNAs.
MA445206 - JP 2018138019-A/17132: Polycomb-Associated Non-Coding RNAs.

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

Protein P10645 (Reactome details) participates in the following event(s):

R-HSA-6808566 CHGA-derived peptide binds the bacterial cell surface
R-HSA-6803157 Antimicrobial peptides
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2R9E9, CMGA_HUMAN, ENST00000216492.1, ENST00000216492.2, ENST00000216492.3, ENST00000216492.4, ENST00000216492.5, ENST00000216492.6, ENST00000216492.7, ENST00000216492.8, ENST00000216492.9, NM_001275, P10645, Q53FA8, Q6NR84, Q96E84, Q96GL7, Q9BQB5, uc317crh.1, uc317crh.2
UCSC ID: ENST00000216492.10_7
RefSeq Accession: NM_001275.4
Protein: P10645 (aka CMGA_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.