Human Gene CA9 (uc003zxo.4) Description and Page Index
  Description: Homo sapiens carbonic anhydrase IX (CA9), mRNA.
RefSeq Summary (NM_001216): Carbonic anhydrases (CAs) are a large family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide. They participate in a variety of biological processes, including respiration, calcification, acid-base balance, bone resorption, and the formation of aqueous humor, cerebrospinal fluid, saliva, and gastric acid. They show extensive diversity in tissue distribution and in their subcellular localization. CA IX is a transmembrane protein and is one of only two tumor-associated carbonic anhydrase isoenzymes known. It is expressed in all clear-cell renal cell carcinoma, but is not detected in normal kidney or most other normal tissues. It may be involved in cell proliferation and transformation. This gene was mapped to 17q21.2 by fluorescence in situ hybridization, however, radiation hybrid mapping localized it to 9p13-p12. [provided by RefSeq, Jun 2014]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC014950.1, SRR3476690.458455.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2142586 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000378357.9/ ENSP00000367608.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr9:35,673,915-35,681,154 Size: 7,240 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr9:35,673,957-35,681,022 Size: 7,066 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:35,673,915-35,681,154)mRNA (may differ from genome)Protein (459 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CAH9_HUMAN
DESCRIPTION: RecName: Full=Carbonic anhydrase 9; EC=4.2.1.1; AltName: Full=Carbonate dehydratase IX; AltName: Full=Carbonic anhydrase IX; Short=CA-IX; Short=CAIX; AltName: Full=Membrane antigen MN; AltName: Full=P54/58N; AltName: Full=Renal cell carcinoma-associated antigen G250; Short=RCC-associated antigen G250; AltName: Full=pMW1; Flags: Precursor;
FUNCTION: Reversible hydration of carbon dioxide. Participates in pH regulation. May be involved in the control of cell proliferation and transformation. Appears to be a novel specific biomarker for a cervical neoplasia.
CATALYTIC ACTIVITY: H(2)CO(3) = CO(2) + H(2)O.
COFACTOR: Zinc.
ENZYME REGULATION: Inhibited by coumarins, saccharin, sulfonamide derivatives such as acetazolamide (AZA) and Foscarnet (phosphonoformate trisodium salt).
BIOPHYSICOCHEMICAL PROPERTIES: pH dependence: Optimum pH is 6.5;
SUBUNIT: Forms oligomers linked by disulfide bonds.
SUBCELLULAR LOCATION: Nucleus. Nucleus, nucleolus. Cell membrane; Single-pass type I membrane protein. Cell projection, microvillus membrane; Single-pass type I membrane protein. Note=Found on the surface microvilli and in the nucleus, particularly in nucleolus.
TISSUE SPECIFICITY: Expressed primarily in carcinoma cells lines. Expression is restricted to very few normal tissues and the most abundant expression is found in the epithelial cells of gastric mucosa.
INDUCTION: By hypoxia.
PTM: Asn-346 bears high-mannose type glycan structures.
SIMILARITY: Belongs to the alpha-carbonic anhydrase family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CA9
CDC HuGE Published Literature: CA9

-  MalaCards Disease Associations
  MalaCards Gene Search: CA9
Diseases sorted by gene-association score: renal cell carcinoma (11), clear cell renal cell carcinoma (8), kidney cancer (7), renal clear cell carcinoma (6), hypoxia (6), cervical cancer, somatic (4), lung cancer (3), clear cell papillary renal cell carcinoma (3), breast cancer (2), squamous cell carcinoma, head and neck (2), renal cell carcinoma, papillary (2), nodular prostate (2), breast mucinous carcinoma (1), renal pelvis carcinoma (1), retinal hemangioblastoma (1), lacrimal gland adenocarcinoma (1), ovarian mucinous neoplasm (1), nephrogenic adenofibroma (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D010100 Oxygen
  • D013749 Tetrachlorodibenzodioxin
  • C025205 1,10-phenanthroline
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C093973 2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-one
  • C085911 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one
  • D000667 Ampicillin
  • D001205 Ascorbic Acid
  • D001564 Benzo(a)pyrene
  • D001959 Bromates
          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: 321.62 RPKM in Stomach
Total median expression: 415.42 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 -10.8042-0.257 Picture PostScript Text
3' UTR -35.80132-0.271 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
IPR001148 - Carbonic_anhydrase_a
IPR023561 - Carbonic_anhydrase_a-class
IPR018338 - Carbonic_anhydrase_a-class_CS
IPR018429 - Carbonic_anhydrase_CA9

Pfam Domains:
PF00194 - Eukaryotic-type carbonic anhydrase

SCOP Domains:
51069 - Carbonic anhydrase

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

2HKF
- X-ray

3IAI
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q16790
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004089 carbonate dehydratase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016829 lyase activity
GO:0046872 metal ion binding

Biological Process:
GO:0001666 response to hypoxia
GO:0002009 morphogenesis of an epithelium
GO:0015701 bicarbonate transport
GO:0033574 response to testosterone
GO:0042493 response to drug
GO:0046903 secretion
GO:0061418 regulation of transcription from RNA polymerase II promoter in response to hypoxia

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016323 basolateral plasma membrane
GO:0031528 microvillus membrane
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  LF206430 - JP 2014500723-A/13933: Polycomb-Associated Non-Coding RNAs.
BD243189 - MN gene and protein.
DD272278 - MN/CA IX-SPECIFIC MONOCLONAL ANTIBODIES GENERATED FROM MN/CA IX-DEFICIENT MICE AND METHODS OF USE.
DJ054919 - MN Gene and Protein.
DL135774 - MN Gene and Protein.
FW350870 - MN/CA IX-SPECIFIC MONOCLONAL ANTIBODIES GENERATED FROM MN/CA IX-DEFICIENT MICE AND METHODS OF USE.
FW361688 - MN/CA9 Splice Variants.
HI380745 - Sequence 66 from Patent EP2076611.
HV041854 - JP 2009114198-A/45: MN/CA IX-SPECIFIC MONOCLONAL ANTIBODIES GENERATED FROM MN/CA IX-DEFICIENT MICE AND METHODS OF USE.
HV781757 - JP 2010088443-A/38: MN Gene and Protein.
HW478203 - JP 2013060452-A/45: MN/CA IX-SPECIFIC MONOCLONAL ANTIBODIES GENERATED FROM MN/CA IX-DEFICIENT MICE AND METHODS OF USE.
HZ072579 - JP 2014057596-A/45: MN/CA9 Splice Variants.
BC014950 - Homo sapiens carbonic anhydrase IX, mRNA (cDNA clone MGC:22967 IMAGE:4865275), complete cds.
EF122496 - Homo sapiens truncated carbonic anhydrase 9 mRNA, complete cds, alternatively spliced.
X66839 - H.sapiens MaTu MN mRNA for p54/58N protein.
LF206431 - JP 2014500723-A/13934: Polycomb-Associated Non-Coding RNAs.
AJ010588 - Homo sapiens mRNA for renal cell carcinoma associated antigen G250.
JD513831 - Sequence 494855 from Patent EP1572962.
CU677133 - Synthetic construct Homo sapiens gateway clone IMAGE:100019500 5' read CA9 mRNA.
DQ895404 - Synthetic construct Homo sapiens clone IMAGE:100009864; FLH184067.01L; RZPDo839B11143D carbonic anhydrase IX (CA9) gene, encodes complete protein.
KJ896528 - Synthetic construct Homo sapiens clone ccsbBroadEn_05922 CA9 gene, encodes complete protein.
DQ892208 - Synthetic construct clone IMAGE:100004838; FLH184071.01X; RZPDo839B11144D carbonic anhydrase IX (CA9) gene, encodes complete protein.
KU177952 - Homo sapiens carbonic anhydrase IX isoform 1 (CA9) mRNA, partial cds.
KU177953 - Homo sapiens carbonic anhydrase IX isoform 2 (CA9) mRNA, complete cds, alternatively spliced.
LF354333 - JP 2014500723-A/161836: Polycomb-Associated Non-Coding RNAs.
LF354334 - JP 2014500723-A/161837: Polycomb-Associated Non-Coding RNAs.
JD486502 - Sequence 467526 from Patent EP1572962.
JD045196 - Sequence 26220 from Patent EP1572962.
JD136534 - Sequence 117558 from Patent EP1572962.
MA442007 - JP 2018138019-A/13933: Polycomb-Associated Non-Coding RNAs.
MA442008 - JP 2018138019-A/13934: Polycomb-Associated Non-Coding RNAs.
MA589910 - JP 2018138019-A/161836: Polycomb-Associated Non-Coding RNAs.
MA589911 - JP 2018138019-A/161837: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00910 - Nitrogen metabolism

Reactome (by CSHL, EBI, and GO)

Protein Q16790 (Reactome details) participates in the following event(s):

R-HSA-1475017 Carbonic anhydrase dehydrates bicarbonate (plasma membrane)
R-HSA-1475025 Carbonic anhydrase hydrates carbon dioxide (plasma membrane)
R-HSA-1234158 Regulation of gene expression by Hypoxia-inducible Factor
R-HSA-1234174 Regulation of Hypoxia-inducible Factor (HIF) by oxygen
R-HSA-2262749 Cellular response to hypoxia
R-HSA-1475029 Reversible hydration of carbon dioxide
R-HSA-2262752 Cellular responses to stress
R-HSA-1430728 Metabolism
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: CAH9_HUMAN, G250, MN, NM_001216, NP_001207, Q16790, Q5T4R1
UCSC ID: uc003zxo.4
RefSeq Accession: NM_001216
Protein: Q16790 (aka CAH9_HUMAN)
CCDS: CCDS6585.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001216.2
exon count: 11CDS single in 3' UTR: no RNA size: 1561
ORF size: 1380CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2924.00frame shift in genome: no % Coverage: 99.55
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.