Human Gene CARD9 (uc004chg.3) Description and Page Index
  Description: Homo sapiens caspase recruitment domain family, member 9 (CARD9), transcript variant 1, mRNA.
RefSeq Summary (NM_052813): The protein encoded by this gene is a member of the CARD protein family, which is defined by the presence of a characteristic caspase-associated recruitment domain (CARD). CARD is a protein interaction domain known to participate in activation or suppression of CARD containing members of the caspase family, and thus plays an important regulatory role in cell apoptosis. This protein was identified by its selective association with the CARD domain of BCL10, a postive regulator of apoptosis and NF-kappaB activation, and is thought to function as a molecular scaffold for the assembly of a BCL10 signaling complex that activates NF-kappaB. Several alternatively spliced transcript variants have been observed, but their full-length nature is not clearly defined. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr9:139,257,441-139,268,133 Size: 10,693 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr9:139,258,754-139,266,530 Size: 7,777 Coding Exon Count: 12 

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 (chr9:139,257,441-139,268,133)mRNA (may differ from genome)Protein (536 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: CARD9_HUMAN
DESCRIPTION: RecName: Full=Caspase recruitment domain-containing protein 9; Short=hCARD9;
FUNCTION: Activates NF-kappa-B via BCL10.
SUBUNIT: Self-associates. CARD9 and BCL10 bind to each other by CARD-CARD interaction.
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Highly expressed in spleen. Also detected in liver, placenta, lung, peripheral blood leukocytes and in brain.
DISEASE: Defects in CARD9 are the cause of familial candidiasis type 2 (CANDF2) [MIM:212050]. Chronic mucocutaneous candidiasis is characterized by impaired clearance of fungal infections and results in colonization and infections of the mucosa or skin, predominantly with Candida albicans. CANDF2 is an autosomal recessive chronic mucocutaneous candidiasis.
SIMILARITY: Contains 1 CARD domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CARD9
CDC HuGE Published Literature: CARD9
Positive Disease Associations: Colitis, Ulcerative , Crohn Disease , Spondylitis, Ankylosing , ulcerative colitis
Related Studies:
  1. Colitis, Ulcerative
    Jeffrey C Barrett et al. Nature genetics 2009, Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region., Nature genetics. [PubMed 19915572]
  2. Colitis, Ulcerative
    Dermot P B McGovern et al. Nature genetics 2010, Genome-wide association identifies multiple ulcerative colitis susceptibility loci., Nature genetics. [PubMed 20228799]
  3. Colitis, Ulcerative
    Carl A Anderson et al. Nature genetics 2011, Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47., Nature genetics. [PubMed 21297633]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CARD9
Diseases sorted by gene-association score: candidiasis, familial, 2, autosomal recessive* (1650), candidiasis (31), phaeohyphomycosis (25), dermatophytosis (25), deep dermatophytosis (18), meningoencephalitis (13), subcutaneous mycosis (12), cd3gamma deficiency (9), adenoiditis (9), tinea capitis (8), opportunistic mycosis (8), plantar fasciitis (7), immunodeficiency with hyper-igm, type 3 (7), chromoblastomycosis (6), primary systemic mycosis (6), coccidioidomycosis (5), cryptococcosis (4)
* = Manually curated disease association

-  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: 9.79 RPKM in Spleen
Total median expression: 68.90 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 -62.90166-0.379 Picture PostScript Text
3' UTR -684.851313-0.522 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
IPR001315 - CARD
IPR011029 - DEATH-like

Pfam Domains:
PF00619 - Caspase recruitment domain

SCOP Domains:
47986 - DEATH domain

ModBase Predicted Comparative 3D Structure on Q9H257
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019904 protein domain specific binding
GO:0042803 protein homodimerization activity
GO:0050700 CARD domain binding

Biological Process:
GO:0002223 stimulatory C-type lectin receptor signaling pathway
GO:0002376 immune system process
GO:0007249 I-kappaB kinase/NF-kappaB signaling
GO:0009620 response to fungus
GO:0032494 response to peptidoglycan
GO:0032495 response to muramyl dipeptide
GO:0032755 positive regulation of interleukin-6 production
GO:0032760 positive regulation of tumor necrosis factor production
GO:0032874 positive regulation of stress-activated MAPK cascade
GO:0042493 response to drug
GO:0042534 regulation of tumor necrosis factor biosynthetic process
GO:0042981 regulation of apoptotic process
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0043330 response to exogenous dsRNA
GO:0045076 regulation of interleukin-2 biosynthetic process
GO:0045087 innate immune response
GO:0045089 positive regulation of innate immune response
GO:0045408 regulation of interleukin-6 biosynthetic process
GO:0046330 positive regulation of JNK cascade
GO:0050830 defense response to Gram-positive bacterium
GO:0051607 defense response to virus

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  LF205596 - JP 2014500723-A/13099: Polycomb-Associated Non-Coding RNAs.
BC070091 - Homo sapiens caspase recruitment domain family, member 9, mRNA (cDNA clone IMAGE:30343821).
BC146915 - Homo sapiens DNL-type zinc finger, mRNA (cDNA clone MGC:182018 IMAGE:9056843), complete cds.
BC146924 - Homo sapiens DNL-type zinc finger, mRNA (cDNA clone MGC:182027 IMAGE:9056852), complete cds.
BC171835 - Homo sapiens cDNA clone IMAGE:9054489, containing frame-shift errors.
LF346393 - JP 2014500723-A/153896: Polycomb-Associated Non-Coding RNAs.
LF346394 - JP 2014500723-A/153897: Polycomb-Associated Non-Coding RNAs.
JD196166 - Sequence 177190 from Patent EP1572962.
JD389926 - Sequence 370950 from Patent EP1572962.
AF311287 - Homo sapiens caspase recruitment domain protein 9 mRNA, complete cds.
BC035805 - Homo sapiens caspase recruitment domain family, member 9, mRNA (cDNA clone IMAGE:5745585), with apparent retained intron.
BC008877 - Homo sapiens caspase recruitment domain family, member 9, mRNA (cDNA clone MGC:14973 IMAGE:4139529), complete cds.
AK127481 - Homo sapiens cDNA FLJ45573 fis, clone BRTHA3011149, highly similar to Homo sapiens caspase recruitment domain protein 9.
AK292081 - Homo sapiens cDNA FLJ76920 complete cds, highly similar to Homo sapiens caspase recruitment domain family, member 9 (CARD9), mRNA.
AK024001 - Homo sapiens cDNA FLJ13939 fis, clone Y79AA1000827.
JD239236 - Sequence 220260 from Patent EP1572962.
JD097101 - Sequence 78125 from Patent EP1572962.
JD097102 - Sequence 78126 from Patent EP1572962.
JD513369 - Sequence 494393 from Patent EP1572962.
JD513368 - Sequence 494392 from Patent EP1572962.
JD235438 - Sequence 216462 from Patent EP1572962.
JD513367 - Sequence 494391 from Patent EP1572962.
JD341234 - Sequence 322258 from Patent EP1572962.
JD550050 - Sequence 531074 from Patent EP1572962.
KJ894539 - Synthetic construct Homo sapiens clone ccsbBroadEn_03933 CARD9 gene, encodes complete protein.
DQ893526 - Synthetic construct clone IMAGE:100006156; FLH195604.01X; RZPDo839E03152D caspase recruitment domain family, member 9 (CARD9) gene, encodes complete protein.
EU176781 - Synthetic construct Homo sapiens clone IMAGE:100011555; FLH195603.01L; RZPDo839B05256D caspase recruitment domain family, member 9 (CARD9) gene, encodes complete protein.
JD099057 - Sequence 80081 from Patent EP1572962.
AB527615 - Synthetic construct DNA, clone: pF1KB9953, Homo sapiens CARD9 gene for caspase recruitment domain family, member 9, without stop codon, in Flexi system.
JD462456 - Sequence 443480 from Patent EP1572962.
JD167802 - Sequence 148826 from Patent EP1572962.
JD470808 - Sequence 451832 from Patent EP1572962.
JD187589 - Sequence 168613 from Patent EP1572962.
JD539314 - Sequence 520338 from Patent EP1572962.
AK295647 - Homo sapiens cDNA FLJ57991 complete cds, highly similar to Caspase recruitment domain-containing protein9.
JD072453 - Sequence 53477 from Patent EP1572962.
JD226637 - Sequence 207661 from Patent EP1572962.
KJ903060 - Synthetic construct Homo sapiens clone ccsbBroadEn_12454 CARD9 gene, encodes complete protein.
CU679165 - Synthetic construct Homo sapiens gateway clone IMAGE:100017365 5' read CARD9 mRNA.
AK309043 - Homo sapiens cDNA, FLJ99084.
JD156485 - Sequence 137509 from Patent EP1572962.
JD427316 - Sequence 408340 from Patent EP1572962.
JD457339 - Sequence 438363 from Patent EP1572962.
JD187155 - Sequence 168179 from Patent EP1572962.
JD186936 - Sequence 167960 from Patent EP1572962.
JD134717 - Sequence 115741 from Patent EP1572962.
MA581970 - JP 2018138019-A/153896: Polycomb-Associated Non-Coding RNAs.
MA581971 - JP 2018138019-A/153897: Polycomb-Associated Non-Coding RNAs.
MA441173 - JP 2018138019-A/13099: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04621 - NOD-like receptor signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein Q9H257 (Reactome details) participates in the following event(s):

R-HSA-741395 CARD9 binds RIP2 (and NOD2)
R-HSA-5607740 PKC-delta phosphorylates CARD9
R-HSA-168638 NOD1/2 Signaling Pathway
R-HSA-5607764 CLEC7A (Dectin-1) signaling
R-HSA-168643 Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: CARD9_HUMAN, NM_052813, NP_434700, Q5SXM5, Q5SXM6, Q9H257, Q9H854
UCSC ID: uc004chg.3
RefSeq Accession: NM_052813
Protein: Q9H257 (aka CARD9_HUMAN or CAR9_HUMAN)
CCDS: CCDS6997.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_052813.4
exon count: 13CDS single in 3' UTR: no RNA size: 2147
ORF size: 1611CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3419.00frame shift in genome: no % Coverage: 98.88
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.