Human Gene CLEC9A (uc001qxa.3) Description and Page Index
  Description: Homo sapiens C-type lectin domain family 9, member A (CLEC9A), mRNA.
RefSeq Summary (NM_207345): CLEC9A is a group V C-type lectin-like receptor (CTLR) that functions as an activation receptor and is expressed on myeloid lineage cells (Huysamen et al., 2008 [PubMed 18408006]).[supplied by OMIM, Aug 2008]. 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 :: AY358265.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000355819.6/ ENSP00000348074.1 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:10,183,276-10,218,565 Size: 35,290 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr12:10,205,287-10,218,231 Size: 12,945 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:10,183,276-10,218,565)mRNA (may differ from genome)Protein (241 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtOMIM
PubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CLC9A_HUMAN
DESCRIPTION: RecName: Full=C-type lectin domain family 9 member A;
FUNCTION: Functions as an endocytic receptor on a small subset of myeloid cells specialized for the uptake and processing of material from dead cells. Recognizes filamentous form of actin in association with particular actin-binding domains of cytoskeletal proteins, including spectrin, exposed when cell membranes are damaged, and mediate the cross-presentation of dead-cell associated antigens in a Syk-dependent manner.
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Membrane; Single-pass type II membrane protein.
TISSUE SPECIFICITY: In peripheral blood highly restricted on the surface of BDCA31(+) dendritic cells and on a small subset of CD14(+) and CD16(-) monocytes.
PTM: N-glycosylated.
SIMILARITY: Contains 1 C-type lectin domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CLEC9A
CDC HuGE Published Literature: CLEC9A
Positive Disease Associations: Alkaline Phosphatase
Related Studies:
  1. Alkaline Phosphatase
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.25 RPKM in Testis
Total median expression: 12.98 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -157.90613-0.258 Picture PostScript Text
3' UTR -66.23334-0.198 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
IPR001304 - C-type_lectin
IPR016186 - C-type_lectin-like
IPR018378 - C-type_lectin_CS
IPR016187 - C-type_lectin_fold

Pfam Domains:
PF00059 - Lectin C-type domain

SCOP Domains:
56436 - C-type lectin-like

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

3VPP
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q6UXN8
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 orthologNo orthologGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
   FlyBase  
   Protein Sequence  
   Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0030246 carbohydrate binding

Biological Process:
GO:0006897 endocytosis
GO:0006898 receptor-mediated endocytosis
GO:0050715 positive regulation of cytokine secretion

Cellular Component:
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AY358265 - Homo sapiens clone DNA182968 HEEE9341 (UNQ9341) mRNA, complete cds.
AK307335 - Homo sapiens cDNA, FLJ97283.
AB590792 - Synthetic construct DNA, clone: pFN21AE1220, Homo sapiens CLEC9A gene for C-type lectin domain family 9, member A, without stop codon, in Flexi system.
EU339276 - Homo sapiens CLEC9A (CLEC9A) mRNA, complete cds.
JD171059 - Sequence 152083 from Patent EP1572962.
JD550199 - Sequence 531223 from Patent EP1572962.
JD358954 - Sequence 339978 from Patent EP1572962.
JD560158 - Sequence 541182 from Patent EP1572962.
JD540533 - Sequence 521557 from Patent EP1572962.
JD322892 - Sequence 303916 from Patent EP1572962.
JD424944 - Sequence 405968 from Patent EP1572962.
JD516978 - Sequence 498002 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B0ZBM2, CLC9A_HUMAN, NM_207345, NP_997228, Q6UXN8, UNQ9341/PRO34046
UCSC ID: uc001qxa.3
RefSeq Accession: NM_207345
Protein: Q6UXN8 (aka CLC9A_HUMAN)
CCDS: CCDS8611.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_207345.2
exon count: 9CDS single in 3' UTR: no RNA size: 1673
ORF size: 726CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 1299.50frame shift in genome: no % Coverage: 100.00
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.