Human Gene CLEC10A (uc010clv.2)
  Description: Homo sapiens C-type lectin domain family 10, member A (CLEC10A), transcript variant 2, mRNA.
RefSeq Summary (NM_006344): This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may function as a cell surface antigen. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:6,978,114-6,983,600 Size: 5,487 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr17:6,978,873-6,982,131 Size: 3,259 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:6,978,114-6,983,600)mRNA (may differ from genome)Protein (256 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIPubMedReactomeUniProtKB
Wikipedia

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CLEC10A
CDC HuGE Published Literature: CLEC10A

-  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: 5.67 RPKM in Small Intestine - Terminal Ileum
Total median expression: 85.43 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 -89.50303-0.295 Picture PostScript Text
3' UTR -271.42759-0.358 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
  Pfam Domains:
PF00059 - Lectin C-type domain
PF03954 - Hepatic lectin, N-terminal domain

SCOP Domains:
56436 - C-type lectin-like

ModBase Predicted Comparative 3D Structure on Q8IUN9-3
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 orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC039011 - Homo sapiens C-type lectin domain family 10, member A, mRNA (cDNA clone MGC:47699 IMAGE:5751735), complete cds.
BC027858 - Homo sapiens C-type lectin domain family 10, member A, mRNA (cDNA clone MGC:34439 IMAGE:5225381), complete cds.
D50532 - Homo sapiens mRNA for macrophage lectin 2, complete cds.
JD313164 - Sequence 294188 from Patent EP1572962.
JD304366 - Sequence 285390 from Patent EP1572962.
JD056287 - Sequence 37311 from Patent EP1572962.
JD172726 - Sequence 153750 from Patent EP1572962.
JD439018 - Sequence 420042 from Patent EP1572962.
JD104113 - Sequence 85137 from Patent EP1572962.
CU691636 - Synthetic construct Homo sapiens gateway clone IMAGE:100020797 5' read CLEC10A mRNA.
KJ898219 - Synthetic construct Homo sapiens clone ccsbBroadEn_07613 CLEC10A gene, encodes complete protein.
AK291975 - Homo sapiens cDNA FLJ78539 complete cds, highly similar to Homo sapiens C-type lectin domain family 10, member A, mRNA.
AK292363 - Homo sapiens cDNA FLJ75226 complete cds, highly similar to Homo sapiens C-type lectin domain family 10, member A, mRNA.
KJ902110 - Synthetic construct Homo sapiens clone ccsbBroadEn_11504 CLEC10A gene, encodes complete protein.
JD103496 - Sequence 84520 from Patent EP1572962.
JD322166 - Sequence 303190 from Patent EP1572962.
JD370610 - Sequence 351634 from Patent EP1572962.

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

Protein Q8IUN9 (Reactome details) participates in the following event(s):

R-HSA-8858500 CLEC10A binds Tn-MUC1
R-HSA-5621480 Dectin-2 family
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: AK292363, CLECSF13, CLECSF14, HML, Q8IUN9-3
UCSC ID: uc010clv.2
RefSeq Accession: NM_006344
Protein: Q8IUN9-3, splice isoform of Q8IUN9

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK292363.1
exon count: 7CDS single in 3' UTR: no RNA size: 1504
ORF size: 771CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1626.00frame 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: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 936# 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.