Human Gene CLEC4M (uc010dvt.3)
  Description: Homo sapiens C-type lectin domain family 4, member M (CLEC4M), transcript variant 1, mRNA.
RefSeq Summary (NM_001144909): This gene encodes a C-type lectin that functions in cell adhesion and pathogen recognition. This receptor recognizes a wide range of evolutionarily divergent pathogens with a large impact on public health, including tuberculosis mycobacteria, and viruses including Ebola, hepatitis C, HIV-1, influenza A, West Nile virus and the SARS-CoV acute respiratory syndrome coronavirus. The protein is organized into four distinct domains: a C-terminal carbohydrate recognition domain, a flexible tandem-repeat neck domain of variable length, a transmembrane region and an N-terminal cytoplasmic domain involved in internalization. This gene is closely related in terms of both sequence and function to a neighboring gene, CD209 (Gene ID: 30835), also known as DC-SIGN. The two genes differ in viral recognition and expression patterns, with this gene showing high expression in endothelial cells of the liver, lymph node and placenta. Polymorphisms in the tandem repeat neck domain are associated with resistance to SARS infection. [provided by RefSeq, May 2020].
Transcript (Including UTRs)
   Position: hg19 chr19:7,828,035-7,834,491 Size: 6,457 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr19:7,828,153-7,833,874 Size: 5,722 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:7,828,035-7,834,491)mRNA (may differ from genome)Protein (353 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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): CLEC4M
CDC HuGE Published Literature: CLEC4M
Positive Disease Associations: Cell Adhesion Molecules , Coronary Artery Disease , SARS infection
Related Studies:
  1. Cell Adhesion Molecules
    , , . [PubMed 0]
  2. Coronary Artery Disease
    , , . [PubMed 0]
  3. SARS infection
    Chan VS et al. 2006, Homozygous L-SIGN (CLEC4M) plays a protective role in SARS coronavirus infection, Nature genetics. 2006 Jan;38(1):38-46. [PubMed 16369534]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CLEC4M
Diseases sorted by gene-association score: japanese encephalitis (26), severe acute respiratory syndrome (18), west nile virus (17), encephalitis (13), hepatitis c virus (12), hepatitis c (7), hiv-1 (4), viral infectious disease (2)

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

+  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: 14.88 RPKM in Liver
Total median expression: 23.47 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 -40.10118-0.340 Picture PostScript Text
3' UTR -187.39617-0.304 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

SCOP Domains:
56436 - C-type lectin-like

ModBase Predicted Comparative 3D Structure on Q9H2X3-8
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 BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK292278 - Homo sapiens cDNA FLJ77783 complete cds, highly similar to Homo sapiens CD209 antigen-like (CD209L), mRNA.
BC038851 - Homo sapiens C-type lectin domain family 4, member M, mRNA (cDNA clone MGC:47866 IMAGE:5166966), complete cds.
AF290887 - Homo sapiens L-SIGN mRNA, complete cds.
AK314704 - Homo sapiens cDNA, FLJ95558.
AK304499 - Homo sapiens cDNA FLJ52840 complete cds, highly similar to C-type lectin domain family 4 member M.
JD231731 - Sequence 212755 from Patent EP1572962.
JD206134 - Sequence 187158 from Patent EP1572962.
AB015629 - Homo sapiens mRNA for type II membrane protein similar to HIV gp120-binding C-type lectin, complete cds, clone:HP01347.
AF245219 - Homo sapiens probable mannose binding C-type lectin DC-SIGNR mRNA, complete cds.
AK298084 - Homo sapiens cDNA FLJ55003 complete cds, highly similar to Homo sapiens C-type lectin domain family 4, member M (CLEC4M), transcript variant 6, mRNA.
AK023750 - Homo sapiens cDNA FLJ13688 fis, clone PLACE2000062, highly similar to Homo sapiens mRNA for type II membrane protein.
BC110614 - Homo sapiens C-type lectin domain family 4, member M, mRNA (cDNA clone MGC:129964 IMAGE:40032453), complete cds.
KJ902090 - Synthetic construct Homo sapiens clone ccsbBroadEn_11484 CLEC4M gene, encodes complete protein.
DQ893779 - Synthetic construct Homo sapiens clone IMAGE:100008239; FLH167490.01L; RZPDo839B0589D C-type lectin domain family 4, member M (CLEC4M) gene, encodes complete protein.
KJ898195 - Synthetic construct Homo sapiens clone ccsbBroadEn_07589 CLEC4M gene, encodes complete protein.
AY343913 - Homo sapiens L-SIGN variant (CD209L) mRNA, complete cds.
AY042234 - Homo sapiens mDC-SIGN2 type I isoform (CD209L) mRNA, complete cds, alternatively spliced.
AY042235 - Homo sapiens mDC-SIGN2 type III isoform (CD209L) mRNA, complete cds, alternatively spliced.
AY042236 - Homo sapiens mDC-SIGN2 type IV isoform (CD209L) mRNA, complete cds, alternatively spliced.
AY042237 - Homo sapiens mDC-SIGN2 type VI isoform (CD209L) mRNA, complete cds, alternatively spliced.
AY042238 - Homo sapiens sDC-SIGN2 type I isoform (CD209L) mRNA, complete cds, alternatively spliced.
AY042239 - Homo sapiens sDC-SIGN2 type II isoform (CD209L) mRNA, complete cds, alternatively spliced.
AY042240 - Homo sapiens sDC-SIGN2 type III isoform (CD209L) mRNA, complete cds, alternatively spliced.
JD555088 - Sequence 536112 from Patent EP1572962.
JD462147 - Sequence 443171 from Patent EP1572962.
JD094413 - Sequence 75437 from Patent EP1572962.
JD249117 - Sequence 230141 from Patent EP1572962.
JD276142 - Sequence 257166 from Patent EP1572962.
JD251588 - Sequence 232612 from Patent EP1572962.
JD249348 - Sequence 230372 from Patent EP1572962.
JD535830 - Sequence 516854 from Patent EP1572962.
JD111353 - Sequence 92377 from Patent EP1572962.
JD516861 - Sequence 497885 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CD209L, CD209L1, CD299, NM_001144909, NP_001138381, Q9H2X3-8
UCSC ID: uc010dvt.3
RefSeq Accession: NM_001144909
Protein: Q9H2X3-8 CCDS: CCDS12187.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001144909.1
exon count: 7CDS single in 3' UTR: no RNA size: 1838
ORF size: 1200CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2420.00frame shift in genome: no % Coverage: 97.77
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: 562# 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.