Human Gene CD300LF (uc002jlg.3) Description and Page Index
  Description: Homo sapiens CD300 molecule-like family member f (CD300LF), mRNA.
RefSeq Summary (NM_139018): This gene encodes a member of the CD300 protein family. Members of this family are cell surface glycoproteins with a single IgV-like extracellular domain, and are involved in the regulation of immune response. The encoded protein is an inhibitory receptor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014].
Transcript (Including UTRs)
   Position: hg19 chr17:72,690,452-72,709,108 Size: 18,657 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr17:72,691,235-72,709,005 Size: 17,771 Coding Exon Count: 7 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:72,690,452-72,709,108)mRNA (may differ from genome)Protein (290 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CLM1_HUMAN
DESCRIPTION: RecName: Full=CMRF35-like molecule 1; Short=CLM-1; AltName: Full=CD300 antigen-like family member F; AltName: Full=Immune receptor expressed on myeloid cells 1; Short=IREM-1; AltName: Full=Immunoglobulin superfamily member 13; Short=IgSF13; AltName: Full=NK inhibitory receptor; AltName: CD_antigen=CD300f; Flags: Precursor;
FUNCTION: Acts as an inhibitory receptor for myeloid cells and mast cells. Inhibits osteoclast formation.
SUBUNIT: Interacts with PTPN6/SHP-1 in a tyrosine phosphorylation dependent manner.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (Potential).
TISSUE SPECIFICITY: Highly expressed in spleen, peripheral blood leukocyte and monocyte, and lung. Weakly expressed in thymus, heart, brain, placenta, liver, skeletal muscle, kidney, pancreas, prostate, testis, ovary, small intestine or colon. Expressed selectively in monocytes and monocyte-related cells.
PTM: Phosphorylated on tyrosine.
SIMILARITY: Belongs to the CD300 family.
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CD300LF
CDC HuGE Published Literature: CD300LF
Positive Disease Associations: fibrinogen
Related Studies:
  1. fibrinogen
    Danik ,et al. 2009, Novel Loci, Including Those Related to Crohn Disease, Psoriasis, and Inflammation Identified in a Genome-Wide Association Study of Fibrinogen in 17,686 Women: The Women's Genome Health Study, Circulation. Cardiovascular genetics 2009 2- 2 : 134-41. [PubMed 20031577]
  2. Fibrinogen
    Jacqueline S Danik et al. Circulation. Cardiovascular genetics 2009, Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study., Circulation. Cardiovascular genetics. [PubMed 20031577]
    A genome-wide survey of the human genome identifies novel loci related to common chronic inflammatory diseases as genetic determinants of fibrinogen levels, in addition to loci that relate to the inflammatory cascade, the urea cycle, and the fibrinogen gene cluster.

-  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: 31.80 RPKM in Whole Blood
Total median expression: 79.06 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 -28.90103-0.281 Picture PostScript Text
3' UTR -274.06783-0.350 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
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR013106 - Ig_V-set

Pfam Domains:
PF07686 - Immunoglobulin V-set domain
PF15330 - SHP2-interacting transmembrane adaptor protein, SIT

SCOP Domains:
48726 - Immunoglobulin

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

2NMS
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8TDQ1
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
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001786 phosphatidylserine binding
GO:0005136 interleukin-4 receptor binding
GO:0008289 lipid binding
GO:0097001 ceramide binding

Biological Process:
GO:0002376 immune system process
GO:0033004 negative regulation of mast cell activation
GO:0034125 negative regulation of MyD88-dependent toll-like receptor signaling pathway
GO:0035666 TRIF-dependent toll-like receptor signaling pathway
GO:0035772 interleukin-13-mediated signaling pathway
GO:0050776 regulation of immune response
GO:1902216 positive regulation of interleukin-4-mediated signaling pathway
GO:2000426 negative regulation of apoptotic cell clearance
GO:2000427 positive regulation of apoptotic cell clearance

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF251706 - Homo sapiens NK inhibitory receptor precursor (NKIR) mRNA, complete cds.
AY358545 - Homo sapiens clone DNA125200 PIGR (UNQ3105) mRNA, complete cds.
BC028199 - Homo sapiens CD300 molecule-like family member f, mRNA (cDNA clone MGC:40116 IMAGE:5207520), complete cds.
AK092757 - Homo sapiens cDNA FLJ35438 fis, clone SMINT2002884, weakly similar to CMRF35 ANTIGEN PRECURSOR.
AX747710 - Sequence 1235 from Patent EP1308459.
JD151152 - Sequence 132176 from Patent EP1572962.
JD250755 - Sequence 231779 from Patent EP1572962.
JD148631 - Sequence 129655 from Patent EP1572962.
JD516139 - Sequence 497163 from Patent EP1572962.
JD038191 - Sequence 19215 from Patent EP1572962.
JD092257 - Sequence 73281 from Patent EP1572962.
AK298752 - Homo sapiens cDNA FLJ52935 complete cds, highly similar to CMRF35-like-molecule 1 precursor.
JD473051 - Sequence 454075 from Patent EP1572962.
JD508705 - Sequence 489729 from Patent EP1572962.
JD053532 - Sequence 34556 from Patent EP1572962.
JD157316 - Sequence 138340 from Patent EP1572962.
AF375480 - Homo sapiens immune receptor expressed on myeloid cells splice variant 1 (IREM1) mRNA, complete cds; alternatively spliced.
AF375481 - Homo sapiens immune receptor expressed on myeloid cells splice variant 2 (IREM1) mRNA, complete cds; alternatively spliced.
AY303545 - Homo sapiens inhibitory receptor IREM1 (IREM1) mRNA, complete cds.
JD341665 - Sequence 322689 from Patent EP1572962.
JD370654 - Sequence 351678 from Patent EP1572962.
JD084556 - Sequence 65580 from Patent EP1572962.
JD385802 - Sequence 366826 from Patent EP1572962.
AK315165 - Homo sapiens cDNA, FLJ96140, highly similar to Homo sapiens NK inhibitory receptor precursor (NKIR), mRNA.
KJ905002 - Synthetic construct Homo sapiens clone ccsbBroadEn_14396 CD300LF gene, encodes complete protein.
DQ153249 - Homo sapiens unknown mRNA.

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

Protein Q8TDQ1 (Reactome details) participates in the following event(s):

R-HSA-5696358 TREM,CD300 binds lipids
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2RCL2, C9JDN3, CD300F, CLM1, CLM1_HUMAN, IGSF13, IREM1, NKIR, NM_139018, NP_620587, Q3Y6P0, Q6UX24, Q7Z6A6, Q7Z7I4, Q7Z7I5, Q8N6D0, Q8NAF5, Q8TDQ1, UNQ3105/PRO10111
UCSC ID: uc002jlg.3
RefSeq Accession: NM_139018
Protein: Q8TDQ1 (aka CLM1_HUMAN)
CCDS: CCDS11704.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_139018.3
exon count: 7CDS single in 3' UTR: no RNA size: 1759
ORF size: 873CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1946.00frame 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: 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.