Cd1d1 CD1d1 molecule [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cd1d1provided by RGD
Official Full Name: CD1d1 moleculeprovided by RGD
Primary source: RGD:2296
See related: Ensembl:ENSRNOG00000016451 AllianceGenome:RGD:2296
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Cd1; Cd1d
Summary: Predicted to enable several functions, including T cell receptor binding activity; lipid antigen binding activity; and lipopeptide binding activity. Predicted to be involved in several processes, including antigen processing and presentation, endogenous lipid antigen via MHC class Ib; antigen processing and presentation, exogenous lipid antigen via MHC class Ib; and regulation of T cell proliferation. Predicted to act upstream of or within several processes, including positive regulation of cytokine production; positive regulation of leukocyte activation; and positive thymic T cell selection. Predicted to be located in several cellular components, including cell surface; endosome; and lysosome. Predicted to be active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in pulmonary tuberculosis. Orthologous to human CD1D (CD1d molecule). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 272.8), Muscle (RPKM 260.8) and 8 other tissues See more
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Genomic context

Location:: 2q34

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (174721522..174725029, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (172423582..172427089, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (186330298..186333805, complement)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CD1d is expressed in non-lymphatic tissues such as paneth cells and exocrine pancreas.
Title: CD1d expression in paneth cells and rat exocrine pancreas revealed by novel monoclonal antibodies which differentially affect NKT cell activation.

Submit: New GeneRIF Correction

General gene information

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Markers

D2Wox42 (e-PCR)
- UniSTS:240039

RH133461 (e-PCR)
- UniSTS:216744

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables T cell receptor binding	ISO Inferred from Sequence Orthology more info
enables cell adhesion molecule binding	ISO Inferred from Sequence Orthology more info
enables endogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables endogenous lipid antigen binding	ISO Inferred from Sequence Orthology more info
enables exogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables exogenous lipid antigen binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables lipid antigen binding	ISO Inferred from Sequence Orthology more info
enables lipid antigen binding	ISS Inferred from Sequence or Structural Similarity more info
enables lipopeptide binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in NK T cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within antigen processing and presentation	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation, exogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within antigen processing and presentation, exogenous lipid antigen via MHC class Ib	ISO Inferred from Sequence Orthology more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of NK T cell activation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of NK T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of T cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of interleukin-2 production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of interleukin-4 production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of macrophage activation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of type II interferon production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive thymic T cell selection	ISO Inferred from Sequence Orthology more info
involved_in regulation of immature T cell proliferation in thymus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of immune response	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in early endosome	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in external side of plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: antigen-presenting glycoprotein CD1d

Names: CD1D antigen; CD1d1 antigen; T-cell surface glycoprotein CD1d

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_017079.1 → NP_058775.1 antigen-presenting glycoprotein CD1d precursor

See identical proteins and their annotated locations for NP_058775.1

Status: PROVISIONAL

Source sequence(s)

D26439

UniProtKB/Swiss-Prot

Q63493

UniProtKB/TrEMBL

Q9R1S6

Related

ENSRNOP00000022150.2, ENSRNOT00000022150.3

Conserved Domains (2) summary

cd07698
Location:204 → 296

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam16497
Location:22 → 199

MHC_I_3; MHC-I family domain