Cd4 Cd4 molecule [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cd4provided by RGD
Official Full Name: Cd4 moleculeprovided by RGD
Primary source: RGD:2306
See related: EnsemblRapid:ENSRNOG00000071219 AllianceGenome:RGD:2306
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: p55; W3/25
Summary: Enables immunoglobulin binding activity; protein tyrosine kinase binding activity; and signaling receptor binding activity. Involved in several processes, including cellular response to ionomycin; positive regulation of calcium ion transport into cytosol; and response to vitamin D. Located in external side of plasma membrane. Used to study septic arthritis and sialadenitis. Biomarker of amphetamine abuse. Human ortholog(s) of this gene implicated in immunodeficiency 79. Orthologous to human CD4 (CD4 molecule). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 876.1), Spleen (RPKM 309.4) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q42

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (159355147..159381636, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (157668878..157695366, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (157381862..157408357, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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 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?

C4d Deposition after Allogeneic Renal Transplantation in Rats Is Involved in Initial Apoptotic Cell Clearance.
Title: C4d Deposition after Allogeneic Renal Transplantation in Rats Is Involved in Initial Apoptotic Cell Clearance.
Adoptive transfusion of CD4+CD25+ Regulatory T Cells into Experimental Autoimmune Neuritis model rats has significant therapeutic effects.
Title: Therapeutic Effect of CD4+CD25+ Regulatory T Cells Amplified In Vitro on Experimental Autoimmune Neuritis in Rats.
Increased C4d deposition may be amenable to identify early myocardial infarction after cardiac arrest.
Title: C4d Deposition Reveals Myocardial Infarction After Cardiac Arrest--Experimental Study.
Data show several homologies across human, rat and mouse in the kinetic of loss of several LAgs such as CD5, CD4 and CD28.
Title: Loss of surface antigens is a conserved feature of apoptotic lymphocytes from several mammalian species.
Clear trend toward worse graft survival in patients with focal C4d after kidney transplantaation.
Title: Focal C4d+ in renal allografts is associated with the presence of donor-specific antibodies and decreased allograft survival.
Capillary C4d deposition is a marker of antibody-mediated rejection in kidney transplantation and can be detected by various staining methods.
Title: Analysis of different staining techniques for c4d detection in renal allograft biopsies.
In this EAE model, perivascular cells, microglia and macrophages showed different dynamics; microglial cells expressed CD4 during the recovery phase, suggesting microglial CD4 expression in the resolution of the immune response.
Title: CD4 microglial expression correlates with spontaneous clinical improvement in the acute Lewis rat EAE model.
C4d deposition and cellular infiltrates as markers of acute rejection in rat models of orthotopic lung transplantation.
Title: C4d deposition and cellular infiltrates as markers of acute rejection in rat models of orthotopic lung transplantation.
testicular macrophages expressed the markers CD45 and MAC387 and most also expressed CD4.
Title: Study of the HIV-1 receptors CD4, CXCR4, CCR5 and CCR3 in the human and rat testis.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables MHC class II protein binding	IEA Inferred from Electronic Annotation more info
enables MHC class II protein binding	ISO Inferred from Sequence Orthology more info
enables MHC class II protein complex binding	IEA Inferred from Electronic Annotation more info
enables MHC class II protein complex binding	ISO Inferred from Sequence Orthology more info
enables MHC class II protein complex binding	ISS Inferred from Sequence or Structural Similarity more info
enables coreceptor activity	IEA Inferred from Electronic Annotation more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables immunoglobulin binding	IDA Inferred from Direct Assay more info	PubMed
enables interleukin-16 binding	IEA Inferred from Electronic Annotation more info
enables interleukin-16 binding	ISO Inferred from Sequence Orthology more info
enables interleukin-16 receptor activity	IEA Inferred from Electronic Annotation more info
enables interleukin-16 receptor activity	ISO Inferred from Sequence Orthology more info
enables lipid binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein tyrosine kinase binding	IDA Inferred from Direct Assay more info	PubMed
enables protein tyrosine kinase binding	IEA Inferred from Electronic Annotation more info
enables protein tyrosine kinase binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of T cell activation	ISO Inferred from Sequence Orthology more info
involved_in T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in T cell selection	IEA Inferred from Electronic Annotation more info
involved_in T cell selection	ISO Inferred from Sequence Orthology more info
involved_in T cell selection	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of calcium-mediated signaling	ISO Inferred from Sequence Orthology more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cellular response to granulocyte macrophage colony-stimulating factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to granulocyte macrophage colony-stimulating factor stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to ionomycin	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within defense response to Gram-negative bacterium	ISO Inferred from Sequence Orthology more info
involved_in helper T cell enhancement of adaptive immune response	ISO Inferred from Sequence Orthology more info
involved_in interleukin-15-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in interleukin-15-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in macrophage differentiation	IEA Inferred from Electronic Annotation more info
involved_in macrophage differentiation	ISO Inferred from Sequence Orthology more info
involved_in maintenance of protein location in cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within maintenance of protein location in cell	ISO Inferred from Sequence Orthology more info
acts_upstream_of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ERK1 and ERK2 cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MAPK cascade	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of T cell activation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of calcium ion transport into cytosol	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of calcium-mediated signaling	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of kinase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of monocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of monocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein kinase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral entry into host cell	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of viral entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in regulation of T cell activation	IEA Inferred from Electronic Annotation more info
involved_in regulation of T cell activation	ISO Inferred from Sequence Orthology more info
involved_in regulation of calcium ion transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of calcium ion transport	ISO Inferred from Sequence Orthology more info
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to ethanol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to methamphetamine hydrochloride	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to vitamin D	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum lumen	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in external side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in external side of plasma membrane	IEA Inferred from Electronic Annotation more info
located_in external side of plasma membrane	ISO Inferred from Sequence Orthology more info
located_in membrane raft	IEA Inferred from Electronic Annotation more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: T-cell surface glycoprotein CD4

Names: CD4 antigen; T-cell surface antigen T4/Leu-3; W3/25 antigen

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_012705.1 → NP_036837.1 T-cell surface glycoprotein CD4 precursor

See identical proteins and their annotated locations for NP_036837.1

Status: PROVISIONAL

Source sequence(s)

M15768

UniProtKB/Swiss-Prot

P05540

UniProtKB/TrEMBL

A0AA76ENJ6, A6ILM7

Related

ENSRNOP00000098012.2, ENSRNOT00000120323.2

Conserved Domains (5) summary

cd07690
Location:30 → 123

Ig1_CD4; First immunoglobulin (Ig) domain of CD4

smart00410
Location:30 → 121

IG_like; Immunoglobulin like

pfam05790
Location:127 → 206

C2-set; Immunoglobulin C2-set domain

pfam09191
Location:211 → 315

CD4-extracel; CD4, extracellular

pfam12104
Location:425 → 452

Tcell_CD4_C; T cell CD4 receptor C terminal region

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

159355147..159381636 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006237331.5 → XP_006237393.1 T-cell surface glycoprotein CD4 isoform X1

See identical proteins and their annotated locations for XP_006237393.1

UniProtKB/Swiss-Prot

P05540

UniProtKB/TrEMBL

A0AA76ENJ6, A6ILM7

Conserved Domains (5) summary

cd07690
Location:30 → 123

Ig1_CD4; First immunoglobulin (Ig) domain of CD4

smart00410
Location:30 → 121

IG_like; Immunoglobulin like

pfam05790
Location:127 → 206

C2-set; Immunoglobulin C2-set domain

pfam09191
Location:211 → 315

CD4-extracel; CD4, extracellular

pfam12104
Location:425 → 452

Tcell_CD4_C; T cell CD4 receptor C terminal region
XM_039107080.2 → XP_038963008.1 T-cell surface glycoprotein CD4 isoform X2

UniProtKB/TrEMBL

A0AA76ENJ6

Conserved Domains (4) summary

pfam05790
Location:127 → 206

C2-set; Immunoglobulin C2-set domain

pfam09191
Location:211 → 315

CD4-extracel; CD4, extracellular

cd00096
Location:211 → 217

Ig; Ig strand A [structural motif]

cd07690
Location:28 → 124

IgV_1_CD4; First immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the V-set of IgSF domains