RAET1G retinoic acid early transcript 1G [Homo sapiens (human)] - Gene

Summary

Official Symbol: RAET1Gprovided by HGNC
Official Full Name: retinoic acid early transcript 1Gprovided by HGNC
Primary source: HGNC:HGNC:16795
See related: Ensembl:ENSG00000203722 MIM:609244; AllianceGenome:HGNC:16795
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ULBP5
Summary: This gene encodes a member of the major histocompatibility complex (MHC) class I family of proteins. Although the encoded protein includes C-terminal transmembrane and cytoplasmic domains, proteolytic processing results in the removal of these domains and subsequent tethering to the plasma membrane by a glycosylphosphatidylinositol (GPI)-anchor. The encoded protein is one of several related ligands of the natural killer group 2, member D (NKG2D) receptor, which functions as an activating receptor in innate and adaptive immunity. This gene is present in a gene cluster on chromosome 6. [provided by RefSeq, Jul 2015]
Expression: Biased expression in esophagus (RPKM 1.3), adrenal (RPKM 0.9) and 11 other tissues See more
Orthologs: all
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Genomic context

Location:: 6q25.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (149916878..149923121, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (151116222..151122465, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (150238014..150244257, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Human anaplastic thyroid carcinoma cells are sensitive to NK cell-mediated lysis via ULBP2/5/6 and chemoattract NK cells.
Title: Human anaplastic thyroid carcinoma cells are sensitive to NK cell-mediated lysis via ULBP2/5/6 and chemoattract NK cells.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
RAET1G is regulated post-translationally to produce a GPI-anchored isoform
Title: Post-translational modification of the NKG2D ligand RAET1G leads to cell surface expression of a glycosylphosphatidylinositol-linked isoform.
Observational study of genotype prevalence. (HuGE Navigator)
Title: Single nucleotide polymorphism analysis of the NKG2D ligand cluster on the long arm of chromosome 6: Extensive polymorphisms and evidence of diversity between human populations.
RAET1G, like ULBP2, appears broadly expressed, but exhibits a lower apparent avidity for NKG2D due to a mutation in the center of the MHC-like fold.
Title: Differential NKG2D binding to highly related human NKG2D ligands ULBP2 and RAET1G is determined by a single amino acid in the alpha2 domain.
the expression patterns of ULBP5RAET1G are very similar to the well-characterised NKG2D ligand, MICA. However the two isoforms of ULBP5/RAET1G have very different cellular localisations that are likely to reflect unique functionality.
Title: Cellular expression, trafficking, and function of two isoforms of human ULBP5/RAET1G.
Binds the activating receptor NKG2D and the the human cytomegalovirus protein UL16.
Title: Two human ULBP/RAET1 molecules with transmembrane regions are ligands for NKG2D.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	HIV-1 (SF2) Nef downregulates RAET1G (ULBP5); downregulation is dependent upon residues G2 and F195 and a di-lysine motif in Nef as shown in A3.01 T cells and HeLa TZM-bl cells	PubMed
Vpu	vpu	HIV-1 (NL4-3) Vpu downregulates RAET1G (ULBP5); downregulation is dependent upon amino acids R30/K31, V25/Y29, the acidic di-leucine motif in Vpu helix 2 as shown in A3.01 T cells and HeLa TZM-bl cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables natural killer cell lectin-like receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in natural killer cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of natural killer cell cytokine production	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	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 extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: UL-16 binding protein 5

Names: retinoic acid early transcript 1G protein

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_001001788.4 → NP_001001788.2 UL-16 binding protein 5 preproprotein

See identical proteins and their annotated locations for NP_001001788.2

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as RAET1G1) represents the longer transcript and encodes the protein.

Source sequence(s)

AY172579, AY172580, HY165961

Consensus CDS

CCDS43514.1

UniProtKB/Swiss-Prot

Q6H3X2, Q6H3X3

Related

ENSP00000356329.2, ENST00000367360.7

Conserved Domains (1) summary

cl08246
Location:29 → 198

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RNA

NR_130110.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as RAET1G2) uses an alternate splice site at an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AY172580, HY165961

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

149916878..149923121 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011535800.4 → XP_011534102.1 UL-16 binding protein 5 isoform X2

Conserved Domains (1) summary

cl08246
Location:29 → 198

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
XM_017010831.3 → XP_016866320.1 UL-16 binding protein 5 isoform X1

Conserved Domains (1) summary

cl08246
Location:29 → 198

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
XM_047418729.1 → XP_047274685.1 UL-16 binding protein 5 isoform X3

UniProtKB/TrEMBL

Q4V9S8

Related

ENSP00000356330.2, ENST00000367361.6

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

151116222..151122465 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054355347.1 → XP_054211322.1 UL-16 binding protein 5 isoform X2
XM_054355346.1 → XP_054211321.1 UL-16 binding protein 5 isoform X1
XM_054355348.1 → XP_054211323.1 UL-16 binding protein 5 isoform X3

UniProtKB/TrEMBL

Q4V9S8