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NR6A1 nuclear receptor subfamily 6 group A member 1 [ Homo sapiens (human) ]

Gene ID: 2649, updated on 27-Nov-2024

Summary

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Official Symbol
NR6A1provided by HGNC
Official Full Name
nuclear receptor subfamily 6 group A member 1provided by HGNC
Primary source
HGNC:HGNC:7985
See related
Ensembl:ENSG00000148200 MIM:602778; AllianceGenome:HGNC:7985
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
RTR; GCNF; NR61; hRTR; CT150; GCNF1; hGCNF
Summary
This gene encodes an orphan nuclear receptor which is a member of the nuclear hormone receptor family. Its expression pattern suggests that it may be involved in neurogenesis and germ cell development. The protein can homodimerize and bind DNA, but in vivo targets have not been identified. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2013]
Expression
Biased expression in testis (RPKM 11.0), thyroid (RPKM 1.5) and 7 other tissues See more
Orthologs
mouse all
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Genomic context

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See NR6A1 in Genome Data Viewer
Location:
9q33.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (124517275..124771311, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (136715509..136969568, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (127279554..127533590, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127212355-127212879 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127212880-127213404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127213405-127213929 Neighboring gene adhesion G protein-coupled receptor D2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127244219-127244996 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:127248727-127248904 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127263337-127263838 Neighboring gene NR5A1 5' promoter region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127274335-127274887 Neighboring gene nuclear receptor subfamily 5 group A member 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:127297992-127298492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28986 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:127336756-127337955 Neighboring gene RAN binding protein 1 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr9:127379928-127380429 Neighboring gene RNA, 7SL, cytoplasmic 302, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28988 Neighboring gene MIR181A2 host gene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127457301-127457846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:127469911-127470422 Neighboring gene microRNA 181a-2 Neighboring gene uncharacterized LOC124902269 Neighboring gene microRNA 181b-2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:127483243-127483752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127490193-127490694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127490695-127491194 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:127496997-127497528 Neighboring gene uncharacterized LOC124900274 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:127507402-127507902 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:127522805-127523360 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:127523361-127523915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:127533372-127533939 Neighboring gene uncharacterized LOC107987126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20266 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127561206-127561720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127561721-127562234 Neighboring gene olfactomedin like 2A Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127573487-127573987 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127573988-127574490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:127574992-127575493

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Genomic structure of the gene for mouse germ-cell nuclear factor (GCNF). II. Comparison with the genomic structure of the human GCNF gene. Süsens U, et al. Genome Biol, 2001. PMID 11387038, Free PMC Article
  2. NR6A1 regulates lipid metabolism through mammalian target of rapamycin complex 1 in HepG2 cells. Wang Y, et al. Cell Commun Signal, 2019 Jul 17. PMID 31315616, Free PMC Article
  3. DNA binding, protein interaction and differential expression of the human germ cell nuclear factor. Schmitz TP, et al. Biochim Biophys Acta, 1999 Sep 3. PMID 10524192
  4. Characterization of the human germ cell nuclear factor gene. Süsens U, et al. Biochim Biophys Acta, 1996 Dec 11. PMID 8982251
  5. Characterization of the DNA-binding and dimerization properties of the nuclear orphan receptor germ cell nuclear factor. Greschik H, et al. Mol Cell Biol, 1999 Jan. PMID 9858592, Free PMC Article

See all (38) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Integrated analysis of histone lysine lactylation (Kla)-specific genes suggests that NR6A1, OSBP2 and UNC119B are novel therapeutic targets for hepatocellular carcinoma.
    Title: Integrated analysis of histone lysine lactylation (Kla)-specific genes suggests that NR6A1, OSBP2 and UNC119B are novel therapeutic targets for hepatocellular carcinoma.
  2. Novel LAMC2 fusion protein has tumor-promoting properties in ovarian carcinoma.
    Title: Novel LAMC2 fusion protein has tumor-promoting properties in ovarian carcinoma.
  3. hsa_circ_001653 up-regulates NR6A1 expression and elicits gastric cancer progression by binding to microRNA-377.
    Title: hsa_circ_001653 up-regulates NR6A1 expression and elicits gastric cancer progression by binding to microRNA-377.
  4. the role of NR6A1 in the lipogenesis in HepG2 cells
    Title: NR6A1 regulates lipid metabolism through mammalian target of rapamycin complex 1 in HepG2 cells.
  5. GCNF acts as a transcriptional repressor in the regulation of OCT4 gene expression through cooperative interaction with three NR binding elements in pluripotent NCCIT cells.
    Title: GCNF regulates OCT4 expression through its interactions with nuclear receptor binding elements in NCCIT cells.
  6. the genes, and up-regulated 64% in undifferentiated hES cells. In addition, GCNF also showed a regulatory gene pattern that is different from RA treatment during hES cell differentiation
    Title: Germ Cell Nuclear Factor (GCNF) Represses Oct4 Expression and Globally Modulates Gene Expression in Human Embryonic Stem (hES) Cells.
  7. Findings show a role for Gcnf as a regulator of iPS cell pluripotency gene expression. It also demonstrates that reactivation of the Gcnf gene may serve as a marker to distinguish completely reprogrammed iPS cells from incompletely pluripotent cells.
    Title: Epigenetic reprogramming of the germ cell nuclear factor gene is required for proper differentiation of induced pluripotent cells.
  8. Our results show that cellular levels of NR6A1 are correlated with disease progression in prostate cancer.
    Title: Expression screening of cancer/testis genes in prostate cancer identifies NR6A1 as a novel marker of disease progression and aggressiveness.
  9. These experiments confirmed that NR6A1 works as a regulator for hypocretin transcription.
    Title: Transcriptional regulation of the hypocretin/orexin gene by NR6A1.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of sex hormones, gonadotropins and sex hormone-binding protein in Chinese men.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables estrogen response element binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in intracellular receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription regulator complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
nuclear receptor subfamily 6 group A member 1
Names
retinoic acid receptor-related testis-associated receptor
retinoid receptor-related testis-specific receptor

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)

  1. NM_001278546.2 → NP_001265475.1  nuclear receptor subfamily 6 group A member 1 isoform 4

    See identical proteins and their annotated locations for NP_001265475.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 4), compared to isoform 1.
    Source sequence(s)
    AL354928, AL354979, S83309
    Consensus CDS
    CCDS65127.1
    UniProtKB/TrEMBL
    F1DAM1
    Related
    ENSP00000362686.3, ENST00000373584.7
    Conserved Domains (2) summary
    cd06953
    Location:252 → 463
    NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4
    cd07169
    Location:48 → 137
    NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

  2. NM_001410996.1 → NP_001397925.1  nuclear receptor subfamily 6 group A member 1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL158075, AL354928, AL354979
    Consensus CDS
    CCDS94481.1
    Related
    ENSP00000341135.4, ENST00000344523.8

  3. NM_001489.5 → NP_001480.3  nuclear receptor subfamily 6 group A member 1 isoform 2

    See identical proteins and their annotated locations for NP_001480.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses two alternate in-frame splice sites compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AA467752, AL354928, AL354979, BC030600
    Consensus CDS
    CCDS55340.1
    UniProtKB/Swiss-Prot
    Q15406
    Related
    ENSP00000413701.2, ENST00000416460.6
    Conserved Domains (2) summary
    cd06953
    Location:251 → 462
    NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4
    cd07169
    Location:48 → 137
    NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

  4. NM_033334.4 → NP_201591.2  nuclear receptor subfamily 6 group A member 1 isoform 1

    See identical proteins and their annotated locations for NP_201591.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL354928, AL354979, U80802
    Consensus CDS
    CCDS35137.1
    UniProtKB/Swiss-Prot
    O00551, O00603, Q15406, Q5T6F4, Q8NHQ0, Q92898, Q99802
    UniProtKB/TrEMBL
    F1D8S0
    Related
    ENSP00000420267.1, ENST00000487099.7
    Conserved Domains (2) summary
    cd06953
    Location:256 → 467
    NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4
    cd07169
    Location:52 → 141
    NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    124517275..124771311 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423226.1 → XP_047279182.1  nuclear receptor subfamily 6 group A member 1 isoform X2

  2. XM_005251918.6 → XP_005251975.1  nuclear receptor subfamily 6 group A member 1 isoform X1

    Conserved Domains (2) summary
    cd06953
    Location:214 → 425
    NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4
    cd07169
    Location:10 → 99
    NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    136715509..136969568 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362730.1 → XP_054218705.1  nuclear receptor subfamily 6 group A member 1 isoform X1

  2. XM_054362731.1 → XP_054218706.1  nuclear receptor subfamily 6 group A member 1 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_033335.2: Suppressed sequence

    Description
    NM_033335.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15406.2 GenPept UniProtKB/Swiss-Prot:Q15406

Gene LinkOut

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