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

    Gene ID: 2649, updated on 27-Dec-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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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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