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

    Gene ID: 2649, updated on 9-Dec-2024

    Summary

    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
    NEW
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001278546.2NP_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:252463
      NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4
      cd07169
      Location:48137
      NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers
    2. NM_001410996.1NP_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_001489.5NP_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:251462
      NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4
      cd07169
      Location:48137
      NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers
    4. NM_033334.4NP_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:256467
      NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4
      cd07169
      Location:52141
      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_047423226.1XP_047279182.1  nuclear receptor subfamily 6 group A member 1 isoform X2

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

      Conserved Domains (2) summary
      cd06953
      Location:214425
      NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4
      cd07169
      Location:1099
      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_054362730.1XP_054218705.1  nuclear receptor subfamily 6 group A member 1 isoform X1

    2. XM_054362731.1XP_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.