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

Gene ID: 2649, updated on 29-Mar-2020

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
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

Genomic context

See NR6A1 in Genome Data Viewer
Location:
9q33.3
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (124517275..124771311, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (127279554..127533589, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376270 Neighboring gene adhesion G protein-coupled receptor D2 Neighboring gene NR5A1 5' promoter region Neighboring gene nuclear receptor subfamily 5 group A member 1 Neighboring gene RAN binding protein 1 pseudogene Neighboring gene RNA, 7SL, cytoplasmic 302, pseudogene Neighboring gene MIR181A2 host gene Neighboring gene microRNA 181a-2 Neighboring gene microRNA 181b-2 Neighboring gene uncharacterized LOC107987126 Neighboring gene olfactomedin like 2A

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

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
 
intracellular receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
host cell nucleus IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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/Swiss-Prot
    Q15406
    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_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
  3. 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
    Q15406
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_005251918.5XP_005251975.1  nuclear receptor subfamily 6 group A member 1 isoform X2

    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
  2. XM_005251917.5XP_005251974.1  nuclear receptor subfamily 6 group A member 1 isoform X1

    UniProtKB/Swiss-Prot
    Q15406
    Related
    ENSP00000341135.4, ENST00000344523.8
    Conserved Domains (2) summary
    cd06953
    Location:255466
    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

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.
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