U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 2649, updated on 2-Nov-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
Try the new Gene table
Try the new Transcript table

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 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.