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

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: mouse all
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Genomic context

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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Novel LAMC2 fusion protein has tumor-promoting properties in ovarian carcinoma.
Title: Novel LAMC2 fusion protein has tumor-promoting properties in ovarian carcinoma.
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.
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.
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.
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.
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.
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.
These experiments confirmed that NR6A1 works as a regulator for hypocretin transcription.
Title: Transcriptional regulation of the hypocretin/orexin gene by NR6A1.
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 EBI GWAS CatalogPubMed

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

SHGC-9435 (e-PCR)
- UniSTS:40195

STS-X99975 (e-PCR)
- UniSTS:52529

RH121360 (e-PCR)
- UniSTS:134206

SHGC-34240 (e-PCR)
- UniSTS:20110

AFMA212WE1 (e-PCR)
- UniSTS:81580

STS-X99975 (e-PCR)
- UniSTS:14509

RH91255 (e-PCR)
- UniSTS:90802

RH138284 (e-PCR)
- UniSTS:220371

D9S1840 (e-PCR), detects polymorphism
- UniSTS:8679

WI-11569 (e-PCR)
- UniSTS:19949

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)

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
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
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
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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

124517275..124771311 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060933.1 Alternate T2T-CHM13v2.0

Range

136715509..136969568 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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.