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Protein

Nuclear receptor subfamily 6 group A member 1

Gene

nr6a1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Probable orphan nuclear receptor. Binds to a response element containing repeats of the motif 5'-AGGTCA-3'. Required for anterior-posterior patterning during organogenesis. Acts with chordin to play a role in patterning the midbrain-hindbrain. Isoform Em is required for integrin-mediated cell matrix interaction during neurulation and for the morphogenetic movements leading to formation of the neural tube. Also mediates the effect of retinoic acid on primary neurogenesis.5 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi11 – 8676Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri14 – 3421NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri50 – 6920NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • animal organ development Source: UniProtKB
  • anterior/posterior pattern specification Source: UniProtKB
  • cell migration Source: UniProtKB
  • midbrain-hindbrain boundary development Source: UniProtKB
  • neurogenesis Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Receptor

Keywords - Biological processi

Differentiation, Neurogenesis, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear receptor subfamily 6 group A member 1
Alternative name(s):
Germ cell nuclear factor
Short name:
GCNF
Short name:
xGCNF
Gene namesi
Name:nr6a1By similarity
Synonyms:gcnf1 Publication
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-487596. nr6a1.

Subcellular locationi

  • Cytoplasm 2 Publications
  • Nucleus PROSITE-ProRule annotation2 Publications

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 435435Nuclear receptor subfamily 6 group A member 1PRO_0000289151Add
BLAST

Expressioni

Tissue specificityi

Transiently expressed in differentiating cells of all embryonic germ layers. Expressed in an anterior to posterior concentration gradient from late gastrula to midneurula stages. Shows a complicated spatio-temporal pattern of expression during neurulation, being predominant in the neural plate and neural crest in midneurula embryos. At late tailbud (stage 30), mainly expressed in the head mesenchyme, gill arches and tail tip. Expression persists in the epidermis, somites and endoderm, and in the central nervous system, expression is restricted to the midbrain, hindbrain and part of the spinal cord. Isoforms Oo and Em are both expressed in the brain and isoform Oo is expressed in the germ cells of both the adult testis and ovary.4 Publications

Developmental stagei

Isoform Oo is expressed both maternally and zygotically, being predominantly expressed in oocytes and embryos before the midblastula transition but present at later stages at very low levels. Isoform Em is expressed zygotically between late gastrula stage and late tailbud stage 30, being predominant during tailbud stages.4 Publications

Inductioni

By retinoic acid.1 Publication

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Structurei

3D structure databases

ProteinModelPortaliP70033.
SMRiP70033. Positions 14-79.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the nuclear hormone receptor family. NR6 subfamily.Sequence analysis
Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri14 – 3421NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri50 – 6920NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOVERGENiHBG052664.
KOiK08561.

Family and domain databases

Gene3Di1.10.565.10. 3 hits.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 2 hits.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform Em1 Publication (identifier: P70033-1) [UniParc]FASTAAdd to basket
Also known as: xlEm1 Publication

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MDTWEDDRVD QRACLICGDR ATGLHYGIIS CEGCKGFFKR SICNKRVYRC
60 70 80 90 100
SRDKNCVMSR KQRNRCQYCR LLKCLQMGMN RKAIREDGMP GGRNKSIGPV
110 120 130 140 150
QISDEEVERI MSGQEFEEEA NTSWSNNGDS DHSSPGNAVS ESNQPSPVST
160 170 180 190 200
PSSSRSMELN GFSSLRDQYL GTPGPTHYQY LPHLFSFSAH PTIIPAQSRS
210 220 230 240 250
LDPQSHTLIN QLLTAEDIEP LNTPMLIEDG YKVTQSELFA LLCRLADELL
260 270 280 290 300
FRQITWVKKL PFFCDLSIKD YTCLLSTTWQ ELILLSSITT YSKQIFGDLT
310 320 330 340 350
DVTSKYSPSE DELHRFSEDG MEVMERLIYL FRKFSQLKVS NEEYVCMKAI
360 370 380 390 400
NFLNQDIQGI SSASQVEQLN KRYWYVCQDF TEYRYPHQPN RFPDLMMCLP
410 420 430
EVRYIAGKLV NVPLEQLPLL FKAFLHSCKT IVTKE
Note: Embryonic form.1 Publication
Length:435
Mass (Da):50,005
Last modified:May 29, 2007 - v2
Checksum:iB8DDF322E0686BA6
GO
Isoform Oo1 Publication (identifier: P70033-2) [UniParc]FASTAAdd to basket
Also known as: xlOo1 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     1-5: MDTWE → MEVERSTSGLMDSTGFYKEPAGETEHTAAGNMSDLSSDGIKINSFV

Note: Oocyte form.1 Publication
Show »
Length:476
Mass (Da):54,223
Checksum:iE82C5C7039BBE02D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti41 – 411S → T in AAC60126 (PubMed:9025060).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 55MDTWE → MEVERSTSGLMDSTGFYKEP AGETEHTAAGNMSDLSSDGI KINSFV in isoform Oo. 1 PublicationVSP_052452

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U58683 mRNA. Translation: AAC60126.1.
AY130967 mRNA. Translation: AAM95452.1.
RefSeqiNP_001084102.1. NM_001090633.1.
UniGeneiXl.37734.

Genome annotation databases

GeneIDi399304.
KEGGixla:399304.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U58683 mRNA. Translation: AAC60126.1.
AY130967 mRNA. Translation: AAM95452.1.
RefSeqiNP_001084102.1. NM_001090633.1.
UniGeneiXl.37734.

3D structure databases

ProteinModelPortaliP70033.
SMRiP70033. Positions 14-79.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi399304.
KEGGixla:399304.

Organism-specific databases

CTDi2649.
XenbaseiXB-GENE-487596. nr6a1.

Phylogenomic databases

HOVERGENiHBG052664.
KOiK08561.

Family and domain databases

Gene3Di1.10.565.10. 3 hits.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 2 hits.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNR6A1_XENLA
AccessioniPrimary (citable) accession number: P70033
Secondary accession number(s): Q8JG52
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: May 29, 2007
Last modified: March 16, 2016
This is version 92 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.