Retinoic acid receptor gamma-B - Danio rerio (Zebrafish)

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A2T928 (RARGB_DANRE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 41. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Retinoic acid receptor gamma-B
Short name=RAR-gamma-B

Alternative name(s):
Nuclear receptor subfamily 1 group B member 3-B

Gene names

Name:	rargb
Synonyms:	nr1b3b

Organism

Danio rerio (Zebrafish) (Brachydanio rerio) [Reference proteome]

Taxonomic identifier

7955 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Cyprinidae › Danio

Protein attributes

Sequence length	489 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The rar/rxr heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5 By similarity. Required for hindbrain development. Ref.2
Subunit structure	Heterodimer; with an rxr molecule By similarity. Binds DNA preferentially as a rar/rxr heterodimer By similarity.
Subcellular location	Nucleus By similarity.
Developmental stage	Expressed both maternally and zygotically. Expressed ubiquitously throughout gastrulation. At the tailbud stage, expressed at higher levels in the anterior and tailbud. Also expressed in migrating cranial neural crest cells. Ref.1 Ref.2
Sequence similarities	Belongs to the nuclear hormone receptor family. NR1 subfamily. Contains 1 nuclear receptor DNA-binding domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	retinoic acid receptor activity Inferred from electronic annotation. Source: InterPro sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro steroid hormone receptor activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 489

489

Retinoic acid receptor gamma-B

PRO_0000299171

Regions

DNA binding

62 – 137

Nuclear receptor

Zinc finger

65 – 85

NR C4-type

Zinc finger

101 – 120

NR C4-type

Compositional bias

53 – 59

Poly-Pro

Compositional bias

141 – 144

Poly-Lys

Compositional bias

342 – 345

Poly-Arg

Sequences

Sequence

Length

Mass (Da)

Tools

A2T928 [UniParc].

Last modified March 6, 2007. Version 1.
Checksum: F181AE31C836F2C8
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FASTA

489

55,571

        10         20         30         40         50         60 
MRDVFREATP MTCRSPLPDL RDMMEKLTVF EPTIDSTVET QSTSSEEMIP SSPSPPPPPR 

        70         80         90        100        110        120 
VYKPCFVCQD KSSGYHYGVS SCEGCKGFFR RSIQKNMVYT CHRDKNCQIN KVTRNRCQYC 

       130        140        150        160        170        180 
RLRKCFEVGM SKEAVRNDRN KKKKDVKEEV VLPESYELSG ELEELVNKVS KAHRETFPSL 

       190        200        210        220        230        240 
CQLGKYTTNS SADHRVQLDL GLWDKFSELS TKCIIKIVEF AKRLPGFTSL TIADQITLLK 

       250        260        270        280        290        300 
SACLDILMLR ICTRYTPEQD TMTFSDGLTL NRTQMHNAGF GPLTDLVFAF AGQLLPLEMD 

       310        320        330        340        350        360 
DTETGLLSAI CLICGDRMDL EEPHRVDQLQ EPLLEALKIY ARRRRPNKPH MFPRMLMKVT 

       370        380        390        400        410        420 
DLRGISTKGA ERAITLKMEI PGPMPPLIRE MLENPEIFED SSDSNDSGAA AVVPAPNIKR 

       430        440        450        460        470        480 
MGQRQAAWVK GERPEWVRGR RRGSKSRYKA GFKAGKARSR DSPDNNGEIR QGDERSEMSV 


RAEQDFALE

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References

[1]	"Comparison of the expression patterns of newly identified zebrafish retinoic acid and retinoid X receptors." Waxman J.S., Yelon D. Dev. Dyn. 236:587-595(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], DEVELOPMENTAL STAGE. Tissue: Embryo.
[2]	"Combinatorial roles for zebrafish retinoic acid receptors in the hindbrain, limbs and pharyngeal arches." Linville A., Radtke K., Waxman J.S., Yelon D., Schilling T.F. Dev. Biol. 325:60-70(2009) [PubMed] [Europe PMC] [Abstract] Cited for: DEVELOPMENTAL STAGE, INDUCTION, FUNCTION.

Cross-references

Sequence databases
EMBL GenBank DDBJ	EF028131 mRNA. Translation: ABM89228.1.
IPI	IPI00679293.
RefSeq	NP_001076779.1. NM_001083310.1.
UniGene	Dr.135572.
3D structure databases
ProteinModelPortal	A2T928.
SMR	A2T928. Positions 59-137, 158-395.
ModBase	Search...
Protein-protein interaction databases
STRING	7955.ENSDARP00000052545.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	100034753.
KEGG	dre:100034753.
Organism-specific databases
CTD	100034753.
ZFIN	ZDB-GENE-070314-1. rargb.
Phylogenomic databases
eggNOG	NOG297448.
HOVERGEN	HBG005606.
OrthoDB	EOG4F7NK7.
Family and domain databases
Gene3D	1.10.565.10. 1 hit. 3.30.50.10. 1 hit.
InterPro	IPR008946. Nucl_hormone_rcpt_ligand-bd. IPR000536. Nucl_hrmn_rcpt_lig-bd_core. IPR003078. Retinoic_acid_rcpt. IPR001723. Str_hrmn_rcpt. IPR001628. Znf_hrmn_rcpt. IPR013088. Znf_NHR/GATA. [Graphical view]
Pfam	PF00104. Hormone_recep. 1 hit. PF00105. zf-C4. 1 hit. [Graphical view]
PRINTS	PR01292. RETNOICACIDR. PR00398. STRDHORMONER. PR00047. STROIDFINGER.
SMART	SM00430. HOLI. 1 hit. SM00399. ZnF_C4. 1 hit. [Graphical view]
SUPFAM	SSF48508. Str_ncl_receptor. 1 hit.
PROSITE	PS00031. NUCLEAR_REC_DBD_1. 1 hit. PS51030. NUCLEAR_REC_DBD_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	20788475.

Entry information

Entry name

RARGB_DANRE

Accession

Primary (citable) accession number: A2T928

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 21, 2007
Last sequence update:	March 6, 2007
Last modified:	April 3, 2013
This is version 41 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Other

Entry information

Relevant documents