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A2T928

- RARGB_DANRE

UniProt

A2T928 - RARGB_DANRE

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Protein

Retinoic acid receptor gamma-B

Gene
rargb, nr1b3b
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at transcript leveli

Functioni

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.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi62 – 13776Nuclear receptorAdd
BLAST
Zinc fingeri65 – 8521NR C4-typeAdd
BLAST
Zinc fingeri101 – 12020NR C4-typeAdd
BLAST

GO - Molecular functioni

  1. retinoic acid receptor activity Source: InterPro
  2. sequence-specific DNA binding Source: InterPro
  3. steroid hormone receptor activity Source: InterPro
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. determination of digestive tract left/right asymmetry Source: ZFIN
  2. determination of heart left/right asymmetry Source: ZFIN
  3. determination of left/right asymmetry in lateral mesoderm Source: ZFIN
  4. determination of liver left/right asymmetry Source: ZFIN
  5. determination of pancreatic left/right asymmetry Source: ZFIN
  6. intrahepatic bile duct development Source: ZFIN
  7. negative regulation of BMP signaling pathway Source: ZFIN
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
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 namesi
Name:rargb
Synonyms:nr1b3b
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437: Unplaced

Organism-specific databases

ZFINiZDB-GENE-070314-1. rargb.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 489489Retinoic acid receptor gamma-BPRO_0000299171Add
BLAST

Expressioni

Developmental stagei

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.2 Publications

Interactioni

Subunit structurei

Heterodimer; with an rxr molecule By similarity. Binds DNA preferentially as a rar/rxr heterodimer By similarity.

Protein-protein interaction databases

STRINGi7955.ENSDARP00000052545.

Structurei

3D structure databases

ProteinModelPortaliA2T928.
SMRiA2T928. Positions 59-137, 158-395.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi53 – 597Poly-Pro
Compositional biasi141 – 1444Poly-Lys
Compositional biasi342 – 3454Poly-Arg

Sequence similaritiesi

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri65 – 8521NR C4-typeAdd
BLAST
Zinc fingeri101 – 12020NR C4-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG297448.
HOVERGENiHBG005606.
PhylomeDBiA2T928.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR008946. 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]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR01292. RETNOICACIDR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A2T928-1 [UniParc]FASTAAdd to Basket

« Hide

MRDVFREATP MTCRSPLPDL RDMMEKLTVF EPTIDSTVET QSTSSEEMIP    50
SSPSPPPPPR VYKPCFVCQD KSSGYHYGVS SCEGCKGFFR RSIQKNMVYT 100
CHRDKNCQIN KVTRNRCQYC RLRKCFEVGM SKEAVRNDRN KKKKDVKEEV 150
VLPESYELSG ELEELVNKVS KAHRETFPSL CQLGKYTTNS SADHRVQLDL 200
GLWDKFSELS TKCIIKIVEF AKRLPGFTSL TIADQITLLK SACLDILMLR 250
ICTRYTPEQD TMTFSDGLTL NRTQMHNAGF GPLTDLVFAF AGQLLPLEMD 300
DTETGLLSAI CLICGDRMDL EEPHRVDQLQ EPLLEALKIY ARRRRPNKPH 350
MFPRMLMKVT DLRGISTKGA ERAITLKMEI PGPMPPLIRE MLENPEIFED 400
SSDSNDSGAA AVVPAPNIKR MGQRQAAWVK GERPEWVRGR RRGSKSRYKA 450
GFKAGKARSR DSPDNNGEIR QGDERSEMSV RAEQDFALE 489
Length:489
Mass (Da):55,571
Last modified:March 6, 2007 - v1
Checksum:iF181AE31C836F2C8
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
EF028131 mRNA. Translation: ABM89228.1.
RefSeqiNP_001076779.1. NM_001083310.1.
UniGeneiDr.135572.

Genome annotation databases

GeneIDi100034753.
KEGGidre:100034753.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
EF028131 mRNA. Translation: ABM89228.1 .
RefSeqi NP_001076779.1. NM_001083310.1.
UniGenei Dr.135572.

3D structure databases

ProteinModelPortali A2T928.
SMRi A2T928. Positions 59-137, 158-395.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 7955.ENSDARP00000052545.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 100034753.
KEGGi dre:100034753.

Organism-specific databases

CTDi 100034753.
ZFINi ZDB-GENE-070314-1. rargb.

Phylogenomic databases

eggNOGi NOG297448.
HOVERGENi HBG005606.
PhylomeDBi A2T928.

Miscellaneous databases

NextBioi 20788475.

Family and domain databases

Gene3Di 1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProi 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 ]
Pfami PF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view ]
PRINTSi PR01292. RETNOICACIDR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTi SM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view ]
SUPFAMi SSF48508. SSF48508. 1 hit.
PROSITEi PS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiRARGB_DANRE
AccessioniPrimary (citable) accession number: A2T928
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 21, 2007
Last sequence update: March 6, 2007
Last modified: April 16, 2014
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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