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Protein

Retinoic acid receptor gamma-B

Gene

rargb

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: 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.By similarity1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi62 – 13776Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri65 – 8521NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri101 – 12020NR C4-typePROSITE-ProRule annotationAdd
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:rargbImported
Synonyms:nr1b3b
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-070314-1. rargb.

Subcellular locationi

Nucleus PROSITE-ProRule annotation

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. 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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi53 – 597Poly-ProSequence Analysis
Compositional biasi141 – 1444Poly-LysSequence Analysis
Compositional biasi342 – 3454Poly-Arg

Sequence similaritiesi

Belongs to the nuclear hormone receptor family. NR1 subfamily.Sequence Analysis
Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

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

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG297448.
HOVERGENiHBG005606.
InParanoidiA2T928.
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

        10         20         30         40         50
MRDVFREATP MTCRSPLPDL RDMMEKLTVF EPTIDSTVET QSTSSEEMIP
60 70 80 90 100
SSPSPPPPPR VYKPCFVCQD KSSGYHYGVS SCEGCKGFFR RSIQKNMVYT
110 120 130 140 150
CHRDKNCQIN KVTRNRCQYC RLRKCFEVGM SKEAVRNDRN KKKKDVKEEV
160 170 180 190 200
VLPESYELSG ELEELVNKVS KAHRETFPSL CQLGKYTTNS SADHRVQLDL
210 220 230 240 250
GLWDKFSELS TKCIIKIVEF AKRLPGFTSL TIADQITLLK SACLDILMLR
260 270 280 290 300
ICTRYTPEQD TMTFSDGLTL NRTQMHNAGF GPLTDLVFAF AGQLLPLEMD
310 320 330 340 350
DTETGLLSAI CLICGDRMDL EEPHRVDQLQ EPLLEALKIY ARRRRPNKPH
360 370 380 390 400
MFPRMLMKVT DLRGISTKGA ERAITLKMEI PGPMPPLIRE MLENPEIFED
410 420 430 440 450
SSDSNDSGAA AVVPAPNIKR MGQRQAAWVK GERPEWVRGR RRGSKSRYKA
460 470 480
GFKAGKARSR DSPDNNGEIR QGDERSEMSV RAEQDFALE
Length:489
Mass (Da):55,571
Last modified:March 5, 2007 - v1
Checksum:iF181AE31C836F2C8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
EF028131 mRNA. Translation: ABM89228.1.
RefSeqiNP_001076779.1. NM_001083310.1.
UniGeneiDr.135572.

3D structure databases

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

Protein-protein interaction databases

STRINGi7955.ENSDARP00000052545.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100034753.
KEGGidre:100034753.

Organism-specific databases

CTDi100034753.
ZFINiZDB-GENE-070314-1. rargb.

Phylogenomic databases

eggNOGiNOG297448.
HOVERGENiHBG005606.
InParanoidiA2T928.
PhylomeDBiA2T928.

Miscellaneous databases

NextBioi20788475.

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]
ProtoNetiSearch...

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(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], DEVELOPMENTAL STAGE.
    Tissue: Embryo1 Publication.
  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(2008) [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 20, 2007
Last sequence update: March 5, 2007
Last modified: January 6, 2015
This is version 50 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

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 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.