ARL6_DANRE
ID ARL6_DANRE Reviewed; 186 AA.
AC Q5M9P8;
DT 08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=ADP-ribosylation factor-like protein 6;
GN Name=arl6; ORFNames=si:dkey-24h22.2, zgc:101762;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (ISOFORM 1).
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Olfactory epithelium;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (DEC-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP ALTERNATIVE SPLICING (ISOFORM 2), FUNCTION, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=20333246; DOI=10.1371/journal.pgen.1000884;
RA Pretorius P.R., Baye L.M., Nishimura D.Y., Searby C.C., Bugge K., Yang B.,
RA Mullins R.F., Stone E.M., Sheffield V.C., Slusarski D.C.;
RT "Identification and functional analysis of the vision-specific BBS3 (ARL6)
RT long isoform.";
RL PLoS Genet. 6:E1000884-E1000884(2010).
CC -!- FUNCTION: Probably involved in membrane protein trafficking at the base
CC of the ciliary organelle. May function in cilia biogenesis. Isoform 2
CC is required for proper retinal function and organization.
CC {ECO:0000269|PubMed:20333246}.
CC -!- SUBCELLULAR LOCATION: Cell projection, cilium membrane {ECO:0000250};
CC Peripheral membrane protein {ECO:0000250}; Cytoplasmic side
CC {ECO:0000250}. Cytoplasm, cytoskeleton, cilium axoneme {ECO:0000250}.
CC Cytoplasm, cytoskeleton, cilium basal body {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=bbs3;
CC IsoId=Q5M9P8-1; Sequence=Displayed;
CC Name=2; Synonyms=bbs3l;
CC IsoId=Q5M9P8-2; Sequence=VSP_040513;
CC -!- TISSUE SPECIFICITY: Expressed in brain, heart and eye. Isoform 2 is
CC expressed only in the retina. {ECO:0000269|PubMed:20333246}.
CC -!- DEVELOPMENTAL STAGE: Expressed throughout all the development stages.
CC Isoform 2 is not expressed until 48 hours post fertilization.
CC {ECO:0000269|PubMed:20333246}.
CC -!- DISRUPTION PHENOTYPE: Results in the cardinal features of Bardet-Biedl
CC syndrome in zebrafish, including defects to the ciliated Kupffer's
CC vesicle and delayed retrograde melanosome transport. Isoform 2 defects
CC does not result in Kupffer vesicle or melanosome transport defects, but
CC rather leads to impaired visual function and mislocalization of the
CC photopigment green cone opsin. Isoform 2, but not isoform 1, is
CC sufficient to rescue both the vision defect as well as green opsin
CC localization in the retina. {ECO:0000269|PubMed:20333246}.
CC -!- SIMILARITY: Belongs to the small GTPase superfamily. Arf family.
CC {ECO:0000305}.
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DR EMBL; BX901972; CAX13374.1; -; Genomic_DNA.
DR EMBL; BC086734; AAH86734.1; -; mRNA.
DR RefSeq; NP_001008733.1; NM_001008733.1. [Q5M9P8-1]
DR AlphaFoldDB; Q5M9P8; -.
DR SMR; Q5M9P8; -.
DR STRING; 7955.ENSDARP00000046093; -.
DR PaxDb; Q5M9P8; -.
DR Ensembl; ENSDART00000046094; ENSDARP00000046093; ENSDARG00000032056. [Q5M9P8-1]
DR Ensembl; ENSDART00000180898; ENSDARP00000152357; ENSDARG00000113281. [Q5M9P8-1]
DR Ensembl; ENSDART00000191432; ENSDARP00000147421; ENSDARG00000032056. [Q5M9P8-2]
DR Ensembl; ENSDART00000192938; ENSDARP00000155069; ENSDARG00000032056. [Q5M9P8-1]
DR GeneID; 494134; -.
DR KEGG; dre:494134; -.
DR CTD; 84100; -.
DR ZFIN; ZDB-GENE-041219-2; arl6.
DR eggNOG; KOG0070; Eukaryota.
DR GeneTree; ENSGT00940000156459; -.
DR HOGENOM; CLU_040729_9_1_1; -.
DR InParanoid; Q5M9P8; -.
DR OMA; WQIVPSN; -.
DR OrthoDB; 1271528at2759; -.
DR PhylomeDB; Q5M9P8; -.
DR TreeFam; TF105466; -.
DR Reactome; R-DRE-5620922; BBSome-mediated cargo-targeting to cilium.
DR PRO; PR:Q5M9P8; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 1.
DR Bgee; ENSDARG00000032056; Expressed in testis and 19 other tissues.
DR ExpressionAtlas; Q5M9P8; baseline and differential.
DR GO; GO:0005930; C:axoneme; IBA:GO_Central.
DR GO; GO:0060170; C:ciliary membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005525; F:GTP binding; IBA:GO_Central.
DR GO; GO:0003924; F:GTPase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0060271; P:cilium assembly; IMP:BHF-UCL.
DR GO; GO:0007368; P:determination of left/right symmetry; IMP:BHF-UCL.
DR GO; GO:0007369; P:gastrulation; IMP:ZFIN.
DR GO; GO:0006886; P:intracellular protein transport; IBA:GO_Central.
DR GO; GO:0070121; P:Kupffer's vesicle development; IMP:ZFIN.
DR GO; GO:0032402; P:melanosome transport; IMP:BHF-UCL.
DR GO; GO:0033339; P:pectoral fin development; IGI:ZFIN.
DR GO; GO:0061512; P:protein localization to cilium; IBA:GO_Central.
DR GO; GO:0008593; P:regulation of Notch signaling pathway; IMP:ZFIN.
DR GO; GO:0050896; P:response to stimulus; IEA:UniProtKB-KW.
DR GO; GO:0016192; P:vesicle-mediated transport; IBA:GO_Central.
DR GO; GO:0007601; P:visual perception; IMP:ZFIN.
DR CDD; cd04157; Arl6; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR041839; Arl6.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR005225; Small_GTP-bd_dom.
DR InterPro; IPR024156; Small_GTPase_ARF.
DR InterPro; IPR006689; Small_GTPase_ARF/SAR.
DR PANTHER; PTHR11711; PTHR11711; 1.
DR Pfam; PF00025; Arf; 1.
DR PRINTS; PR00328; SAR1GTPBP.
DR SMART; SM00178; SAR; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00231; small_GTP; 1.
DR PROSITE; PS51417; ARF; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Cell membrane; Cell projection; Cilium;
KW Cilium biogenesis/degradation; Cytoplasm; Cytoskeleton; GTP-binding;
KW Lipoprotein; Magnesium; Membrane; Metal-binding; Myristate;
KW Nucleotide-binding; Reference proteome; Sensory transduction; Vision.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000255"
FT CHAIN 2..186
FT /note="ADP-ribosylation factor-like protein 6"
FT /id="PRO_0000404211"
FT BINDING 24..31
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 50
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 50
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 69..73
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 72
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 130..133
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 164
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT LIPID 2
FT /note="N-myristoyl glycine"
FT /evidence="ECO:0000255"
FT VAR_SEQ 179..186
FT /note="DQIRAMKT -> EQIALSNQSDENVKPS (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_040513"
SQ SEQUENCE 186 AA; 21007 MW; ED4162A9B899ADD7 CRC64;
MGLFDKLAGW LGLKKKEVNV LCLGLDNSGK TTIINQLKPS NAQAQDIVPT IGFSIEKFKT
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSGDKL RMVVAKEELD TLLNHPDIKH
RRIPLLFFAN KMDLRDALSA VKVSQLLCLE NIKDKPWHIC ASDAVKGEGL LEGVDWLQDQ
IRAMKT
