ID   COG4_DANRE              Reviewed;         781 AA.
AC   Q29RB1;
DT   08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT   04-APR-2006, sequence version 1.
DT   03-AUG-2022, entry version 98.
DE   RecName: Full=Conserved oligomeric Golgi complex subunit 4;
DE            Short=COG complex subunit 4;
DE   AltName: Full=Component of oligomeric Golgi complex 4;
GN   Name=cog4; ORFNames=zgc:136860;
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].
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].
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX   PubMed=30290151; DOI=10.1016/j.ajhg.2018.09.003;
RA   Ferreira C.R., Xia Z.J., Clement A., Parry D.A., Davids M., Taylan F.,
RA   Sharma P., Turgeon C.T., Blanco-Sanchez B., Ng B.G., Logan C.V.,
RA   Wolfe L.A., Solomon B.D., Cho M.T., Douglas G., Carvalho D.R., Bratke H.,
RA   Haug M.G., Phillips J.B., Wegner J., Tiemeyer M., Aoki K., Nordgren A.,
RA   Hammarsjoe A., Duker A.L., Rohena L., Hove H.B., Ek J., Adams D.,
RA   Tifft C.J., Onyekweli T., Weixel T., Macnamara E., Radtke K., Powis Z.,
RA   Earl D., Gabriel M., Russi A.H.S., Brick L., Kozenko M., Tham E.,
RA   Raymond K.M., Phillips J.A. III, Tiller G.E., Wilson W.G., Hamid R.,
RA   Malicdan M.C.V., Nishimura G., Grigelioniene G., Jackson A.,
RA   Westerfield M., Bober M.B., Gahl W.A., Freeze H.H.;
RT   "A recurrent de novo heterozygous COG4 substitution leads to Saul-Wilson
RT   syndrome, disrupted vesicular trafficking, and altered proteoglycan
RT   glycosylation.";
RL   Am. J. Hum. Genet. 103:553-567(2018).
CC   -!- FUNCTION: Required for normal Golgi function (PubMed:30290151). Plays a
CC       role in the vesicular trafficking between the endoplasmic reticulum and
CC       the Golgi apparatus (By similarity). {ECO:0000250|UniProtKB:Q9H9E3,
CC       ECO:0000269|PubMed:30290151}.
CC   -!- SUBUNIT: Monomer. Component of the conserved oligomeric Golgi (COG)
CC       complex which is composed of eight different subunits and is required
CC       for normal Golgi morphology and localization.
CC       {ECO:0000250|UniProtKB:Q9H9E3}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
CC       {ECO:0000250|UniProtKB:Q9H9E3}. Golgi apparatus membrane
CC       {ECO:0000250|UniProtKB:Q9H9E3}; Peripheral membrane protein
CC       {ECO:0000250|UniProtKB:Q9H9E3}; Cytoplasmic side
CC       {ECO:0000250|UniProtKB:Q9H9E3}. Note=Mosty cytosolic, with about 5%
CC       membrane-bound. {ECO:0000250|UniProtKB:Q9H9E3}.
CC   -!- TISSUE SPECIFICITY: Widely expressed, including in larval inner ear
CC       anterior macula, brain, retina and ceratobranchial arches
CC       (PubMed:30290151). Expressed in larval chondrocytes and hair cells of
CC       the anterior macula (at protein level) (PubMed:30290151).
CC       {ECO:0000269|PubMed:30290151}.
CC   -!- DISRUPTION PHENOTYPE: Zebrafish mutants are significantly shorter than
CC       their wild-type counterparts. Mutants have craniofacial defects with a
CC       smaller jaw, smaller inner ears, slightly smaller eyes, and stubby
CC       pectoral fins. They exhibit malformation of the inner ear, with
CC       abnormally shaped semicircular canals. Mechanosensory hair cells in the
CC       inner ear and neuromasts have reduced numbers of hair bundles. Response
CC       to auditory stimuli is greatly reduced. Animals show defects in
CC       proteoglycan secretion and reduced collagen COL1A2 expression in fins,
CC       but normal collagen type II expression in the jaw. Golgi apparatus
CC       structure is disrupted in mutant cells, with defects in the processing
CC       of N- and O-linked glycans and decreased glycosphingolipid complexity.
CC       {ECO:0000269|PubMed:30290151}.
CC   -!- SIMILARITY: Belongs to the COG4 family. {ECO:0000305}.
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DR   EMBL; CR376738; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CR848675; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; BC114292; AAI14293.1; -; mRNA.
DR   RefSeq; NP_001034912.1; NM_001039823.1.
DR   AlphaFoldDB; Q29RB1; -.
DR   STRING; 7955.ENSDARP00000070899; -.
DR   PaxDb; Q29RB1; -.
DR   Ensembl; ENSDART00000076425; ENSDARP00000070899; ENSDARG00000054264.
DR   GeneID; 569049; -.
DR   KEGG; dre:569049; -.
DR   CTD; 25839; -.
DR   ZFIN; ZDB-GENE-060312-33; cog4.
DR   eggNOG; KOG0412; Eukaryota.
DR   GeneTree; ENSGT00940000154065; -.
DR   HOGENOM; CLU_014853_2_0_1; -.
DR   InParanoid; Q29RB1; -.
DR   OMA; SECQQRV; -.
DR   OrthoDB; 376278at2759; -.
DR   PhylomeDB; Q29RB1; -.
DR   TreeFam; TF105835; -.
DR   Reactome; R-DRE-6807878; COPI-mediated anterograde transport.
DR   Reactome; R-DRE-6811438; Intra-Golgi traffic.
DR   PRO; PR:Q29RB1; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 7.
DR   Bgee; ENSDARG00000054264; Expressed in somite and 41 other tissues.
DR   GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR   GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0017119; C:Golgi transport complex; IBA:GO_Central.
DR   GO; GO:0007030; P:Golgi organization; IBA:GO_Central.
DR   GO; GO:0048213; P:Golgi vesicle prefusion complex stabilization; IBA:GO_Central.
DR   GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR   GO; GO:0006029; P:proteoglycan metabolic process; IMP:ZFIN.
DR   GO; GO:0006890; P:retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum; IBA:GO_Central.
DR   GO; GO:0001501; P:skeletal system development; IMP:ZFIN.
DR   InterPro; IPR013167; COG_su4.
DR   Pfam; PF08318; COG4; 1.
DR   SMART; SM00762; Cog4; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; Golgi apparatus; Membrane; Protein transport;
KW   Reference proteome; Transport.
FT   CHAIN           1..781
FT                   /note="Conserved oligomeric Golgi complex subunit 4"
FT                   /id="PRO_0000446920"
FT   REGION          614..736
FT                   /note="D domain"
FT                   /evidence="ECO:0000250|UniProtKB:Q9H9E3"
FT   REGION          737..781
FT                   /note="E domain; essential for proper cell surface
FT                   glycosylation"
FT                   /evidence="ECO:0000250|UniProtKB:Q9H9E3"
SQ   SEQUENCE   781 AA;  87587 MW;  F286FFB8E18CDD5A CRC64;
     MEEAASPARR RGGPAGVSAV QTDTIEALTE LEDLERVYAQ LCAEEAEVQV ELDALVGQQN
     NIETKMLSLQ RMGPNLQLIE GDAVQLSGMI NFTCSLAENV SSKVRQLDLT KKRLYQAIQR
     ADDILDLKFC TDGVQTALRN QDYEQAAAHI HRYLSLDQSV IELSKQGGEG SAVEASLALL
     QEAERNLKTL VTTRLEEAVA TGDLPQVERF FKILPLLGLH EQGLARFAQY LCSQLASKAE
     ENLILAVGSD LGERRAPVIF ADTLTLLLEG IARIVETHQP IVETYYGPGR LHTLLAHLQK
     ECDKQAQKIV DKFIQQRDYN NKFQVVQSNM MRGMTTDKIE PRDLDPVLCE VTLMNSRAEL
     YFRFLRRRIV ADFEVADAMA DEAVIQEHQQ SLEQLLKNCQ LSRTMQELIG YYIPMEEYYM
     RESVNKAVAM DTAEVGQLSS SVVDDVFYIV KKCISRALTS SSSDCVCAMI NHATSVLETD
     FREVLVCKLR AGYPVSALQD LQRGVSSAVS LMQSSLQQGK ITNLTQTLGI ESQEQAKSAY
     LVTLNNVEVC SENISTLKKN LESDCAKLFS QGASSDHAKE KIDSCLSDLV NTSSKFKDLL
     QEGLQELNNT AIRPQVKPWI SSFLSVSHNI EEEEFSEYEA NDPFVQQLIV QLEQLMAEFK
     VGLSPVIYDT LTSLMTSLIA MEMEKTVFKC TFSRLGGLQF DKELRALVAY LSSVTSWTIR
     DKFARLTQMA TILNLERVSE ILDYWGPNSG PLTWRLTPAE VRQVLALRVD FRSEDIKRLR
     L