LOCUS       NM_015386               2820 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens component of oligomeric golgi complex 4 (COG4),
            transcript variant 1, mRNA.
ACCESSION   NM_015386
VERSION     NM_015386.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2820)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   2  (bases 1 to 2820)
  AUTHORS   Ferreira,C.R., Niiler,T., Duker,A.L., Jackson,A.P. and Bober,M.B.
  TITLE     Growth in individuals with Saul-Wilson syndrome
  JOURNAL   Am J Med Genet A 182 (9), 2110-2116 (2020)
   PUBMED   32652690
  REMARK    GeneRIF: Growth in individuals with Saul-Wilson syndrome.
REFERENCE   3  (bases 1 to 2820)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   4  (bases 1 to 2820)
  AUTHORS   Ferreira,C.R., Xia,Z.J., Clement,A., Parry,D.A., Davids,M.,
            Taylan,F., Sharma,P., Turgeon,C.T., Blanco-Sanchez,B., Ng,B.G.,
            Logan,C.V., Wolfe,L.A., Solomon,B.D., Cho,M.T., Douglas,G.,
            Carvalho,D.R., Bratke,H., Haug,M.G., Phillips,J.B., Wegner,J.,
            Tiemeyer,M., Aoki,K., Nordgren,A., Hammarsjo,A., Duker,A.L.,
            Rohena,L., Hove,H.B., Ek,J., Adams,D., Tifft,C.J., Onyekweli,T.,
            Weixel,T., Macnamara,E., Radtke,K., Powis,Z., Earl,D., Gabriel,M.,
            Russi,A.H.S., Brick,L., Kozenko,M., Tham,E., Raymond,K.M.,
            Phillips,J.A. 3rd, Tiller,G.E., Wilson,W.G., Hamid,R.,
            Malicdan,M.C.V., Nishimura,G., Grigelioniene,G., Jackson,A.,
            Westerfield,M., Bober,M.B., Gahl,W.A. and Freeze,H.H.
  CONSRTM   Undiagnosed Diseases Network; Scottish Genome Partnership
  TITLE     A Recurrent De Novo Heterozygous COG4 Substitution Leads to
            Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered
            Proteoglycan Glycosylation
  JOURNAL   Am J Hum Genet 103 (4), 553-567 (2018)
   PUBMED   30290151
  REMARK    GeneRIF: A specific heterozygous COG4 substitution as the molecular
            basis of Saul-Wilson syndrome.
REFERENCE   5  (bases 1 to 2820)
  AUTHORS   Hillman,R.T., Green,R.E. and Brenner,S.E.
  TITLE     An unappreciated role for RNA surveillance
  JOURNAL   Genome Biol 5 (2), R8 (2004)
   PUBMED   14759258
REFERENCE   6  (bases 1 to 2820)
  AUTHORS   Loh,E. and Hong,W.
  TITLE     Sec34 is implicated in traffic from the endoplasmic reticulum to
            the Golgi and exists in a complex with GTC-90 and ldlBp
  JOURNAL   J Biol Chem 277 (24), 21955-21961 (2002)
   PUBMED   11929878
REFERENCE   7  (bases 1 to 2820)
  AUTHORS   Ungar,D., Oka,T., Brittle,E.E., Vasile,E., Lupashin,V.V.,
            Chatterton,J.E., Heuser,J.E., Krieger,M. and Waters,M.G.
  TITLE     Characterization of a mammalian Golgi-localized protein complex,
            COG, that is required for normal Golgi morphology and function
  JOURNAL   J Cell Biol 157 (3), 405-415 (2002)
   PUBMED   11980916
REFERENCE   8  (bases 1 to 2820)
  AUTHORS   Whyte,J.R. and Munro,S.
  TITLE     The Sec34/35 Golgi transport complex is related to the exocyst,
            defining a family of complexes involved in multiple steps of
            membrane traffic
  JOURNAL   Dev Cell 1 (4), 527-537 (2001)
   PUBMED   11703943
REFERENCE   9  (bases 1 to 2820)
  AUTHORS   Ferreira,C.
  TITLE     Saul-Wilson Syndrome
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   32078278
REFERENCE   10 (bases 1 to 2820)
  AUTHORS   Sparks,S.E. and Krasnewich,D.M.
  TITLE     Congenital Disorders of N-Linked Glycosylation and Multiple Pathway
            Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301507
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK096557.1, BP282697.1,
            AU125729.1 and AL050101.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 24, 2018 this sequence version replaced NM_015386.2.
            
            Summary: The protein encoded by this gene is a component of an
            oligomeric protein complex involved in the structure and function
            of the Golgi apparatus. Defects in this gene may be a cause of
            congenital disorder of glycosylation type IIj. Two transcript
            variants encoding different isoforms have been found for this
            gene.[provided by RefSeq, Aug 2010].
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660809.118636.1,
                                           SRR1803616.277363.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000323786.10/ ENSP00000315775.5
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-265               AK096557.1         1-265
            266-555             BP282697.1         230-519
            556-1072            AU125729.1         34-550
            1073-2820           AL050101.1         375-2122
FEATURES             Location/Qualifiers
     source          1..2820
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q22.1"
     gene            1..2820
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /note="component of oligomeric golgi complex 4"
                     /db_xref="GeneID:25839"
                     /db_xref="HGNC:HGNC:18620"
                     /db_xref="MIM:606976"
     exon            1..182
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     CDS             12..2381
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /note="isoform 1 is encoded by transcript variant 1;
                     complexed with Dor1p; conserved oligomeric Golgi complex
                     protein 4; COG complex subunit 4"
                     /codon_start=1
                     /product="conserved oligomeric Golgi complex subunit 4
                     isoform 1"
                     /protein_id="NP_056201.2"
                     /db_xref="CCDS:CCDS10892.2"
                     /db_xref="GeneID:25839"
                     /db_xref="HGNC:HGNC:18620"
                     /db_xref="MIM:606976"
                     /translation="MGTKMADLDSPPKLSGVQQPSEGVGGGRCSEISAELIRSLTELQ
                     ELEAVYERLCGEEKVVERELDALLEQQNTIESKMVTLHRMGPNLQLIEGDAKQLAGMI
                     TFTCNLAENVSSKVRQLDLAKNRLYQAIQRADDILDLKFCMDGVQTALRSEDYEQAAA
                     HTHRYLCLDKSVIELSRQGKEGSMIDANLKLLQEAEQRLKAIVAEKFAIATKEGDLPQ
                     VERFFKIFPLLGLHEEGLRKFSEYLCKQVASKAEENLLMVLGTDMSDRRAAVIFADTL
                     TLLFEGIARIVETHQPIVETYYGPGRLYTLIKYLQVECDRQVEKVVDKFIKQRDYHQQ
                     FRHVQNNLMRNSTTEKIEPRELDPILTEVTLMNARSELYLRFLKKRISSDFEVGDSMA
                     SEEVKQEHQKCLDKLLNNCLLSCTMQELIGLYVTMEEYFMRETVNKAVALDTYEKGQL
                     TSSMVDDVFYIVKKCIGRALSSSSIDCLCAMINLATTELESDFRDVLCNKLRMGFPAT
                     TFQDIQRGVTSAVNIMHSSLQQGKFDTKGIESTDEAKMSFLVTLNNVEVCSENISTLK
                     KTLESDCTKLFSQGIGGEQAQAKFDSCLSDLAAVSNKFRDLLQEGLTELNSTAIKPQV
                     QPWINSFFSVSHNIEEEEFNDYEANDPWVQQFILNLEQQMAEFKASLSPVIYDSLTGL
                     MTSLVAVELEKVVLKSTFNRLGGLQFDKELRSLIAYLTTVTTWTIRDKFARLSQMATI
                     LNLERVTEILDYWGPNSGPLTWRLTPAEVRQVLALRIDFRSEDIKRLRL"
     exon            183..265
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            266..380
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            381..555
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            556..749
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            750..855
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            856..1013
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1014..1072
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1073..1206
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1207..1325
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1326..1492
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1493..1658
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1659..1721
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1722..1838
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1839..1931
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            1932..2015
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            2016..2117
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            2118..2246
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     exon            2247..2820
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2800..2805
                     /regulatory_class="polyA_signal_sequence"
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /note="hexamer: AATAAA"
     polyA_site      2820
                     /gene="COG4"
                     /gene_synonym="CDG2J; COD1; SWILS"
                     /note="major polyA site"
ORIGIN      
        1 ggaagtgccg aatggggacc aagatggcgg accttgattc gcctccgaag ctgtcagggg
       61 tgcagcagcc gtctgagggg gtgggaggtg gccgctgctc cgaaatctcc gctgagctca
      121 ttcgctccct gacagagctg caggagctgg aggctgtata cgaacggctc tgcggcgagg
      181 agaaagtggt ggagagagag ctggatgctc ttttggaaca gcaaaacacc attgaaagta
      241 agatggtcac tctccaccga atgggtccta atctgcagct gattgaggga gatgcaaagc
      301 agctggctgg aatgatcacc tttacctgca acctggctga gaatgtgtcc agcaaagttc
      361 gtcagcttga cctggccaag aaccgcctct atcaggccat tcagagagct gatgacatct
      421 tggacctgaa gttctgcatg gatggagttc agactgcttt gaggagtgaa gattatgagc
      481 aggctgcagc acatactcat cgctacttgt gcctggacaa gtcggtcatt gagctcagcc
      541 gacagggcaa agaggggagc atgattgatg ccaacctgaa attgctgcag gaagctgagc
      601 aacgtctcaa agccattgtg gcagagaagt ttgccattgc caccaaggaa ggtgatctgc
      661 cccaggtgga gcgcttcttc aagatcttcc cactgctggg tttgcatgag gagggattaa
      721 gaaagttctc ggagtacctt tgcaagcagg tggccagtaa agctgaggag aatctgctca
      781 tggtgctggg gacagacatg agtgatcgga gagctgcagt catctttgca gatacactta
      841 ctcttctgtt tgaagggatt gcccgcattg tggagaccca ccagccaata gtggagacct
      901 attatgggcc agggagactc tataccctga tcaaatatct gcaggtggaa tgtgacagac
      961 aggtggagaa ggtggtagac aagttcatca agcaaaggga ctaccaccag cagttccggc
     1021 atgttcagaa caacctgatg agaaattcta caacagaaaa aatcgaacca agagaactgg
     1081 accccatcct gactgaggtc accctgatga atgcccgcag tgagctatac ttacgcttcc
     1141 tcaagaagag gattagctct gattttgagg tgggagactc catggcctca gaggaagtaa
     1201 agcaagagca ccagaagtgt ctggacaaac tcctcaataa ctgccttttg agctgtacca
     1261 tgcaggagct aattggctta tatgttacca tggaggagta cttcatgagg gagactgtca
     1321 ataaggctgt ggctctggac acctatgaga agggccagct gacatccagc atggtggatg
     1381 atgtcttcta cattgttaag aagtgcattg ggcgggctct gtccagctcc agcattgact
     1441 gtctctgtgc catgatcaac ctcgccacca cagagctgga gtctgacttc agggatgttc
     1501 tgtgtaataa gctgcggatg ggctttcctg ccaccacctt ccaggacatc cagcgcgggg
     1561 tgacaagtgc cgtgaacatc atgcacagca gcctccagca aggcaaattt gacacaaaag
     1621 gcatcgagag tactgacgag gcgaagatgt ccttcctggt gactctgaac aacgtggaag
     1681 tctgcagtga aaacatctcc actctgaaga agacactgga gagtgactgc accaagctct
     1741 tcagccaggg cattggaggg gagcaggccc aggccaagtt tgacagctgc ctttctgact
     1801 tggccgccgt gtccaacaaa ttccgagacc tcttgcagga agggctgacg gagctcaaca
     1861 gcacagccat caagccacag gtgcagcctt ggatcaacag ctttttctcc gtctcccaca
     1921 acatcgagga ggaagaattc aatgactatg aggccaacga cccttgggta caacagttca
     1981 tccttaacct ggagcagcaa atggcagagt tcaaggccag cctgtccccg gtcatctacg
     2041 acagcctaac cggcctcatg actagccttg ttgccgtcga gttggagaaa gtggtgctga
     2101 aatccacctt taaccggctg ggtggtctgc agtttgacaa ggagctgagg tcgctcattg
     2161 cctaccttac cacggtgacc acctggacca tccgagacaa gtttgcccgg ctctcccaga
     2221 tggccaccat cctcaatctg gagcgggtga ccgagatcct cgattactgg ggacccaatt
     2281 ccggcccatt gacgtggcgc ctcacccctg ctgaagtgcg ccaggtgctg gccctgcgga
     2341 tagacttccg cagtgaagat atcaagaggc tgcgcctgta gctgcctgga tgagcacacc
     2401 tggctcatca cacttgcagg cctgttccct aaggggcccc agccaaggag ctgagcgagg
     2461 ctgtctggct tgggggagat ctgacagccc agacctttct acggctggca gcagagaaac
     2521 aaagtctgga cccactccat gctctgccct cagacctggc caggtgatgc tctgggggca
     2581 gcatctcccc accgagagaa gcgggctcct aatgaggtgg gaaagccacg gcaggcagcg
     2641 agcagcccag gccagctttc tgcatggatg gtcagtctct tgccctcaaa cactacagca
     2701 aacaagctac ccctgccagt cctagacaac ttgggtacat ctggggacct agcagttagg
     2761 cttgactttg aggagaggct gtgatgttta tgatccctga ataaagctac tccttggaga
//
