LOCUS       NM_015966               1302 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens ERGIC and golgi 3 (ERGIC3), transcript variant 2,
            mRNA.
ACCESSION   NM_015966
VERSION     NM_015966.3
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 1302)
  AUTHORS   Liu,M., Zhao,Q., Zheng,X., Yang,L., Zhao,Y., Li,X. and Wu,M.
  TITLE     Transcriptome changes in ERGIC3-knockdown hepatocellular carcinoma
            cells: ERGIC3 is a novel immune function related gene
  JOURNAL   PeerJ 10, e13369 (2022)
   PUBMED   35602902
  REMARK    GeneRIF: Transcriptome changes in ERGIC3-knockdown hepatocellular
            carcinoma cells: ERGIC3 is a novel immune function related gene.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1302)
  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   3  (bases 1 to 1302)
  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 1302)
  AUTHORS   Yoo,W., Cho,E.B., Kim,S. and Yoon,J.B.
  TITLE     The E3 ubiquitin ligase MARCH2 regulates ERGIC3-dependent
            trafficking of secretory proteins
  JOURNAL   J Biol Chem 294 (28), 10900-10912 (2019)
   PUBMED   31142615
  REMARK    GeneRIF: MARCH2 reduced secretion of alpha1-antitrypsin and
            haptoglobin, and coexpression of the ubiquitination-resistant
            ERGIC3 variant largely restored their secretion, suggesting that
            MARCH2-mediated ERGIC3 ubiquitination is the major cause of the
            decrease in trafficking of ERGIC3-binding secretory proteins.
REFERENCE   5  (bases 1 to 1302)
  AUTHORS   Hong,S.H., Chang,S.H., Cho,K.C., Kim,S., Park,S., Lee,A.Y.,
            Jiang,H.L., Kim,H.J., Lee,S., Yu,K.N., Seo,H.W., Chae,C., Kim,K.P.,
            Park,J. and Cho,M.H.
  TITLE     Endoplasmic reticulum-Golgi intermediate compartment protein 3
            knockdown suppresses lung cancer through endoplasmic reticulum
            stress-induced autophagy
  JOURNAL   Oncotarget 7 (40), 65335-65347 (2016)
   PUBMED   27588471
  REMARK    GeneRIF: these data showed that knockdown of ERGIC3 triggers
            endoplasmic reticulum stress-induced autophagic cancer cell death
REFERENCE   6  (bases 1 to 1302)
  AUTHORS   Ghosh,D., Lippert,D., Krokhin,O., Cortens,J.P. and Wilkins,J.A.
  TITLE     Defining the membrane proteome of NK cells
  JOURNAL   J Mass Spectrom 45 (1), 1-25 (2010)
   PUBMED   19946888
REFERENCE   7  (bases 1 to 1302)
  AUTHORS   Nishikawa,M., Kira,Y., Yabunaka,Y. and Inoue,M.
  TITLE     Identification and characterization of endoplasmic
            reticulum-associated protein, ERp43
  JOURNAL   Gene 386 (1-2), 42-51 (2007)
   PUBMED   17020792
  REMARK    GeneRIF: Plays important roles in cell growth and endoplasmic
            reticulum stress-induced cell death.
REFERENCE   8  (bases 1 to 1302)
  AUTHORS   Breuza,L., Halbeisen,R., Jeno,P., Otte,S., Barlowe,C., Hong,W. and
            Hauri,H.P.
  TITLE     Proteomics of endoplasmic reticulum-Golgi intermediate compartment
            (ERGIC) membranes from brefeldin A-treated HepG2 cells identifies
            ERGIC-32, a new cycling protein that interacts with human Erv46
  JOURNAL   J Biol Chem 279 (45), 47242-47253 (2004)
   PUBMED   15308636
REFERENCE   9  (bases 1 to 1302)
  AUTHORS   Deloukas,P., Matthews,L.H., Ashurst,J., Burton,J., Gilbert,J.G.,
            Jones,M., Stavrides,G., Almeida,J.P., Babbage,A.K., Bagguley,C.L.,
            Bailey,J., Barlow,K.F., Bates,K.N., Beard,L.M., Beare,D.M.,
            Beasley,O.P., Bird,C.P., Blakey,S.E., Bridgeman,A.M., Brown,A.J.,
            Buck,D., Burrill,W., Butler,A.P., Carder,C., Carter,N.P.,
            Chapman,J.C., Clamp,M., Clark,G., Clark,L.N., Clark,S.Y.,
            Clee,C.M., Clegg,S., Cobley,V.E., Collier,R.E., Connor,R.,
            Corby,N.R., Coulson,A., Coville,G.J., Deadman,R., Dhami,P.,
            Dunn,M., Ellington,A.G., Frankland,J.A., Fraser,A., French,L.,
            Garner,P., Grafham,D.V., Griffiths,C., Griffiths,M.N., Gwilliam,R.,
            Hall,R.E., Hammond,S., Harley,J.L., Heath,P.D., Ho,S., Holden,J.L.,
            Howden,P.J., Huckle,E., Hunt,A.R., Hunt,S.E., Jekosch,K.,
            Johnson,C.M., Johnson,D., Kay,M.P., Kimberley,A.M., King,A.,
            Knights,A., Laird,G.K., Lawlor,S., Lehvaslaiho,M.H., Leversha,M.,
            Lloyd,C., Lloyd,D.M., Lovell,J.D., Marsh,V.L., Martin,S.L.,
            McConnachie,L.J., McLay,K., McMurray,A.A., Milne,S., Mistry,D.,
            Moore,M.J., Mullikin,J.C., Nickerson,T., Oliver,K., Parker,A.,
            Patel,R., Pearce,T.A., Peck,A.I., Phillimore,B.J.,
            Prathalingam,S.R., Plumb,R.W., Ramsay,H., Rice,C.M., Ross,M.T.,
            Scott,C.E., Sehra,H.K., Shownkeen,R., Sims,S., Skuce,C.D.,
            Smith,M.L., Soderlund,C., Steward,C.A., Sulston,J.E., Swann,M.,
            Sycamore,N., Taylor,R., Tee,L., Thomas,D.W., Thorpe,A., Tracey,A.,
            Tromans,A.C., Vaudin,M., Wall,M., Wallis,J.M., Whitehead,S.L.,
            Whittaker,P., Willey,D.L., Williams,L., Williams,S.A., Wilming,L.,
            Wray,P.W., Hubbard,T., Durbin,R.M., Bentley,D.R., Beck,S. and
            Rogers,J.
  TITLE     The DNA sequence and comparative analysis of human chromosome 20
  JOURNAL   Nature 414 (6866), 865-871 (2001)
   PUBMED   11780052
REFERENCE   10 (bases 1 to 1302)
  AUTHORS   Scanlan,M.J., Gout,I., Gordon,C.M., Williamson,B., Stockert,E.,
            Gure,A.O., Jager,D., Chen,Y.T., Mackay,A., O'Hare,M.J. and Old,L.J.
  TITLE     Humoral immunity to human breast cancer: antigen definition and
            quantitative analysis of mRNA expression
  JOURNAL   Cancer Immun 1, 4 (2001)
   PUBMED   12747765
  REMARK    Publication Status: Online-Only
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AF077030.1.
            
            On Jun 2, 2019 this sequence version replaced NM_015966.2.
            
            Transcript Variant: This variant (2) lacks an alternate in-frame
            exon compared to variant 1. The resulting isoform (b) has the same
            N- and C-termini but is shorter compared to isoform a.
            
            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 :: SRR5189655.118257.1, AF077030.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000348547.7/ ENSP00000341358.2
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1302              AF077030.1         8-1309
FEATURES             Location/Qualifiers
     source          1..1302
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20q11.22"
     gene            1..1302
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /note="ERGIC and golgi 3"
                     /db_xref="GeneID:51614"
                     /db_xref="HGNC:HGNC:15927"
                     /db_xref="MIM:616971"
     exon            1..108
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     CDS             21..1172
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /note="isoform b is encoded by transcript variant 2;
                     serologically defined breast cancer antigen 84;
                     endoplasmic reticulum-Golgi intermediate compartment
                     protein 3; endoplasmic reticulum-localized protein ERp43;
                     serologically defined breast cancer antigen NY-BR-84"
                     /codon_start=1
                     /product="endoplasmic reticulum-Golgi intermediate
                     compartment protein 3 isoform b"
                     /protein_id="NP_057050.1"
                     /db_xref="CCDS:CCDS13257.1"
                     /db_xref="GeneID:51614"
                     /db_xref="HGNC:HGNC:15927"
                     /db_xref="MIM:616971"
                     /translation="MEALGKLKQFDAYPKTLEDFRVKTCGGATVTIVSGLLMLLLFLS
                     ELQYYLTTEVHPELYVDKSRGDKLKINIDVLFPHMPCAYLSIDAMDVAGEQQLDVEHN
                     LFKQRLDKDGIPVSSEAERHELGKVEVTVFDPDSLDPDRCESCYGAEAEDIKCCNTCE
                     DVREAYRRRGWAFKNPDTIEQCRREGFSQKMQEQKNEGCQVYGFLEVNKVAGNFHFAP
                     GKSFQQSHVHVHDLQSFGLDNINMTHYIQHLSFGEDYPGIVNPLDHTNVTAPQASMMF
                     QYFVKVVPTVYMKVDGEVLRTNQFSVTRHEKVANGLLGDQGLPGVFVLYELSPMMVKL
                     TEKHRSFTHFLTGVCAIIGGMFTVAGLIDSLIYHSARAIQKKIDLGKTT"
     exon            109..179
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            180..267
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            268..387
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            388..481
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            482..647
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            648..705
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            706..737
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            738..834
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            835..899
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            900..1036
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            1037..1092
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     exon            1093..1302
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1274..1279
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /note="hexamer: GATAAA"
     polyA_site      1302
                     /gene="ERGIC3"
                     /gene_synonym="C20orf47; C2orf47; CGI-54; dJ477O4.2;
                     Erv46; NY-BR-84; PRO0989; SDBCAG84"
                     /note="major polyA site"
ORIGIN      
        1 cccctttccg gccggtcccc atggaggcgc tggggaagct gaagcagttc gatgcctacc
       61 ccaagacttt ggaggacttc cgggtcaaga cctgcggggg cgccaccgtg accattgtca
      121 gtggccttct catgctgcta ctgttcctgt ccgagctgca gtattacctc accacggagg
      181 tgcatcctga gctctacgtg gacaagtcgc ggggagataa actgaagatc aacatcgatg
      241 tactttttcc gcacatgcct tgtgcctatc tgagtattga tgccatggat gtggccggag
      301 aacagcagct ggatgtggaa cacaacctgt tcaagcaacg actagataaa gatggcatcc
      361 ccgtgagctc agaggctgag cggcatgagc ttgggaaagt cgaggtgacg gtgtttgacc
      421 ctgactccct ggaccctgat cgctgtgaga gctgctatgg tgctgaggca gaagatatca
      481 agtgctgtaa cacctgtgaa gatgtgcggg aggcatatcg ccgtagaggc tgggccttca
      541 agaacccaga tactattgag cagtgccggc gagagggctt cagccagaag atgcaggagc
      601 agaagaatga aggctgccag gtgtatggct tcttggaagt caataaggtg gccggaaact
      661 tccactttgc ccctgggaag agcttccagc agtcccatgt gcacgtccat gacttgcaga
      721 gctttggcct tgacaacatc aacatgaccc actacatcca gcacctgtca tttggggagg
      781 actatccagg cattgtgaac cccctggacc acaccaatgt cactgcgccc caagcctcca
      841 tgatgttcca gtactttgtg aaggtggtgc ccactgtgta catgaaggtg gacggagagg
      901 tactgaggac aaatcagttc tctgtgacca gacatgagaa ggttgccaat gggctgttgg
      961 gcgaccaagg ccttcccgga gtcttcgtcc tctatgagct ctcgcccatg atggtgaagc
     1021 tgacggagaa gcacaggtcc ttcacccact tcctgacagg tgtgtgcgcc atcattgggg
     1081 gcatgttcac agtggctgga ctcatcgatt cgctcatcta ccactcagca cgagccatcc
     1141 agaagaaaat tgatctaggg aagacaacgt agtcaccctc ggtgcttcct ctgtctcctc
     1201 tttctccctg gcctgtggtt gtcccccagc ctctgccacc ctccacctcc tcggtcagcc
     1261 ccagccccag gttgataaat ctattgattg attgtgatag ta
//
