LOCUS       NM_001655               3994 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens archain 1 (ARCN1), transcript variant 1, mRNA.
ACCESSION   NM_001655
VERSION     NM_001655.5
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 3994)
  AUTHORS   Tidwell,T., Deshotel,M., Palumbos,J., Miller,C., Bayrak-Toydemir,P.
            and Carey,J.C.
  TITLE     Novel de novo ARCN1 intronic variant causes rhizomelic short
            stature with microretrognathia and developmental delay
  JOURNAL   Cold Spring Harb Mol Case Stud 6 (6), a005728 (2020)
   PUBMED   33154040
  REMARK    GeneRIF: Novel de novo ARCN1 intronic variant causes rhizomelic
            short stature with microretrognathia and developmental delay.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3994)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   3  (bases 1 to 3994)
  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 3994)
  AUTHORS   Izumi,K., Brett,M., Nishi,E., Drunat,S., Tan,E.S., Fujiki,K.,
            Lebon,S., Cham,B., Masuda,K., Arakawa,M., Jacquinet,A.,
            Yamazumi,Y., Chen,S.T., Verloes,A., Okada,Y., Katou,Y.,
            Nakamura,T., Akiyama,T., Gressens,P., Foo,R., Passemard,S.,
            Tan,E.C., El Ghouzzi,V. and Shirahige,K.
  TITLE     ARCN1 Mutations Cause a Recognizable Craniofacial Syndrome Due to
            COPI-Mediated Transport Defects
  JOURNAL   Am J Hum Genet 99 (2), 451-459 (2016)
   PUBMED   27476655
  REMARK    GeneRIF: report of a clinically recognizable craniofacial disorder
            characterized by facial dysmorphisms, severe micrognathia,
            rhizomelic shortening, microcephalic dwarfism, and mild
            developmental delay due to loss-of-function heterozygous mutations
            in ARCN1, which encodes the coatomer subunit delta of COPI
REFERENCE   5  (bases 1 to 3994)
  AUTHORS   Hu,Y., Jiang,L., Lai,W., Qin,Y., Zhang,T., Wang,S. and Ye,X.
  TITLE     MicroRNA-33a disturbs influenza A virus replication by targeting
            ARCN1 and inhibiting viral ribonucleoprotein activity
  JOURNAL   J Gen Virol 97 (1), 27-38 (2016)
   PUBMED   26498766
  REMARK    GeneRIF: The authors demonstrated that miR-33a could impede
            influenza A virus replication at the stage of virus internalization
            by suppressing ARCN1 expression.
REFERENCE   6  (bases 1 to 3994)
  AUTHORS   Schekman,R. and Orci,L.
  TITLE     Coat proteins and vesicle budding
  JOURNAL   Science 271 (5255), 1526-1533 (1996)
   PUBMED   8599108
  REMARK    Review article
REFERENCE   7  (bases 1 to 3994)
  AUTHORS   Cukierman,E., Huber,I., Rotman,M. and Cassel,D.
  TITLE     The ARF1 GTPase-activating protein: zinc finger motif and Golgi
            complex localization
  JOURNAL   Science 270 (5244), 1999-2002 (1995)
   PUBMED   8533093
REFERENCE   8  (bases 1 to 3994)
  AUTHORS   Radice,P., Pensotti,V., Jones,C., Perry,H., Pierotti,M.A. and
            Tunnacliffe,A.
  TITLE     The human archain gene, ARCN1, has highly conserved homologs in
            rice and Drosophila
  JOURNAL   Genomics 26 (1), 101-106 (1995)
   PUBMED   7782067
REFERENCE   9  (bases 1 to 3994)
  AUTHORS   Orcl,L., Palmer,D.J., Amherdt,M. and Rothman,J.E.
  TITLE     Coated vesicle assembly in the Golgi requires only coatomer and ARF
            proteins from the cytosol
  JOURNAL   Nature 364 (6439), 732-734 (1993)
   PUBMED   8355790
REFERENCE   10 (bases 1 to 3994)
  AUTHORS   Waters,M.G., Serafini,T. and Rothman,J.E.
  TITLE     'Coatomer': a cytosolic protein complex containing subunits of
            non-clathrin-coated Golgi transport vesicles
  JOURNAL   Nature 349 (6306), 248-251 (1991)
   PUBMED   1898986
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB216489.1, BC093636.1,
            CR988766.1, AU125652.1, BC080638.1 and AA856562.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_001655.4.
            
            Summary: This gene maps in a region, which include the mixed
            lineage leukemia and Friend leukemia virus integration 1 genes,
            where multiple disease-associated chromosome translocations occur.
            It is an intracellular protein. Archain sequences are well
            conserved among eukaryotes and this protein may play a fundamental
            role in eukaryotic cell biology. It has similarities to heat shock
            proteins and clathrin-associated proteins, and may be involved in
            vesicle structure or trafficking. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            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 :: SRR1660809.157670.1,
                                           SRR1803616.34747.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000264028.5/ ENSP00000264028.4
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-51                DB216489.1         23-73
            52-1739             BC093636.1         1-1688
            1740-2034           CR988766.1         416-710
            2035-2564           AU125652.1         21-550
            2565-3632           BC080638.1         2519-3586
            3633-3994           AA856562.1         17-378              c
FEATURES             Location/Qualifiers
     source          1..3994
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q23.3"
     gene            1..3994
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /note="archain 1"
                     /db_xref="GeneID:372"
                     /db_xref="HGNC:HGNC:649"
                     /db_xref="MIM:600820"
     exon            1..142
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     CDS             140..1675
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /note="isoform 1 is encoded by transcript variant 1;
                     coatomer protein delta-COP; coatomer protein complex,
                     subunit delta; archain vesicle transport protein 1;
                     coatomer delta subunit; delta-coat protein; COPI coat
                     complex subunit delta"
                     /codon_start=1
                     /product="coatomer subunit delta isoform 1"
                     /protein_id="NP_001646.2"
                     /db_xref="CCDS:CCDS8400.1"
                     /db_xref="GeneID:372"
                     /db_xref="HGNC:HGNC:649"
                     /db_xref="MIM:600820"
                     /translation="MVLLAAAVCTKAGKAIVSRQFVEMTRTRIEGLLAAFPKLMNTGK
                     QHTFVETESVRYVYQPMEKLYMVLITTKNSNILEDLETLRLFSRVIPEYCRALEENEI
                     SEHCFDLIFAFDEIVALGYRENVNLAQIRTFTEMDSHEEKVFRAVRETQEREAKAEMR
                     RKAKELQQARRDAERQGKKAPGFGGFGSSAVSGGSTAAMITETIIETDKPKVAPAPAR
                     PSGPSKALKLGAKGKEVDNFVDKLKSEGETIMSSSMGKRTSEATKMHAPPINMESVHM
                     KIEEKITLTCGRDGGLQNMELHGMIMLRISDDKYGRIRLHVENEDKKGVQLQTHPNVD
                     KKLFTAESLIGLKNPEKSFPVNSDVGVLKWRLQTTEESFIPLTINCWPSESGNGCDVN
                     IEYELQEDNLELNDVVITIPLPSGVGAPVIGEIDGEYRHDSRRNTLEWCLPVIDAKNK
                     SGSLEFSIAGQPNDFFPVQVSFVSKKNYCNIQVTKVTQVDGNSPVRFSTETTFLVDKY
                     EIL"
     exon            143..406
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     exon            407..586
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     exon            587..792
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     exon            793..957
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     exon            958..1123
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     exon            1124..1271
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     exon            1272..1380
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     exon            1381..1585
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     exon            1586..3994
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3868..3873
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /note="hexamer: AATAAA"
     polyA_site      3889
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /note="major polyA site"
     regulatory      3960..3965
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
                     /note="hexamer: ATTAAA"
     polyA_site      3994
                     /gene="ARCN1"
                     /gene_synonym="COPD; SRMMD; SSMG"
ORIGIN      
        1 atcttggcaa gaggcgaagc ggcagcggtt cctgtcaagg gggcagcagg tccagagctg
       61 ctggtgctcc cgttccccag accctacccc tatccccagt ggagccggag tgcgggcgcg
      121 ccccaccacc gccctcacca tggtgctgtt ggcagcagcg gtctgcacaa aagcaggaaa
      181 ggctattgtt tctcgacagt ttgtggaaat gacccgaact cggattgagg gcttattagc
      241 agcttttcca aagctcatga acactggaaa acaacatacg tttgttgaaa cagagagtgt
      301 aagatatgtc taccagccta tggagaaact gtatatggta ctgatcacta ccaaaaacag
      361 caacatttta gaagatttgg agaccctaag gctcttctca agagtgatcc ctgaatattg
      421 ccgagcctta gaagagaatg aaatatctga gcactgtttt gatttgattt ttgcttttga
      481 tgaaattgtc gcactgggat accgggagaa tgttaacttg gcacagatca gaaccttcac
      541 agaaatggat tctcatgagg agaaggtgtt cagagccgtc agagagactc aagaacgtga
      601 agctaaggct gagatgcgtc gtaaagcaaa ggaattacaa caggcccgaa gagatgcaga
      661 gagacagggc aaaaaagcac caggatttgg cggatttggc agctctgcag tatctggagg
      721 cagcacagct gccatgatca cagagaccat cattgaaact gataaaccaa aagtggcacc
      781 tgcaccagcc aggccttcag gccccagcaa ggctttaaaa cttggagcca aaggaaagga
      841 agtagataac tttgtggaca aattaaaatc tgaaggtgaa accatcatgt cctctagtat
      901 gggcaagcgt acttctgaag caaccaaaat gcatgctcca cccattaata tggaaagtgt
      961 acatatgaag attgaagaaa agataacatt aacctgtgga cgagacggag gattacagaa
     1021 tatggagttg catggcatga tcatgcttag gatctcagat gacaagtatg gccgaattcg
     1081 tcttcatgtg gaaaatgaag ataagaaagg ggtgcagcta cagacccatc caaatgtgga
     1141 taaaaaactt ttcactgcag agtctctaat tggcctgaag aatccagaga agtcatttcc
     1201 agtcaacagt gacgtagggg tgctaaagtg gagactacaa accacagagg aatcttttat
     1261 tccactgaca attaattgct ggccctcgga gagtggaaat ggctgtgatg tcaacataga
     1321 atatgagcta caagaagata atttagaact gaatgatgtg gttatcacca tcccactccc
     1381 gtctggtgtc ggcgcgcctg ttatcggtga gatcgatggg gagtatcgac atgacagtcg
     1441 acgaaatacc ctggagtggt gcctgcctgt gattgatgcc aaaaataaga gtggcagcct
     1501 ggagtttagc attgctgggc agcccaatga cttcttccct gttcaagttt cctttgtctc
     1561 caagaaaaat tactgtaaca tacaggttac caaagtgacc caggtagatg gaaacagccc
     1621 cgtcaggttt tccacagaga ccactttcct agtggataag tatgaaattc tgtaatacca
     1681 agaagaggga gctgaaaagg aaaattttca gattaataaa gaagacgcca atgatggctg
     1741 aagagttttt cccagattta caagccactg gagacccctt ttttctgata caatgcacga
     1801 ttctctgcgc gcaaggaccc tcgactcacc cccatgtttc agtgtcacag agacattctt
     1861 tgataaggaa atggcacaaa cataaaggga aaggctgcta attttctttg gcagattgta
     1921 ttggccagca ggaaagcaag ctctccagag aatgccccca gttaaatacc tcctctacct
     1981 ttacctaagt tgctccttta tttttatttt attattatta ttattattat tattattttt
     2041 tgagatggag tctcactttg taacccaggc tggaatgcaa tggcatgatc tcagctcact
     2101 gcaacctccg cctcctgggt tcaagcaagt ctcctgcctc agcctccgag tagctgggac
     2161 tacaggtgca cgccaccacg cctggctaat tttttgtatt ttagtagaga cggggtttca
     2221 ccgtgttgcc caggctggtc gcgaactcct gagctcaggc aatccgccca cctcagcctc
     2281 ccaaagtgtt gggattacag gcatgagcca ccatgcccag ctgctccttt attttaatcc
     2341 ctaaatataa tccctaaata tagttatatt tcatacttag tttgttttta aaaagttttc
     2401 tctgtagaaa attttaatca ttcataccct ttacctttag gtttttcttt ctatacattc
     2461 agtcaggcac tgggatcatc tgtttacagg cattatattt atttggcact cctggaacaa
     2521 gtatatctaa cccattcttg atttttggac tattcaggtg aactatttga ggggtatggg
     2581 gtctagaagt taaaagatac gcatgtcttc tgttcttttc ccgtatcaat tcattccttc
     2641 atctctttgc caagttgttt tcctttcagg gcctgtcctt ccagtttaga acagtaccat
     2701 gaatcccact tgtgtcaata ttaaagatag ctgagaagca cctttcaaat ggcacagtcc
     2761 ctcttcaaga tgtctaaaag aatggttatg tctgtccagt tagggatttc acatccacat
     2821 gtaatcatgt ctgctgctgt tgctacccaa attttcattt ctccacattt tgggtactta
     2881 agctaaaacg taatggccac agtctgtaat ccattcacat tcctcagttt caccacctcc
     2941 ctcttccaga ctgcactctc tgtcatcagt cccctccttt ctaacagaaa tggggttatg
     3001 attttgaagg ctgtgggttc agggagtctt tgccaatcct gttggcccta aactatcaag
     3061 gaggctccat ttcaccattt gattttttgc atttcaggag gcaactgatt gtttcgatat
     3121 gtacatatta ctcacgtata ccccatttcc ttccagtcag cccaacattt tccaccagtc
     3181 tgtccccatc tctgaaatcc ttccttctct ttccccctaa gtcttttgag tgtcatcatg
     3241 tactggtggt ttctcggttc catctcatcc atttcctttt caatggagac tacagcgtca
     3301 gccagctcag ccttggcttt taactcaata ttccagtcca taggggtggt taaaagttgc
     3361 tgcaaggctg caggcactgg cagtgggaag aggcagacga ctagatgact tctgcacttt
     3421 tagctggttg aaaagtacca ctcccactct gaacatctgg ccgtccctgc aaagagtgta
     3481 ctgtgcttga agcagagcac tcacacataa atggctgtgt gtggaattgc ttgccaaaga
     3541 agtttctagc ctttcccttt cccctaactg catcagggaa gaattcttat ctctagcttg
     3601 gtttccacat gaggtttttc tgagaagggc ttgggacaag aagtctgtca tgttagttaa
     3661 gcaggcaaga aatcctacta atccagtttt gtttgaaagt tgtttgtccg tatgattttt
     3721 taaaagtcaa gtttaatttc aaaaaacctt ttttttctga gattactttt ggggtaatat
     3781 ttaaaatgag agacattttg taaccctgta aaatacatag ggaatataac attccagtgt
     3841 atacaaagaa ggcaaattct ttaatcaaat aaagcgcatt ataaaatgag atgtttattg
     3901 gattattgac tcactttggt gtctgcttgt tgattcagga tgctgtaatg ggacctaaca
     3961 ttaaaaatta atgacatgtt ttttttaaga gaaa
//
