LOCUS       NM_001017964            1309 bp    mRNA    linear   PRI 03-OCT-2024
DEFINITION  Homo sapiens YdjC chitooligosaccharide deacetylase homolog (YDJC),
            transcript variant 1, mRNA.
ACCESSION   NM_001017964 XM_097886
VERSION     NM_001017964.2
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 1309)
  AUTHORS   Okada,Y., Wu,D., Trynka,G., Raj,T., Terao,C., Ikari,K., Kochi,Y.,
            Ohmura,K., Suzuki,A., Yoshida,S., Graham,R.R., Manoharan,A.,
            Ortmann,W., Bhangale,T., Denny,J.C., Carroll,R.J., Eyler,A.E.,
            Greenberg,J.D., Kremer,J.M., Pappas,D.A., Jiang,L., Yin,J., Ye,L.,
            Su,D.F., Yang,J., Xie,G., Keystone,E., Westra,H.J., Esko,T.,
            Metspalu,A., Zhou,X., Gupta,N., Mirel,D., Stahl,E.A., Diogo,D.,
            Cui,J., Liao,K., Guo,M.H., Myouzen,K., Kawaguchi,T., Coenen,M.J.,
            van Riel,P.L., van de Laar,M.A., Guchelaar,H.J., Huizinga,T.W.,
            Dieude,P., Mariette,X., Bridges,S.L. Jr., Zhernakova,A., Toes,R.E.,
            Tak,P.P., Miceli-Richard,C., Bang,S.Y., Lee,H.S., Martin,J.,
            Gonzalez-Gay,M.A., Rodriguez-Rodriguez,L., Rantapaa-Dahlqvist,S.,
            Arlestig,L., Choi,H.K., Kamatani,Y., Galan,P., Lathrop,M., Eyre,S.,
            Bowes,J., Barton,A., de Vries,N., Moreland,L.W., Criswell,L.A.,
            Karlson,E.W., Taniguchi,A., Yamada,R., Kubo,M., Liu,J.S., Bae,S.C.,
            Worthington,J., Padyukov,L., Klareskog,L., Gregersen,P.K.,
            Raychaudhuri,S., Stranger,B.E., De Jager,P.L., Franke,L.,
            Visscher,P.M., Brown,M.A., Yamanaka,H., Mimori,T., Takahashi,A.,
            Xu,H., Behrens,T.W., Siminovitch,K.A., Momohara,S., Matsuda,F.,
            Yamamoto,K. and Plenge,R.M.
  CONSRTM   RACI consortium; GARNET consortium
  TITLE     Genetics of rheumatoid arthritis contributes to biology and drug
            discovery
  JOURNAL   Nature 506 (7488), 376-381 (2014)
   PUBMED   24390342
REFERENCE   2  (bases 1 to 1309)
  AUTHORS   van der Harst,P., Zhang,W., Mateo Leach,I., Rendon,A., Verweij,N.,
            Sehmi,J., Paul,D.S., Elling,U., Allayee,H., Li,X.,
            Radhakrishnan,A., Tan,S.T., Voss,K., Weichenberger,C.X.,
            Albers,C.A., Al-Hussani,A., Asselbergs,F.W., Ciullo,M., Danjou,F.,
            Dina,C., Esko,T., Evans,D.M., Franke,L., Gogele,M., Hartiala,J.,
            Hersch,M., Holm,H., Hottenga,J.J., Kanoni,S., Kleber,M.E.,
            Lagou,V., Langenberg,C., Lopez,L.M., Lyytikainen,L.P., Melander,O.,
            Murgia,F., Nolte,I.M., O'Reilly,P.F., Padmanabhan,S., Parsa,A.,
            Pirastu,N., Porcu,E., Portas,L., Prokopenko,I., Ried,J.S.,
            Shin,S.Y., Tang,C.S., Teumer,A., Traglia,M., Ulivi,S., Westra,H.J.,
            Yang,J., Zhao,J.H., Anni,F., Abdellaoui,A., Attwood,A., Balkau,B.,
            Bandinelli,S., Bastardot,F., Benyamin,B., Boehm,B.O., Cookson,W.O.,
            Das,D., de Bakker,P.I., de Boer,R.A., de Geus,E.J., de Moor,M.H.,
            Dimitriou,M., Domingues,F.S., Doring,A., Engstrom,G.,
            Eyjolfsson,G.I., Ferrucci,L., Fischer,K., Galanello,R.,
            Garner,S.F., Genser,B., Gibson,Q.D., Girotto,G., Gudbjartsson,D.F.,
            Harris,S.E., Hartikainen,A.L., Hastie,C.E., Hedblad,B., Illig,T.,
            Jolley,J., Kahonen,M., Kema,I.P., Kemp,J.P., Liang,L.,
            Lloyd-Jones,H., Loos,R.J., Meacham,S., Medland,S.E., Meisinger,C.,
            Memari,Y., Mihailov,E., Miller,K., Moffatt,M.F., Nauck,M.,
            Novatchkova,M., Nutile,T., Olafsson,I., Onundarson,P.T.,
            Parracciani,D., Penninx,B.W., Perseu,L., Piga,A., Pistis,G.,
            Pouta,A., Puc,U., Raitakari,O., Ring,S.M., Robino,A., Ruggiero,D.,
            Ruokonen,A., Saint-Pierre,A., Sala,C., Salumets,A., Sambrook,J.,
            Schepers,H., Schmidt,C.O., Sillje,H.H., Sladek,R., Smit,J.H.,
            Starr,J.M., Stephens,J., Sulem,P., Tanaka,T., Thorsteinsdottir,U.,
            Tragante,V., van Gilst,W.H., van Pelt,L.J., van Veldhuisen,D.J.,
            Volker,U., Whitfield,J.B., Willemsen,G., Winkelmann,B.R.,
            Wirnsberger,G., Algra,A., Cucca,F., d'Adamo,A.P., Danesh,J.,
            Deary,I.J., Dominiczak,A.F., Elliott,P., Fortina,P., Froguel,P.,
            Gasparini,P., Greinacher,A., Hazen,S.L., Jarvelin,M.R., Khaw,K.T.,
            Lehtimaki,T., Maerz,W., Martin,N.G., Metspalu,A., Mitchell,B.D.,
            Montgomery,G.W., Moore,C., Navis,G., Pirastu,M., Pramstaller,P.P.,
            Ramirez-Solis,R., Schadt,E., Scott,J., Shuldiner,A.R., Smith,G.D.,
            Smith,J.G., Snieder,H., Sorice,R., Spector,T.D., Stefansson,K.,
            Stumvoll,M., Tang,W.H., Toniolo,D., Tonjes,A., Visscher,P.M.,
            Vollenweider,P., Wareham,N.J., Wolffenbuttel,B.H., Boomsma,D.I.,
            Beckmann,J.S., Dedoussis,G.V., Deloukas,P., Ferreira,M.A.,
            Sanna,S., Uda,M., Hicks,A.A., Penninger,J.M., Gieger,C.,
            Kooner,J.S., Ouwehand,W.H., Soranzo,N. and Chambers,J.C.
  TITLE     Seventy-five genetic loci influencing the human red blood cell
  JOURNAL   Nature 492 (7429), 369-375 (2012)
   PUBMED   23222517
REFERENCE   3  (bases 1 to 1309)
  AUTHORS   Jostins,L., Ripke,S., Weersma,R.K., Duerr,R.H., McGovern,D.P.,
            Hui,K.Y., Lee,J.C., Schumm,L.P., Sharma,Y., Anderson,C.A.,
            Essers,J., Mitrovic,M., Ning,K., Cleynen,I., Theatre,E.,
            Spain,S.L., Raychaudhuri,S., Goyette,P., Wei,Z., Abraham,C.,
            Achkar,J.P., Ahmad,T., Amininejad,L., Ananthakrishnan,A.N.,
            Andersen,V., Andrews,J.M., Baidoo,L., Balschun,T., Bampton,P.A.,
            Bitton,A., Boucher,G., Brand,S., Buning,C., Cohain,A., Cichon,S.,
            D'Amato,M., De Jong,D., Devaney,K.L., Dubinsky,M., Edwards,C.,
            Ellinghaus,D., Ferguson,L.R., Franchimont,D., Fransen,K.,
            Gearry,R., Georges,M., Gieger,C., Glas,J., Haritunians,T., Hart,A.,
            Hawkey,C., Hedl,M., Hu,X., Karlsen,T.H., Kupcinskas,L.,
            Kugathasan,S., Latiano,A., Laukens,D., Lawrance,I.C., Lees,C.W.,
            Louis,E., Mahy,G., Mansfield,J., Morgan,A.R., Mowat,C., Newman,W.,
            Palmieri,O., Ponsioen,C.Y., Potocnik,U., Prescott,N.J.,
            Regueiro,M., Rotter,J.I., Russell,R.K., Sanderson,J.D., Sans,M.,
            Satsangi,J., Schreiber,S., Simms,L.A., Sventoraityte,J.,
            Targan,S.R., Taylor,K.D., Tremelling,M., Verspaget,H.W., De Vos,M.,
            Wijmenga,C., Wilson,D.C., Winkelmann,J., Xavier,R.J., Zeissig,S.,
            Zhang,B., Zhang,C.K., Zhao,H., Silverberg,M.S., Annese,V.,
            Hakonarson,H., Brant,S.R., Radford-Smith,G., Mathew,C.G.,
            Rioux,J.D., Schadt,E.E., Daly,M.J., Franke,A., Parkes,M.,
            Vermeire,S., Barrett,J.C. and Cho,J.H.
  CONSRTM   International IBD Genetics Consortium (IIBDGC)
  TITLE     Host-microbe interactions have shaped the genetic architecture of
            inflammatory bowel disease
  JOURNAL   Nature 491 (7422), 119-124 (2012)
   PUBMED   23128233
REFERENCE   4  (bases 1 to 1309)
  AUTHORS   Zhernakova,A., Stahl,E.A., Trynka,G., Raychaudhuri,S., Festen,E.A.,
            Franke,L., Westra,H.J., Fehrmann,R.S., Kurreeman,F.A., Thomson,B.,
            Gupta,N., Romanos,J., McManus,R., Ryan,A.W., Turner,G., Brouwer,E.,
            Posthumus,M.D., Remmers,E.F., Tucci,F., Toes,R., Grandone,E.,
            Mazzilli,M.C., Rybak,A., Cukrowska,B., Coenen,M.J., Radstake,T.R.,
            van Riel,P.L., Li,Y., de Bakker,P.I., Gregersen,P.K.,
            Worthington,J., Siminovitch,K.A., Klareskog,L., Huizinga,T.W.,
            Wijmenga,C. and Plenge,R.M.
  TITLE     Meta-analysis of genome-wide association studies in celiac disease
            and rheumatoid arthritis identifies fourteen non-HLA shared loci
  JOURNAL   PLoS Genet 7 (2), e1002004 (2011)
   PUBMED   21383967
REFERENCE   5  (bases 1 to 1309)
  AUTHORS   Franke,A., McGovern,D.P., Barrett,J.C., Wang,K.,
            Radford-Smith,G.L., Ahmad,T., Lees,C.W., Balschun,T., Lee,J.,
            Roberts,R., Anderson,C.A., Bis,J.C., Bumpstead,S., Ellinghaus,D.,
            Festen,E.M., Georges,M., Green,T., Haritunians,T., Jostins,L.,
            Latiano,A., Mathew,C.G., Montgomery,G.W., Prescott,N.J.,
            Raychaudhuri,S., Rotter,J.I., Schumm,P., Sharma,Y., Simms,L.A.,
            Taylor,K.D., Whiteman,D., Wijmenga,C., Baldassano,R.N., Barclay,M.,
            Bayless,T.M., Brand,S., Buning,C., Cohen,A., Colombel,J.F.,
            Cottone,M., Stronati,L., Denson,T., De Vos,M., D'Inca,R.,
            Dubinsky,M., Edwards,C., Florin,T., Franchimont,D., Gearry,R.,
            Glas,J., Van Gossum,A., Guthery,S.L., Halfvarson,J.,
            Verspaget,H.W., Hugot,J.P., Karban,A., Laukens,D., Lawrance,I.,
            Lemann,M., Levine,A., Libioulle,C., Louis,E., Mowat,C., Newman,W.,
            Panes,J., Phillips,A., Proctor,D.D., Regueiro,M., Russell,R.,
            Rutgeerts,P., Sanderson,J., Sans,M., Seibold,F., Steinhart,A.H.,
            Stokkers,P.C., Torkvist,L., Kullak-Ublick,G., Wilson,D.,
            Walters,T., Targan,S.R., Brant,S.R., Rioux,J.D., D'Amato,M.,
            Weersma,R.K., Kugathasan,S., Griffiths,A.M., Mansfield,J.C.,
            Vermeire,S., Duerr,R.H., Silverberg,M.S., Satsangi,J.,
            Schreiber,S., Cho,J.H., Annese,V., Hakonarson,H., Daly,M.J. and
            Parkes,M.
  TITLE     Genome-wide meta-analysis increases to 71 the number of confirmed
            Crohn's disease susceptibility loci
  JOURNAL   Nat Genet 42 (12), 1118-1125 (2010)
   PUBMED   21102463
REFERENCE   6  (bases 1 to 1309)
  AUTHORS   Dubois,P.C., Trynka,G., Franke,L., Hunt,K.A., Romanos,J.,
            Curtotti,A., Zhernakova,A., Heap,G.A., Adany,R., Aromaa,A.,
            Bardella,M.T., van den Berg,L.H., Bockett,N.A., de la Concha,E.G.,
            Dema,B., Fehrmann,R.S., Fernandez-Arquero,M., Fiatal,S.,
            Grandone,E., Green,P.M., Groen,H.J., Gwilliam,R., Houwen,R.H.,
            Hunt,S.E., Kaukinen,K., Kelleher,D., Korponay-Szabo,I., Kurppa,K.,
            MacMathuna,P., Maki,M., Mazzilli,M.C., McCann,O.T., Mearin,M.L.,
            Mein,C.A., Mirza,M.M., Mistry,V., Mora,B., Morley,K.I.,
            Mulder,C.J., Murray,J.A., Nunez,C., Oosterom,E., Ophoff,R.A.,
            Polanco,I., Peltonen,L., Platteel,M., Rybak,A., Salomaa,V.,
            Schweizer,J.J., Sperandeo,M.P., Tack,G.J., Turner,G., Veldink,J.H.,
            Verbeek,W.H., Weersma,R.K., Wolters,V.M., Urcelay,E., Cukrowska,B.,
            Greco,L., Neuhausen,S.L., McManus,R., Barisani,D., Deloukas,P.,
            Barrett,J.C., Saavalainen,P., Wijmenga,C. and van Heel,D.A.
  TITLE     Multiple common variants for celiac disease influencing immune gene
            expression
  JOURNAL   Nat Genet 42 (4), 295-302 (2010)
   PUBMED   20190752
  REMARK    Erratum:[Nat Genet.2010 May;42(5):465]
REFERENCE   7  (bases 1 to 1309)
  AUTHORS   Imagawa,T., Iino,H., Kanagawa,M., Ebihara,A., Kuramitsu,S. and
            Tsuge,H.
  TITLE     Crystal structure of the YdjC-family protein TTHB029 from Thermus
            thermophilus HB8: structural relationship with peptidoglycan
            N-acetylglucosamine deacetylase
  JOURNAL   Biochem Biophys Res Commun 367 (3), 535-541 (2008)
   PUBMED   18177738
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BI597711.1, BC057814.1 and BQ050386.1.
            
            On Jul 9, 2019 this sequence version replaced NM_001017964.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR14038191.586320.1,
                                           SRR18074967.498106.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968540
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000292778.11/ ENSP00000292778.6
            RefSeq Select criteria :: based on conservation, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-332               BI597711.1         49-380
            333-1304            BC057814.1         413-1384
            1305-1309           BQ050386.1         303-307
FEATURES             Location/Qualifiers
     source          1..1309
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="22"
                     /map="22q11.21"
     gene            1..1309
                     /gene="YDJC"
                     /note="YdjC chitooligosaccharide deacetylase homolog"
                     /db_xref="GeneID:150223"
                     /db_xref="HGNC:HGNC:27158"
                     /db_xref="MIM:619770"
     exon            1..172
                     /gene="YDJC"
                     /inference="alignment:Splign:2.1.0"
     CDS             9..980
                     /gene="YDJC"
                     /note="isoform 1 is encoded by transcript variant 1;
                     UPF0249 protein ydjC homolog; carbohydrate deacetylase;
                     YdjC homolog"
                     /codon_start=1
                     /product="carbohydrate deacetylase isoform 1"
                     /protein_id="NP_001017964.1"
                     /db_xref="CCDS:CCDS33613.1"
                     /db_xref="GeneID:150223"
                     /db_xref="HGNC:HGNC:27158"
                     /db_xref="MIM:619770"
                     /translation="MSRPRMRLVVTADDFGYCPRRDEGIVEAFLAGAVTSVSLLVNGA
                     ATESAAELARRHSIPTGLHANLSEGRPVGPARRGASSLLGPEGFFLGKMGFREAVAAG
                     DVDLPQVREELEAQLSCFRELLGRAPTHADGHQHVHVLPGVCQVFAEALQAYGVRFTR
                     LPLERGVGGCTWLEAPARAFACAVERDARAAVGPFSRHGLRWTDAFVGLSTCGRHMSA
                     HRVSGALARVLEGTLAGHTLTAELMAHPGYPSVPPTGGCGEGPDAFSCSWERLHELRV
                     LTAPTLRAQLAQDGVQLCALDDLDSKRPGEEVPCEPTLEPFLEPSLL"
     exon            173..332
                     /gene="YDJC"
                     /inference="alignment:Splign:2.1.0"
     exon            333..432
                     /gene="YDJC"
                     /inference="alignment:Splign:2.1.0"
     exon            433..610
                     /gene="YDJC"
                     /inference="alignment:Splign:2.1.0"
     exon            611..1309
                     /gene="YDJC"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1285..1290
                     /regulatory_class="polyA_signal_sequence"
                     /gene="YDJC"
                     /note="hexamer: AATAAA"
     polyA_site      1309
                     /gene="YDJC"
                     /note="major polyA site"
ORIGIN      
        1 aggcggccat gtcccgccct cgcatgcgcc tggtggtcac cgcggacgac tttggttact
       61 gcccgcgacg cgatgagggt atcgtggagg cctttctggc cggggctgtg accagcgtgt
      121 ccctgctggt caacggtgcg gccacggaga gcgcggcgga gctggcccgc aggcacagca
      181 tccccacggg cctccacgcc aacctgtccg agggccgccc cgtgggtccg gcccgccgtg
      241 gcgcctcatc gctgctcggc ccggaaggct tcttccttgg caagatggga ttccgggagg
      301 cggtggcggc cggagacgtg gatttgcctc aggtgcggga ggagctcgag gcccaactaa
      361 gctgcttccg ggagctgctg ggcagggccc ccacgcacgc ggacgggcac cagcacgtgc
      421 acgtgctccc aggcgtgtgc caggtgttcg ccgaggcgct gcaggcctat ggggtgcgct
      481 ttacgcgact gccgctggag cgcggtgtgg gtggctgcac ttggctggag gcccccgcgc
      541 gtgccttcgc ctgcgccgtg gagcgcgacg cccgggccgc cgtgggcccc ttctcccgcc
      601 acggcctgcg gtggacagac gccttcgtgg gcctgagcac ttgcggccgg cacatgtccg
      661 ctcaccgcgt gtccggggcc ctggcgcggg tcctggaagg taccctagcg ggccacaccc
      721 tgacagccga gctgatggcg caccccggct accccagtgt gcctcccacc ggcggctgcg
      781 gtgaaggccc cgacgctttc tcttgctctt gggagcggct gcatgagctg cgcgtcctca
      841 ccgcgcccac gctgcgggcc cagcttgccc aggatggcgt gcagctttgc gccctcgacg
      901 acctggactc caagaggcca ggggaggagg tcccctgtga gcccactctg gaacccttcc
      961 tggaaccctc cctactctga ccccctacag acaaccaagc actaatcccc ttagtaccaa
     1021 gaaaggggag ccaggattta gtcctggccc agcccagagc tgggacctgg agcacgatct
     1081 gttgacttcc ctgggtagga cactgccacc tctgggctca ggtcctcatg cctccaaatg
     1141 gcatctagag tttgagcagc cttcttggct gcaggcaggc ctagcctgtg gcagcgggct
     1201 agggcccgca gagcatttgg tgcccctcca tgttgcaatg caaacacctt caccactggg
     1261 gcagtgggga gagatggcta tattaataaa ataacgtgtg tctttcaaa
//
