LOCUS       NM_001415040            3604 bp    mRNA    linear   ROD 03-APR-2024
DEFINITION  Rattus norvegicus coiled-coil domain 39 molecular ruler complex
            subunit (Ccdc39), mRNA.
ACCESSION   NM_001415040 XM_017590855
VERSION     NM_001415040.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 3604)
  AUTHORS   Emmert,A.S., Iwasawa,E., Shula,C., Schultz,P., Lindquist,D.,
            Dunn,R.S., Fugate,E.M., Hu,Y.C., Mangano,F.T. and Goto,J.
  TITLE     Impaired neural differentiation and glymphatic CSF flow in the
            Ccdc39 rat model of neonatal hydrocephalus: genetic interaction
            with L1cam
  JOURNAL   Dis Model Mech 12 (11) (2019)
   PUBMED   31771992
  REMARK    GeneRIF: in Ccdc39(prh/prh) mutant rats demonstrate a possible
            causal role of neuroinflammation in neonatal hydrocephalus
            development, which involves impaired cortical development and
            glymphatic CSF flow.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3604)
  AUTHORS   Abdelhamed,Z., Vuong,S.M., Hill,L., Shula,C., Timms,A., Beier,D.,
            Campbell,K., Mangano,F.T., Stottmann,R.W. and Goto,J.
  TITLE     A mutation in Ccdc39 causes neonatal hydrocephalus with abnormal
            motile cilia development in mice
  JOURNAL   Development 145 (1) (2018)
   PUBMED   29317443
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3604)
  AUTHORS   Solomon,G.M., Francis,R., Chu,K.K., Birket,S.E., Gabriel,G.,
            Trombley,J.E., Lemke,K.L., Klena,N., Turner,B., Tearney,G.J.,
            Lo,C.W. and Rowe,S.M.
  TITLE     Assessment of ciliary phenotype in primary ciliary dyskinesia by
            micro-optical coherence tomography
  JOURNAL   JCI Insight 2 (5), e91702 (2017)
   PUBMED   28289722
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3604)
  AUTHORS   Jeanson,L., Thomas,L., Copin,B., Coste,A., Sermet-Gaudelus,I.,
            Dastot-Le Moal,F., Duquesnoy,P., Montantin,G., Collot,N.,
            Tissier,S., Papon,J.F., Clement,A., Louis,B., Escudier,E.,
            Amselem,S. and Legendre,M.
  TITLE     Mutations in GAS8, a Gene Encoding a Nexin-Dynein Regulatory
            Complex Subunit, Cause Primary Ciliary Dyskinesia with Axonemal
            Disorganization
  JOURNAL   Hum Mutat 37 (8), 776-785 (2016)
   PUBMED   27120127
REFERENCE   5  (bases 1 to 3604)
  AUTHORS   Olbrich,H., Cremers,C., Loges,N.T., Werner,C., Nielsen,K.G.,
            Marthin,J.K., Philipsen,M., Wallmeier,J., Pennekamp,P., Menchen,T.,
            Edelbusch,C., Dougherty,G.W., Schwartz,O., Thiele,H., Altmuller,J.,
            Rommelmann,F. and Omran,H.
  TITLE     Loss-of-Function GAS8 Mutations Cause Primary Ciliary Dyskinesia
            and Disrupt the Nexin-Dynein Regulatory Complex
  JOURNAL   Am J Hum Genet 97 (4), 546-554 (2015)
   PUBMED   26387594
REFERENCE   6  (bases 1 to 3604)
  AUTHORS   Blanchon,S., Legendre,M., Copin,B., Duquesnoy,P., Montantin,G.,
            Kott,E., Dastot,F., Jeanson,L., Cachanado,M., Rousseau,A.,
            Papon,J.F., Beydon,N., Brouard,J., Crestani,B., Deschildre,A.,
            Desir,J., Dollfus,H., Leheup,B., Tamalet,A., Thumerelle,C.,
            Vojtek,A.M., Escalier,D., Coste,A., de Blic,J., Clement,A.,
            Escudier,E. and Amselem,S.
  TITLE     Delineation of CCDC39/CCDC40 mutation spectrum and associated
            phenotypes in primary ciliary dyskinesia
  JOURNAL   J Med Genet 49 (6), 410-416 (2012)
   PUBMED   22693285
REFERENCE   7  (bases 1 to 3604)
  AUTHORS   Nakhleh,N., Francis,R., Giese,R.A., Tian,X., Li,Y., Zariwala,M.A.,
            Yagi,H., Khalifa,O., Kureshi,S., Chatterjee,B., Sabol,S.L.,
            Swisher,M., Connelly,P.S., Daniels,M.P., Srinivasan,A., Kuehl,K.,
            Kravitz,N., Burns,K., Sami,I., Omran,H., Barmada,M., Olivier,K.,
            Chawla,K.K., Leigh,M., Jonas,R., Knowles,M., Leatherbury,L. and
            Lo,C.W.
  TITLE     High prevalence of respiratory ciliary dysfunction in congenital
            heart disease patients with heterotaxy
  JOURNAL   Circulation 125 (18), 2232-2242 (2012)
   PUBMED   22499950
REFERENCE   8  (bases 1 to 3604)
  AUTHORS   Stottmann,R.W., Moran,J.L., Turbe-Doan,A., Driver,E., Kelley,M. and
            Beier,D.R.
  TITLE     Focusing forward genetics: a tripartite ENU screen for
            neurodevelopmental mutations in the mouse
  JOURNAL   Genetics 188 (3), 615-624 (2011)
   PUBMED   21515572
REFERENCE   9  (bases 1 to 3604)
  AUTHORS   Becker-Heck,A., Zohn,I.E., Okabe,N., Pollock,A., Lenhart,K.B.,
            Sullivan-Brown,J., McSheene,J., Loges,N.T., Olbrich,H.,
            Haeffner,K., Fliegauf,M., Horvath,J., Reinhardt,R., Nielsen,K.G.,
            Marthin,J.K., Baktai,G., Anderson,K.V., Geisler,R., Niswander,L.,
            Omran,H. and Burdine,R.D.
  TITLE     The coiled-coil domain containing protein CCDC40 is essential for
            motile cilia function and left-right axis formation
  JOURNAL   Nat Genet 43 (1), 79-84 (2011)
   PUBMED   21131974
REFERENCE   10 (bases 1 to 3604)
  AUTHORS   Merveille,A.C., Davis,E.E., Becker-Heck,A., Legendre,M., Amirav,I.,
            Bataille,G., Belmont,J., Beydon,N., Billen,F., Clement,A.,
            Clercx,C., Coste,A., Crosbie,R., de Blic,J., Deleuze,S.,
            Duquesnoy,P., Escalier,D., Escudier,E., Fliegauf,M., Horvath,J.,
            Hill,K., Jorissen,M., Just,J., Kispert,A., Lathrop,M., Loges,N.T.,
            Marthin,J.K., Momozawa,Y., Montantin,G., Nielsen,K.G., Olbrich,H.,
            Papon,J.F., Rayet,I., Roger,G., Schmidts,M., Tenreiro,H.,
            Towbin,J.A., Zelenika,D., Zentgraf,H., Georges,M., Lequarre,A.S.,
            Katsanis,N., Omran,H. and Amselem,S.
  TITLE     CCDC39 is required for assembly of inner dynein arms and the dynein
            regulatory complex and for normal ciliary motility in humans and
            dogs
  JOURNAL   Nat Genet 43 (1), 72-78 (2011)
   PUBMED   21131972
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000002.1.
            
            On Dec 20, 2022 this sequence version replaced XM_017590855.2.
            
            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 :: SRR26643293.11499.1,
                                           SRR26643429.7807.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760389 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-205               JAXUCZ010000002.1  118631380-118631584 c
            206-325             JAXUCZ010000002.1  118628272-118628391 c
            326-472             JAXUCZ010000002.1  118626121-118626267 c
            473-631             JAXUCZ010000002.1  118624822-118624980 c
            632-724             JAXUCZ010000002.1  118623774-118623866 c
            725-853             JAXUCZ010000002.1  118623554-118623682 c
            854-1045            JAXUCZ010000002.1  118620661-118620852 c
            1046-1149           JAXUCZ010000002.1  118618494-118618597 c
            1150-1282           JAXUCZ010000002.1  118617015-118617147 c
            1283-1477           JAXUCZ010000002.1  118613168-118613362 c
            1478-1642           JAXUCZ010000002.1  118612181-118612345 c
            1643-1780           JAXUCZ010000002.1  118610054-118610191 c
            1781-1989           JAXUCZ010000002.1  118608178-118608386 c
            1990-2113           JAXUCZ010000002.1  118599742-118599865 c
            2114-2273           JAXUCZ010000002.1  118597398-118597557 c
            2274-2380           JAXUCZ010000002.1  118596921-118597027 c
            2381-2521           JAXUCZ010000002.1  118596130-118596270 c
            2522-2698           JAXUCZ010000002.1  118595828-118596004 c
            2699-2772           JAXUCZ010000002.1  118595680-118595753 c
            2773-3604           JAXUCZ010000002.1  118593881-118594712 c
FEATURES             Location/Qualifiers
     source          1..3604
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="2"
                     /map="2q24"
     gene            1..3604
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /note="coiled-coil domain 39 molecular ruler complex
                     subunit"
                     /db_xref="GeneID:310315"
                     /db_xref="RGD:1306277"
     exon            1..205
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     CDS             116..2920
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /note="coiled-coil domain containing 39"
                     /codon_start=1
                     /product="coiled-coil domain-containing protein 39"
                     /protein_id="NP_001401969.1"
                     /db_xref="GeneID:310315"
                     /db_xref="RGD:1306277"
                     /translation="MSSEFLSELHWEDGFAIPVANQENKILEDQLAKLHKEKSNLQDQ
                     LRDYEDRINSMSSHLKNVNQEFLFTQSLYKARECEIESEEHFKAIAERELGRVKDEIQ
                     QLEKEMAIILERKNDKENAIFKATQKLDGLKCQMNWDQQALEAWLEESAHKDSDSLTL
                     QKYSQQDNNKIRALTLKLEKLTMECNEKRKLLDNELTETLSAQLELDKAAQDFRKIHV
                     ERQELIQQWENTIEQMQRRDQEIDNCALALARIKQEAREKEGVVREKIKFLENEVGNN
                     VEYERRISIAERKVSKCRMEYQRQEANRNQLKDELDTLKTTLNRTSSDLEALRKNISK
                     VKKDILDETGRLQKLKHHNEIVKHKLKMITEKTISIEEKATNMEDMLKEEEKNLKEVE
                     VQLNIVKGVLFKKVQELQSAITKEKALGSEIEGTRSSLKHLNQRLHKLDFETLKQQEI
                     MYSQDFYIQQVERRMSRLKGEINSEEKQALEVKIVELRKTMEERKSTLSLLEEQIKKL
                     HNDLYFIKKSNGKNKDEKESLMNKIGELHLFVDRSEKELNKAKAVKEDLMIEDNLLKL
                     QVKRARELLYSKAEEVLSLEKRKQQLCTAMEERVEEIKVHKAMLTSQIRYVDQQRQTV
                     SSEFHERLSKIDKLKNRYEILTVVMLPPEGEEEKTQSYYVIKAAQEKEELQREGDSLD
                     AKISKAEKEIYALQNTLQVLSSCNNNYKQSFKKVTPSSDEYGIKIQLEEQKRSADEKY
                     RCKQRQIRELQEDIQSMENTFEVIEHLANNAREKLSEKQTLSFQLRKETEEQKPKIQR
                     VTKQCGRLRREIRILRQTNDETLEEQDIQLREIIQFHKDIDQMLVNAMENAEIHVIFQ
                     TYFQQNGLELPTAKGPSSRSSSQSSLSSIRSLEDSIPISPPTAKVIELRFPGPPARSD
                     SSRSSSGSNSNIPKGKKLNK"
     exon            206..325
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            326..472
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            473..631
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            632..724
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            725..853
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            854..1045
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            1046..1149
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            1150..1282
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            1283..1477
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            1478..1642
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            1643..1780
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            1781..1989
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            1990..2113
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            2114..2273
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            2274..2380
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            2381..2521
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            2522..2698
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            2699..2772
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
     exon            2773..3604
                     /gene="Ccdc39"
                     /gene_synonym="RGD1306277"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gcctggctgt tgctagggcc gcggaataca gtccggtagg ctctgcagac tccggctgcg
       61 agcttctggg aacggtttgg gggacttggc tgtgctccct tcgagcccgt gcaccatgag
      121 cagtgagttc ctgtcagaac tgcactggga agatgggttc gccattcccg tggccaatca
      181 ggagaacaag atcctggagg accagttagc aaaactacac aaagaaaaat caaacttgca
      241 agatcagctt cgcgactatg aagatcgaat taattctatg tcttctcacc ttaaaaatgt
      301 caatcaagag tttttattta cacagtctct ttacaaagca agggagtgtg aaatcgaaag
      361 tgaagaacat tttaaggcca ttgctgaaag agagctggga cgagtcaagg atgagatcca
      421 acagctggag aaggagatgg ccatcatcct cgagcgcaag aacgacaagg aaaatgctat
      481 atttaaagct actcaaaagc tggatggctt gaaatgtcag atgaactggg accagcaagc
      541 actggaagcc tggctagaag agtctgctca caaagacagc gactcgctca cccttcagaa
      601 gtactctcag caagacaata acaagatcag ggccctgact ctgaagttag aaaagctgac
      661 catggagtgt aatgagaaga ggaagcttct agacaatgaa ctcacggaga cgctaagtgc
      721 gcagttagaa ttagataaag ctgcacagga tttccggaag atccacgtag aacgacagga
      781 gctcattcag cagtgggaga acaccattga gcagatgcag aggcgggatc aggagataga
      841 caactgcgct ctggcattag cacggataaa gcaggaagca agagaaaaag aaggtgtggt
      901 gagagagaag atcaagtttc tggagaatga ggttgggaac aacgtagagt atgaacgaag
      961 aatttctatt gctgagcgta aagtgtcaaa gtgcaggatg gagtaccagc gacaggaagc
     1021 caacagaaat cagctgaagg atgagctgga tactttaaaa accactctca atagaacatc
     1081 cagtgattta gaagctctga ggaaaaacat ttccaaagta aagaaggaca tccttgatga
     1141 aacaggaaga ttacaaaaac tcaaacatca caatgagatt gtaaaacata aattaaagat
     1201 gataactgag aagaccatat ccattgaaga gaaagctacc aacatggaag acatgctgaa
     1261 ggaggaggag aaaaatttga aggaagtgga ggttcaattg aacatagtaa aaggtgtgct
     1321 atttaagaaa gtccaagagt tacagagtgc gataacaaaa gagaaagctc tgggatcaga
     1381 aattgaagga acccgttctt ccttgaaaca tcttaaccaa cggttacaca aactggactt
     1441 tgaaaccctg aagcagcagg aaattatgta cagtcaggat ttttacatcc agcaagtaga
     1501 acgcagaatg tcacgattaa aaggagaaat taattcagag gaaaagcaag cccttgaagt
     1561 aaaaatcgtt gaacttagga agacaatgga agagagaaaa tctacacttt cccttttgga
     1621 agaacagatc aagaagctcc ataatgacct ctacttcatt aagaagtcaa atggtaaaaa
     1681 caaagatgag aaagagtctc tcatgaataa aataggtgaa ctgcaccttt tcgttgatag
     1741 atccgagaag gaactgaaca aagccaaagc tgtgaaagag gatttgatga ttgaggacaa
     1801 tcttttaaag cttcaagtta aacgtgctcg agaactgctt tatagcaaag cagaggaagt
     1861 cctttctctg gagaaaagga aacagcagct gtgcacagcc atggaagaga gagttgaaga
     1921 aattaaagtg cacaaagcca tgcttacctc acagatcaga tatgttgacc agcagcgaca
     1981 aactgtgagt tctgaatttc atgagcggct aagtaaaatt gataagctta agaacagata
     2041 tgaaattctt actgttgtca tgctgcctcc tgagggagaa gaggagaaaa cacagtccta
     2101 ttatgtaata aaggctgctc aagaaaaaga agaacttcaa agggaaggtg acagcttgga
     2161 cgctaagatc agcaaagctg aaaaagaaat ctatgctctg cagaacacct tgcaagttct
     2221 gagcagctgc aacaacaatt acaagcaatc tttcaaaaaa gtgacgccgt caagtgatga
     2281 gtacggaata aaaattcaac tagaagaaca aaaaagaagc gcagatgaga aatacagatg
     2341 caaacaaaga caaatcagag aacttcaaga agatatccag agcatggaga atacttttga
     2401 agttatagaa cacttagcaa ataatgccag agagaaatta tcagagaagc aaaccctctc
     2461 atttcaactt cgtaaggaga ctgaagagca gaagccgaaa atacagcgag taactaagca
     2521 gtgtggaaga ctcagaagag aaatccgcat tttgagacaa acaaatgatg aaactctaga
     2581 agaacaagac attcagctcc gtgaaatcat acagtttcac aaggacattg accaaatgct
     2641 agttaatgcc atggaaaatg cagaaattca tgtcatcttt caaacatatt ttcagcagaa
     2701 tgggttagaa ctacctacag caaaaggccc aagctcaaga tcgtcttccc agtcctcact
     2761 ttcctcaatc aggtcgctgg aggactcaat tcccatctct ccacccacag ctaaagtgat
     2821 agagctcaga ttcccaggac ctccggcaag aagtgatagt tctaggtcta gtagtggcag
     2881 caattccaac atccctaaag gaaaaaagct caacaaataa acattttttt ttttttatct
     2941 tctgtacaaa ttttgaagac aaacgaaaac cttattaata gttaagtctc cctctttttc
     3001 tggggttcca tttattaacg atacaggcta ctaaaatagt accagaagta caaaccagac
     3061 aaaagttctg catggtggct ataaaagctg tttgaaaaaa gaacaaaggt agatttttgt
     3121 ttgttttttt ttttctactg ttttatttat agagaaggaa aactgcagaa ccttagccaa
     3181 gccacacgtg acaaagcaga gggaaatcag tttttttttc actagaacat gtctatagtg
     3241 ttaatgtttt atgaagtaac acgtttataa gattctttca ctaatacact tctaaagatt
     3301 cattctatag ctcaataagg aagtttccat ttactctaga tcacaaaatt actttttaaa
     3361 ataaaaaaca aaaagcaaac aaccgtattc ttcagatctt ttttgggggt tgggtgggca
     3421 tgagggagga ccctggtaaa ggccagtttt ttgtttgttt gtactggtta taatctgtaa
     3481 ccaaaggaca gcatcattcc cactccctca agaaaaagtt tagtaaaaaa gacactgtat
     3541 atgtgtgtat acacatacat ttatctctat atatgcacaa ataaagtgca acttaagctc
     3601 ataa
//
