CCD40_MOUSE
ID CCD40_MOUSE Reviewed; 1192 AA.
AC Q8BI79; A2AFL0; Q5U4C0; Q8BI59;
DT 02-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Coiled-coil domain-containing protein 40 {ECO:0000305};
DE AltName: Full=Protein links {ECO:0000303|PubMed:21131972};
GN Name=Ccdc40 {ECO:0000312|MGI:MGI:2443893};
GN Synonyms=Lnks {ECO:0000303|PubMed:21131972};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
RC STRAIN=C57BL/6J; TISSUE=Cerebellum, and Oviduct;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=C57BL/6J; TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-306, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Lung, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [5]
RP SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=21131972; DOI=10.1038/ng.726;
RA Merveille A.C., Davis E.E., Becker-Heck A., Legendre M., Amirav I.,
RA Bataille G., Belmont J., Beydon N., Billen F., Clement A., Clercx C.,
RA Coste A., Crosbie R., de Blic J., Deleuze S., Duquesnoy P., Escalier D.,
RA Escudier E., Fliegauf M., Horvath J., Hill K., Jorissen M., Just J.,
RA Kispert A., Lathrop M., Loges N.T., Marthin J.K., Momozawa Y.,
RA Montantin G., Nielsen K.G., Olbrich H., Papon J.F., Rayet I., Roger G.,
RA Schmidts M., Tenreiro H., Towbin J.A., Zelenika D., Zentgraf H.,
RA Georges M., Lequarre A.S., Katsanis N., Omran H., Amselem S.;
RT "CCDC39 is required for assembly of inner dynein arms and the dynein
RT regulatory complex and for normal ciliary motility in humans and dogs.";
RL Nat. Genet. 43:72-78(2011).
CC -!- FUNCTION: Required for assembly of dynein regulatory complex (DRC) and
CC inner dynein arm (IDA) complexes, which are responsible for ciliary
CC beat regulation, thereby playing a central role in motility in cilia
CC and flagella. Probably acts together with CCDC39 to form a molecular
CC ruler that determines the 96 nanometer (nm) repeat length and
CC arrangements of components in cilia and flagella. Not required for
CC outer dynein arm complexes assembly. Required for axonemal recruitment
CC of CCDC39. {ECO:0000250|UniProtKB:A8IQT2,
CC ECO:0000250|UniProtKB:Q4G0X9}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:21131972}. Cell
CC projection, cilium {ECO:0000269|PubMed:21131972}. Note=Localizes to
CC cytoplasm and motile cilium. {ECO:0000269|PubMed:21131972}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q8BI79-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8BI79-2; Sequence=VSP_028310, VSP_028312;
CC Name=3;
CC IsoId=Q8BI79-3; Sequence=VSP_028311, VSP_028313, VSP_028314;
CC -!- TISSUE SPECIFICITY: Specifically expressed in the embryonic node and
CC midline. {ECO:0000269|PubMed:21131972}.
CC -!- DISRUPTION PHENOTYPE: Defects are the cause of the lnks phenotype, a
CC phenotype related to primary ciliary dyskinesia (PCD). PCD is
CC characterized by recurrent respiratory infections, situs inversus and
CC ciliary immotility and hydrocephalus. The length of the cilia
CC projecting from the nodal pit cells in mutants is drastically reduced.
CC {ECO:0000269|PubMed:21131972}.
CC -!- SIMILARITY: Belongs to the CCDC40 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH85159.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AK046971; BAC32932.1; -; mRNA.
DR EMBL; AK054172; BAC35680.1; -; mRNA.
DR EMBL; AL672140; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC085159; AAH85159.1; ALT_INIT; mRNA.
DR RefSeq; NP_780639.1; NM_175430.4.
DR AlphaFoldDB; Q8BI79; -.
DR SMR; Q8BI79; -.
DR STRING; 10090.ENSMUSP00000039463; -.
DR iPTMnet; Q8BI79; -.
DR PhosphoSitePlus; Q8BI79; -.
DR MaxQB; Q8BI79; -.
DR PaxDb; Q8BI79; -.
DR PRIDE; Q8BI79; -.
DR ProteomicsDB; 283729; -. [Q8BI79-1]
DR ProteomicsDB; 283730; -. [Q8BI79-2]
DR ProteomicsDB; 283731; -. [Q8BI79-3]
DR Antibodypedia; 9999; 55 antibodies from 15 providers.
DR Ensembl; ENSMUST00000053440; ENSMUSP00000062198; ENSMUSG00000039963. [Q8BI79-3]
DR UCSC; uc007mqc.1; mouse. [Q8BI79-1]
DR UCSC; uc007mqe.1; mouse. [Q8BI79-3]
DR MGI; MGI:2443893; Ccdc40.
DR VEuPathDB; HostDB:ENSMUSG00000039963; -.
DR eggNOG; ENOG502QQ91; Eukaryota.
DR GeneTree; ENSGT00440000035688; -.
DR HOGENOM; CLU_008826_0_0_1; -.
DR InParanoid; Q8BI79; -.
DR OrthoDB; 323186at2759; -.
DR PhylomeDB; Q8BI79; -.
DR TreeFam; TF325559; -.
DR BioGRID-ORCS; 207607; 5 hits in 74 CRISPR screens.
DR ChiTaRS; Ccdc40; mouse.
DR PRO; PR:Q8BI79; -.
DR Proteomes; UP000000589; Chromosome 11.
DR RNAct; Q8BI79; protein.
DR Bgee; ENSMUSG00000039963; Expressed in ventricular system choroidal fissure and 90 other tissues.
DR ExpressionAtlas; Q8BI79; baseline and differential.
DR Genevisible; Q8BI79; MM.
DR GO; GO:0005930; C:axoneme; ISO:MGI.
DR GO; GO:0005929; C:cilium; IDA:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005576; C:extracellular region; IEA:GOC.
DR GO; GO:0031514; C:motile cilium; IDA:MGI.
DR GO; GO:0070286; P:axonemal dynein complex assembly; ISS:UniProtKB.
DR GO; GO:0035082; P:axoneme assembly; IMP:MGI.
DR GO; GO:0003341; P:cilium movement; IMP:UniProtKB.
DR GO; GO:0071907; P:determination of digestive tract left/right asymmetry; ISO:MGI.
DR GO; GO:0007368; P:determination of left/right symmetry; IGI:MGI.
DR GO; GO:0071910; P:determination of liver left/right asymmetry; ISO:MGI.
DR GO; GO:0035469; P:determination of pancreatic left/right asymmetry; ISO:MGI.
DR GO; GO:0060287; P:epithelial cilium movement involved in determination of left/right asymmetry; IMP:UniProtKB.
DR GO; GO:0003351; P:epithelial cilium movement involved in extracellular fluid movement; ISO:MGI.
DR GO; GO:0030317; P:flagellated sperm motility; ISO:MGI.
DR GO; GO:0001947; P:heart looping; ISO:MGI.
DR GO; GO:0036159; P:inner dynein arm assembly; ISO:MGI.
DR GO; GO:0030324; P:lung development; IMP:BHF-UCL.
DR GO; GO:0044458; P:motile cilium assembly; ISO:MGI.
DR GO; GO:0061512; P:protein localization to cilium; IMP:MGI.
DR GO; GO:0003356; P:regulation of cilium beat frequency; ISO:MGI.
DR InterPro; IPR037386; CCDC40.
DR PANTHER; PTHR16275; PTHR16275; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell projection; Ciliopathy; Cilium; Coiled coil;
KW Cytoplasm; Phosphoprotein; Primary ciliary dyskinesia; Reference proteome.
FT CHAIN 1..1192
FT /note="Coiled-coil domain-containing protein 40"
FT /id="PRO_0000305251"
FT REGION 1..78
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 126..153
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 173..196
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 211..246
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 261..289
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 308..369
FT /evidence="ECO:0000255"
FT COILED 425..451
FT /evidence="ECO:0000255"
FT COILED 581..649
FT /evidence="ECO:0000255"
FT COILED 733..768
FT /evidence="ECO:0000255"
FT COILED 830..871
FT /evidence="ECO:0000255"
FT COILED 919..972
FT /evidence="ECO:0000255"
FT COILED 1044..1118
FT /evidence="ECO:0000255"
FT COMPBIAS 54..68
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 306
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT VAR_SEQ 1
FT /note="M -> MAEPEDQADGRSQQEGQQSSAEEDSEQQYTEGPEVSPQLEDNGQEID
FT EGRDPTRSPEEDITTEGGGGSEGEM (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_028310"
FT VAR_SEQ 1
FT /note="M -> MAEPEDQADGSQQEGQQSSAEEDSEQQYTEGPEVSPQLEDNGQEIDE
FT GRDPTRSPEEDITTEGGGGSEGEM (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_028311"
FT VAR_SEQ 744..810
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_028312"
FT VAR_SEQ 1058..1067
FT /note="ATDDCTNTIS -> FIFSLLRVCG (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_028313"
FT VAR_SEQ 1068..1192
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_028314"
FT CONFLICT 88
FT /note="E -> K (in Ref. 3; AAH85159)"
FT /evidence="ECO:0000305"
FT CONFLICT 292
FT /note="E -> K (in Ref. 1; BAC35680)"
FT /evidence="ECO:0000305"
FT CONFLICT 803
FT /note="E -> Q (in Ref. 1; BAC35680)"
FT /evidence="ECO:0000305"
FT CONFLICT 845
FT /note="L -> M (in Ref. 1; BAC35680)"
FT /evidence="ECO:0000305"
FT CONFLICT 866
FT /note="E -> Q (in Ref. 1; BAC35680)"
FT /evidence="ECO:0000305"
FT CONFLICT 884
FT /note="R -> G (in Ref. 1; BAC35680)"
FT /evidence="ECO:0000305"
FT CONFLICT 940
FT /note="S -> A (in Ref. 3; AAH85159)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1192 AA; 136772 MW; A3BBC5ABA0183A3A CRC64;
MMDAEKVSTD GEAISEGEVG SNGETPPETE VEFIGETAPD TDVEFIGETS PGTDVEPTGE
SIQETEVESI GEATPGMDVE PIKKTMTELN VESIGEETSE TDVDSIRKAL RGIDLESITV
AYPPKKAKHR KVRPQAEVES TGRAAPEGEL EVSDHEKVEA LLDELDELSE IVSSPEVSYS
DISPLEMGED DTNVSATSTD TFQQGIYEPI EPIEPTEPPE PAEPPKPAET PEDSTVRAPA
HPYQRDFPMG ARHRFRLSIM GSLTPSDTDD LPLETDEPPQ QESVQSTPRA LEETRIQFLD
QVQSLSPEAL LDRATEGSDE AEEEGSQLIV LDPDHPLMIR FQEALKGYLN RQMDKLKLDV
QELDVATKQT RSQRQELGVN LYGVQQHLAR LQMQLEKSHD RHSLVACERR RKEEELQCAR
SVYNKTCQTA NEERKKLAAL QTEVESLALH LFYMQNIEQD VRDDIQVMKQ VVRKTETEKM
HAEVEKKKQD LFVDQLTERS HQLEENIALF EAQYLSQAED TRVLKKAVTE AITEIDTIAV
EKKRILQQWT TSLVGMKHRN EAYKTVMDAL RECQHQVKST DSEIEVCKKS IMQEEEKNEK
LARLLNRAET EATLVQKMTA QCLSKQEALQ TEFNTYQLAL QDTEEMLNKG YVEHSAVLSE
LQATRQAFHQ EQELRQKMDM SMVDKLQEQG TSSKMTKYFH QLLRKLQKEN TNLVTHLSKI
DGDIAQATLD ITNTNCKIDM HKKTLAEMDK EVKRFNDLIT NSESEIARRT ILIERKQSLI
NFFNKQLEQM VSELGGEEAG PLELEIKRLS KLTEEYNTGV AEAQMTWLRL QQELVQVTHE
REEQLVSVDQ LKKEVHIMEQ KKLRIESKIA HEKKEQKIVS RHMRDLDNDL SKLNMLLDKN
RCSSEELEQN NIATETEFLR TLKDSERETI QMQEKLMELS EEKATLLNSF MEAEHQIMLW
EKKIQLAKEM RSSVDSETGQ TEIRAMKAEI HRMKVRHGQL LKQQEKMIRD MELAVARRET
IVVQAEGQSK IDKKVITKTE FHYQQRELQK KVREMHKATD DCTNTISELE ETQKFLSSSL
QEKQQLLSEM QATTDVLEEE INQLTALKRQ NLLEIVTLQT RGKHLQAAIE GKYVFLHRNS
RSQLMERKRL SVRLSQLNKV LSSVQEDYPQ YQEVLQSIQQ KIATKLETPE PS
