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Protein

Coiled-coil domain-containing protein 39

Gene

CCDC39

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella (PubMed:21131972). Probably acts together with CCDC40 to form a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella (By similarity). Not required for outer dynein arm complexes assembly (PubMed:21131972).By similarity1 Publication

GO - Biological processi

  1. axonemal dynein complex assembly Source: UniProtKB
  2. cilium-dependent cell motility Source: UniProtKB
  3. determination of digestive tract left/right asymmetry Source: BHF-UCL
  4. determination of liver left/right asymmetry Source: BHF-UCL
  5. determination of pancreatic left/right asymmetry Source: BHF-UCL
  6. epithelial cilium movement involved in determination of left/right asymmetry Source: UniProtKB
  7. heart looping Source: BHF-UCL
  8. lung development Source: BHF-UCL
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Coiled-coil domain-containing protein 39Curated
Gene namesi
Name:CCDC39Imported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:25244. CCDC39.

Subcellular locationi

  1. Cytoplasmcytoskeletoncilium axoneme 2 Publications

  2. Note: CCDC40 is required for localization to axonemes.1 Publication

GO - Cellular componenti

  1. axoneme Source: UniProtKB
  2. cytoskeleton Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cell projection, Cilium, Cytoplasm, Cytoskeleton

Pathology & Biotechi

Involvement in diseasei

Ciliary dyskinesia, primary, 14 (CILD14)4 Publications

The disease is caused by mutations affecting the gene represented in this entry. The disease is characterized by primary ciliary dyskinesia with inner dynein arm (IDA) defects and axonemal dizorganisation: defects in CCDC39 and CCDC40 constitute the major cause of this phenotype.

Disease descriptionA disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome.

See also OMIM:613807
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti594 – 5941T → I in a patient with CILD14; unknown pathological significance. 1 Publication
VAR_072468

Keywords - Diseasei

Ciliopathy, Primary ciliary dyskinesia

Organism-specific databases

MIMi613807. phenotype.
Orphaneti244. Primary ciliary dyskinesia.
PharmGKBiPA142672194.

Polymorphism and mutation databases

BioMutaiCCDC39.
DMDMi296439421.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 941941Coiled-coil domain-containing protein 39PRO_0000234493Add
BLAST

Proteomic databases

PaxDbiQ9UFE4.
PRIDEiQ9UFE4.

PTM databases

PhosphoSiteiQ9UFE4.

Expressioni

Tissue specificityi

Mainly expressed in nasal brushings and, to a lesser extent, in lungs and testis.1 Publication

Gene expression databases

BgeeiQ9UFE4.
CleanExiHS_CCDC39.
ExpressionAtlasiQ9UFE4. baseline and differential.
GenevestigatoriQ9UFE4.

Organism-specific databases

HPAiHPA035363.
HPA035364.

Interactioni

Protein-protein interaction databases

BioGridi130945. 2 interactions.
STRINGi9606.ENSP00000405708.

Structurei

3D structure databases

ProteinModelPortaliQ9UFE4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili16 – 122107Sequence AnalysisAdd
BLAST
Coiled coili164 – 273110Sequence AnalysisAdd
BLAST
Coiled coili306 – 605300Sequence AnalysisAdd
BLAST
Coiled coili665 – 825161Sequence AnalysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi871 – 94070Ser-richAdd
BLAST

Sequence similaritiesi

Belongs to the CCDC39 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiNOG117406.
GeneTreeiENSGT00390000015010.
HOGENOMiHOG000060183.
HOVERGENiHBG081041.
InParanoidiQ9UFE4.
OMAiNTEYEKR.
PhylomeDBiQ9UFE4.
TreeFamiTF329312.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UFE4-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSSEFLAELH WEDGFAIPVA NEENKLLEDQ LSKLKDERAS LQDELREYEE
60 70 80 90 100
RINSMTSHFK NVKQELSITQ SLCKARERET ESEEHFKAIA QRELGRVKDE
110 120 130 140 150
IQRLENEMAS ILEKKSDKEN GIFKATQKLD GLKCQMNWDQ QALEAWLEES
160 170 180 190 200
AHKDSDALTL QKYAQQDDNK IRALTLQLER LTLECNQKRK ILDNELTETI
210 220 230 240 250
SAQLELDKAA QDFRKIHNER QELIKQWENT IEQMQKRDGD IDNCALELAR
260 270 280 290 300
IKQETREKEN LVKEKIKFLE SEIGNNTEFE KRISVADRKL LKCRTAYQDH
310 320 330 340 350
ETSRIQLKGE LDSLKATVNR TSSDLEALRK NISKIKKDIH EETARLQKTK
360 370 380 390 400
NHNEIIQTKL KEITEKTMSV EEKATNLEDM LKEEEKDVKE VDVQLNLIKG
410 420 430 440 450
VLFKKAQELQ TETMKEKAVL SEIEGTRSSL KHLNHQLQKL DFETLKQQEI
460 470 480 490 500
MYSQDFHIQQ VERRMSRLKG EINSEEKQAL EAKIVELRKS LEEKKSTCGL
510 520 530 540 550
LETQIKKLHN DLYFIKKAHS KNSDEKQSLM TKINELNLFI DRSEKELDKA
560 570 580 590 600
KGFKQDLMIE DNLLKLEVKR TREMLHSKAE EVLSLEKRKQ QLYTAMEERT
610 620 630 640 650
EEIKVHKTML ASQIRYVDQE RENISTEFRE RLSKIEKLKN RYEILTVVML
660 670 680 690 700
PPEGEEEKTQ AYYVIKAAQE KEELQREGDC LDAKINKAEK EIYALENTLQ
710 720 730 740 750
VLNSCNNNYK QSFKKVTPSS DEYELKIQLE EQKRAVDEKY RYKQRQIREL
760 770 780 790 800
QEDIQSMENT LDVIEHLANN VKEKLSEKQA YSFQLSKETE EQKPKLERVT
810 820 830 840 850
KQCAKLTKEI RLLKDTKDET MEEQDIKLRE MKQFHKVIDE MLVDIIEENT
860 870 880 890 900
EIRIILQTYF QQSGLELPTA STKGSRQSSR SPSHTSLSAR SSRSTSTSTS
910 920 930 940
QSSIKVLELK FPASSSLVGS PSRPSSASSS SSNVKSKKSS K
Length:941
Mass (Da):109,901
Last modified:May 18, 2010 - v3
Checksum:i1B7DAFB1B9A30D14
GO
Isoform 2 (identifier: Q9UFE4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MEYIFPNTGV...CCSSLSAQVM
     667-671: AAQEK → VMSMS
     672-941: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Show »
Length:755
Mass (Da):88,230
Checksum:iB971EE2F7E0F958B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti452 – 4521Y → H in BAG65133 (PubMed:14702039).Curated
Sequence conflicti811 – 8111R → H in BAG65133 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti594 – 5941T → I in a patient with CILD14; unknown pathological significance. 1 Publication
VAR_072468

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 11M → MEYIFPNTGVLWSWLINILC NRRIVWFTSSQLPRGPPASS GGHSFHTLRERSESRLFVES YAAAWQPPGTSGGASCCSSL SAQVM in isoform 2. 1 PublicationVSP_037014
Alternative sequencei667 – 6715AAQEK → VMSMS in isoform 2. 1 PublicationVSP_037015
Alternative sequencei672 – 941270Missing in isoform 2. 1 PublicationVSP_037016Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK304270 mRNA. Translation: BAG65133.1.
AL122120 mRNA. Translation: CAB59277.1.
AC068298 Genomic DNA. No translation available.
CCDSiCCDS46964.1. [Q9UFE4-1]
PIRiT34567.
RefSeqiNP_852091.1. NM_181426.1. [Q9UFE4-1]
UniGeneiHs.712820.

Genome annotation databases

EnsembliENST00000442201; ENSP00000405708; ENSG00000145075. [Q9UFE4-1]
GeneIDi339829.
KEGGihsa:339829.
UCSCiuc010hxe.3. human. [Q9UFE4-1]

Polymorphism and mutation databases

BioMutaiCCDC39.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK304270 mRNA. Translation: BAG65133.1.
AL122120 mRNA. Translation: CAB59277.1.
AC068298 Genomic DNA. No translation available.
CCDSiCCDS46964.1. [Q9UFE4-1]
PIRiT34567.
RefSeqiNP_852091.1. NM_181426.1. [Q9UFE4-1]
UniGeneiHs.712820.

3D structure databases

ProteinModelPortaliQ9UFE4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi130945. 2 interactions.
STRINGi9606.ENSP00000405708.

PTM databases

PhosphoSiteiQ9UFE4.

Polymorphism and mutation databases

BioMutaiCCDC39.
DMDMi296439421.

Proteomic databases

PaxDbiQ9UFE4.
PRIDEiQ9UFE4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000442201; ENSP00000405708; ENSG00000145075. [Q9UFE4-1]
GeneIDi339829.
KEGGihsa:339829.
UCSCiuc010hxe.3. human. [Q9UFE4-1]

Organism-specific databases

CTDi339829.
GeneCardsiGC03M180320.
GeneReviewsiCCDC39.
H-InvDBHIX0003887.
HGNCiHGNC:25244. CCDC39.
HPAiHPA035363.
HPA035364.
MIMi613798. gene.
613807. phenotype.
neXtProtiNX_Q9UFE4.
Orphaneti244. Primary ciliary dyskinesia.
PharmGKBiPA142672194.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG117406.
GeneTreeiENSGT00390000015010.
HOGENOMiHOG000060183.
HOVERGENiHBG081041.
InParanoidiQ9UFE4.
OMAiNTEYEKR.
PhylomeDBiQ9UFE4.
TreeFamiTF329312.

Miscellaneous databases

GenomeRNAii339829.
NextBioi97565.
PROiQ9UFE4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9UFE4.
CleanExiHS_CCDC39.
ExpressionAtlasiQ9UFE4. baseline and differential.
GenevestigatoriQ9UFE4.

Family and domain databases

ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Trachea.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Testis.
  3. "The DNA sequence, annotation and analysis of human chromosome 3."
    Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J.
    , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
    Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: FUNCTION, SUBCELLULAR LOCATION, INVOLVEMENT IN CILD14, TISSUE SPECIFICITY.
  5. Cited for: SUBCELLULAR LOCATION.
  6. Cited for: INVOLVEMENT IN CILD14, VARIANT ILE-594.
  7. "Mutations in CCDC39 and CCDC40 are the major cause of primary ciliary dyskinesia with axonemal disorganization and absent inner dynein arms."
    Antony D., Becker-Heck A., Zariwala M.A., Schmidts M., Onoufriadis A., Forouhan M., Wilson R., Taylor-Cox T., Dewar A., Jackson C., Goggin P., Loges N.T., Olbrich H., Jaspers M., Jorissen M., Leigh M.W., Wolf W.E., Daniels M.L.
    , Noone P.G., Ferkol T.W., Sagel S.D., Rosenfeld M., Rutman A., Dixit A., O'Callaghan C., Lucas J.S., Hogg C., Scambler P.J., Emes R.D., Chung E.M., Shoemark A., Knowles M.R., Omran H., Mitchison H.M., Al-Turki S., Anderson C., Antony D., Barroso I., Beales P., Bentham J., Bertolini S., Bhattacharya S., Calandra S., Carss K., Chatterjee K., Cirak S., Cosgrove C., Daly A., Danecek P., Durbin R., Fitzpatrick D., Floyd J., Foley R., Franklin C., Futema M., Graham C., Humphries S., Hurles M., Joyce C., Leitersdorf E., McCarthy S., Mitchison H.M., Muddyman D., Muntoni F., Neil A., O'Rahilly S., Onoufriadis A., Parker V., Payne F., Plagnol V., Raymond L., Savage D.B., Scambler P., Schmidts M., Schoenmakers N., Seed M., Semple R., Serra E., Stalker J., Van Bockxmeer F., van Kogelenberg M., Vijayarangakannan P., Walter K., Whittall R., Williamson K.
    Hum. Mutat. 34:462-472(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN CILD14.
  8. "Ciliary beat pattern and frequency in genetic variants of primary ciliary dyskinesia."
    Raidt J., Wallmeier J., Hjeij R., Onnebrink J.G., Pennekamp P., Loges N.T., Olbrich H., Haeffner K., Dougherty G.W., Omran H., Werner C.
    Eur. Respir. J. 44:1579-1588(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN CILD14.

Entry informationi

Entry nameiCCD39_HUMAN
AccessioniPrimary (citable) accession number: Q9UFE4
Secondary accession number(s): B4E2H1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: May 18, 2010
Last modified: April 29, 2015
This is version 92 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.