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Protein

Nuclear nucleic acid-binding protein C1D

Gene

C1D

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

Functioni

Plays a role in the recruitment of the RNA exosome complex to pre-rRNA to mediate the 3'-5' end processing of the 5.8S rRNA; this function may include MPHOSPH6. Can activate PRKDC not only in the presence of linear DNA but also in the presence of supercoiled DNA. Can induce apoptosis in a p53/TP53 dependent manner. May regulate the TRAX/TSN complex formation. Potentiates transcriptional repression by NR1D1 and THRB (By similarity).By similarity4 Publications

GO - Molecular functioni

  • DNA binding Source: ProtInc
  • RNA binding Source: UniProtKB
  • transcription corepressor activity Source: Ensembl

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Apoptosis, rRNA processing, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-6791226. Major pathway of rRNA processing in the nucleolus.
SIGNORiQ13901.

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear nucleic acid-binding protein C1D
Short name:
hC1D
Gene namesi
Name:C1D
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:29911. C1D.

Subcellular locationi

  • Nucleus 1 Publication
  • Cytoplasm 1 Publication
  • Nucleusnucleolus 1 Publication

  • Note: EXOSC10 is required for nucleolar localization (PubMed:17412707). Colocalizes with TSNAX in the nucleus (PubMed:11801738).2 Publications

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nuclear exosome (RNase complex) Source: UniProtKB
  • nucleolus Source: HPA
  • nucleoplasm Source: Reactome
  • nucleus Source: HPA
  • transcriptional repressor complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA164717007.

Polymorphism and mutation databases

BioMutaiC1D.
DMDMi74754472.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 141141Nuclear nucleic acid-binding protein C1DPRO_0000316300Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki119 – 119Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Post-translational modificationi

Phosphorylated by PRKDC.1 Publication

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ13901.
MaxQBiQ13901.
PaxDbiQ13901.
PRIDEiQ13901.
TopDownProteomicsiQ13901.

PTM databases

iPTMnetiQ13901.
PhosphoSiteiQ13901.

Expressioni

Tissue specificityi

Ubiquitous. Expressed at very high levels in the hippocampus, medulla oblongata, mammary gland, thyroid and salivary gland. Expressed at high levels in the fetal; lung, liver and kidney. Expressed at low levels in skeletal muscle, appendix, heart, lung and colon.1 Publication

Inductioni

By gamma-radiation.1 Publication

Gene expression databases

BgeeiQ13901.
ExpressionAtlasiQ13901. baseline and differential.
GenevisibleiQ13901. HS.

Organism-specific databases

HPAiHPA037413.
HPA037588.

Interactioni

Subunit structurei

Monomer and homodimer. Interacts with NR1D1, THRA, THRB, NCOR1 and NCOR2 (By similarity). Interacts with EXOSC10; the interaction probably mediates the association with the nuclear form of the RNA exosome. The homodimeric form interacts with TSNAX following gamma-radiation. Interacts with RAC3.By similarity5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EXOSC10Q017805EBI-3844053,EBI-358236
IL23RQ5VWK53EBI-3844053,EBI-10248005

Protein-protein interaction databases

BioGridi115705. 32 interactions.
IntActiQ13901. 8 interactions.
STRINGi9606.ENSP00000348107.

Structurei

3D structure databases

ProteinModelPortaliQ13901.
SMRiQ13901. Positions 8-106.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 100100Required for transcriptional repressionBy similarityAdd
BLAST
Regioni50 – 10051Interaction with NR1D1By similarityAdd
BLAST
Regioni100 – 14142Interaction with NCOR1 and NCOR2By similarityAdd
BLAST

Sequence similaritiesi

Belongs to the C1D family.Curated

Phylogenomic databases

eggNOGiKOG4835. Eukaryota.
ENOG4111ZX6. LUCA.
GeneTreeiENSGT00390000015405.
HOGENOMiHOG000007644.
HOVERGENiHBG097935.
InParanoidiQ13901.
KOiK12592.
OrthoDBiEOG7WQ7TZ.
PhylomeDBiQ13901.
TreeFamiTF314651.

Family and domain databases

InterProiIPR011082. Exosome-assoc_fac/DNA_repair.
IPR007146. Sas10/Utp3/C1D.
[Graphical view]
PANTHERiPTHR15341. PTHR15341. 1 hit.
PfamiPF04000. Sas10_Utp3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q13901-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGEEINEDY PVEIHEYLSA FENSIGAVDE MLKTMMSVSR NELLQKLDPL
60 70 80 90 100
EQAKVDLVSA YTLNSMFWVY LATQGVNPKE HPVKQELERI RVYMNRVKEI
110 120 130 140
TDKKKAGKLD RGAASRFVKN ALWEPKSKNA SKVANKGKSK S
Length:141
Mass (Da):16,019
Last modified:November 1, 1996 - v1
Checksum:i9976A3BBD5620D63
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti76 – 761V → I in BAF83140 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti127 – 1271S → P.
Corresponds to variant rs10444 [ dbSNP | Ensembl ].
VAR_053990

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95592 mRNA. Translation: CAA64845.1.
AK290451 mRNA. Translation: BAF83140.1.
AC079112 Genomic DNA. Translation: AAX88887.1.
CH471053 Genomic DNA. Translation: EAW99884.1.
CH471053 Genomic DNA. Translation: EAW99885.1.
BC005235 mRNA. Translation: AAH05235.1.
BC009584 mRNA. Translation: AAH09584.1.
BC009589 mRNA. Translation: AAH09589.1.
BC016284 mRNA. Translation: AAH16284.1.
CCDSiCCDS1883.1.
RefSeqiNP_001177192.1. NM_001190263.1.
NP_001177194.1. NM_001190265.1.
NP_006324.1. NM_006333.3.
NP_775269.1. NM_173177.2.
UniGeneiHs.602900.
Hs.697447.

Genome annotation databases

EnsembliENST00000355848; ENSP00000348107; ENSG00000197223.
ENST00000409302; ENSP00000386779; ENSG00000197223.
ENST00000410067; ENSP00000386468; ENSG00000197223.
GeneIDi10438.
KEGGihsa:10438.
UCSCiuc002seb.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95592 mRNA. Translation: CAA64845.1.
AK290451 mRNA. Translation: BAF83140.1.
AC079112 Genomic DNA. Translation: AAX88887.1.
CH471053 Genomic DNA. Translation: EAW99884.1.
CH471053 Genomic DNA. Translation: EAW99885.1.
BC005235 mRNA. Translation: AAH05235.1.
BC009584 mRNA. Translation: AAH09584.1.
BC009589 mRNA. Translation: AAH09589.1.
BC016284 mRNA. Translation: AAH16284.1.
CCDSiCCDS1883.1.
RefSeqiNP_001177192.1. NM_001190263.1.
NP_001177194.1. NM_001190265.1.
NP_006324.1. NM_006333.3.
NP_775269.1. NM_173177.2.
UniGeneiHs.602900.
Hs.697447.

3D structure databases

ProteinModelPortaliQ13901.
SMRiQ13901. Positions 8-106.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115705. 32 interactions.
IntActiQ13901. 8 interactions.
STRINGi9606.ENSP00000348107.

PTM databases

iPTMnetiQ13901.
PhosphoSiteiQ13901.

Polymorphism and mutation databases

BioMutaiC1D.
DMDMi74754472.

Proteomic databases

EPDiQ13901.
MaxQBiQ13901.
PaxDbiQ13901.
PRIDEiQ13901.
TopDownProteomicsiQ13901.

Protocols and materials databases

DNASUi10438.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000355848; ENSP00000348107; ENSG00000197223.
ENST00000409302; ENSP00000386779; ENSG00000197223.
ENST00000410067; ENSP00000386468; ENSG00000197223.
GeneIDi10438.
KEGGihsa:10438.
UCSCiuc002seb.4. human.

Organism-specific databases

CTDi10438.
GeneCardsiC1D.
HGNCiHGNC:29911. C1D.
HPAiHPA037413.
HPA037588.
MIMi606997. gene.
neXtProtiNX_Q13901.
PharmGKBiPA164717007.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4835. Eukaryota.
ENOG4111ZX6. LUCA.
GeneTreeiENSGT00390000015405.
HOGENOMiHOG000007644.
HOVERGENiHBG097935.
InParanoidiQ13901.
KOiK12592.
OrthoDBiEOG7WQ7TZ.
PhylomeDBiQ13901.
TreeFamiTF314651.

Enzyme and pathway databases

ReactomeiR-HSA-6791226. Major pathway of rRNA processing in the nucleolus.
SIGNORiQ13901.

Miscellaneous databases

ChiTaRSiC1D. human.
GeneWikiiC1D.
GenomeRNAii10438.
PROiQ13901.
SOURCEiSearch...

Gene expression databases

BgeeiQ13901.
ExpressionAtlasiQ13901. baseline and differential.
GenevisibleiQ13901. HS.

Family and domain databases

InterProiIPR011082. Exosome-assoc_fac/DNA_repair.
IPR007146. Sas10/Utp3/C1D.
[Graphical view]
PANTHERiPTHR15341. PTHR15341. 1 hit.
PfamiPF04000. Sas10_Utp3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "cDNA cloning, recombinant expression and characterization of polypeptides with exceptional DNA affinity."
    Nehls P., Keck T., Greferath R., Spiess E., Glaser T., Rothbarth K., Stammer H., Werner D.
    Nucleic Acids Res. 26:1160-1166(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBUNIT.
    Tissue: Term placenta.
  2. "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].
    Tissue: Brain.
  3. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Bone marrow, Lung and Uterus.
  6. "DNA end-independent activation of DNA-PK mediated via association with the DNA-binding protein C1D."
    Yavuzer U., Smith G.C.M., Bliss T., Werner D., Jackson S.P.
    Genes Dev. 12:2188-2199(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION, PHOSPHORYLATION, INTERACTION WITH PRKDC.
  7. "Identification of a novel Rac3-interacting protein C1D."
    Haataja L., Groffen J., Heisterkamp N.
    Int. J. Mol. Med. 1:665-670(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RAC3.
  8. "Induction of apoptosis by overexpression of the DNA-binding and DNA-PK-activating protein C1D."
    Rothbarth K., Spiess E., Juodka B., Yavuzer U., Nehls P., Stammer H., Werner D.
    J. Cell Sci. 112:2223-2232(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY.
  9. "DNA damage-dependent interaction of the nuclear matrix protein C1D with Translin-associated factor X (TRAX)."
    Erdemir T., Bilican B., Oncel D., Goding C.R., Yavuzer U.
    J. Cell Sci. 115:207-216(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH TSNAX.
  10. "C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing."
    Schilders G., van Dijk E., Pruijn G.J.M.
    Nucleic Acids Res. 35:2564-2572(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH EXOSC10.
  11. "SUMO-2 orchestrates chromatin modifiers in response to DNA damage."
    Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V., Vertegaal A.C.
    Cell Rep. 10:1778-1791(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-119, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiC1D_HUMAN
AccessioniPrimary (citable) accession number: Q13901
Secondary accession number(s): A8K336, D6W5F8, Q05D64
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 130 of the entry and version 1 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 2
    Human chromosome 2: 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

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 one 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.