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Q92600 (RCD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 114. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Cell differentiation protein RCD1 homolog

Short name=Rcd-1
Alternative name(s):
CCR4-NOT transcription complex subunit 9
Gene names
Name:RQCD1
Synonyms:CNOT9, RCD1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length299 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Involved in down-regulation of MYB- and JUN-dependent transcription. May play a role in cell differentiation By similarity. Can bind oligonucleotides, such as poly-G, poly-C or poly-T (in vitro), but the physiological relevance of this is not certain. Does not bind poly-A. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA, expect ESR1-mediated transcription that is not only slightly increased, if at all. Ref.5 Ref.9

Subunit structure

Homodimer. Component of the CCR4-NOT complex; distinct complexes seem to exist that differ in the participation of probably mutually exclusive catalytic subunits. Interacts with MYB, ATF2, RARA, RARB, RARG, RXRA, RXRB and RXRG. Identified in a complex with ATF2 bound to target DNA By similarity. Interacts with NANOS2 By similarity. Directly interacts with ZNF335. Ref.5 Ref.8 Ref.9

Subcellular location

Nucleus By similarity. CytoplasmP-body By similarity. Note: NANOS2 promotes its localization to P-body By similarity.

Tissue specificity

Detected in spleen, thymus, prostate, testis, ovary and intestine. Ref.1

Sequence similarities

Belongs to the RCD1 family.

Sequence caution

The sequence AAH07102.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
   Biological processRNA-mediated gene silencing
Transcription
Transcription regulation
Translation regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityPolymorphism
   Molecular functionActivator
Repressor
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processRNA metabolic process

Traceable author statement. Source: Reactome

cytokine-mediated signaling pathway

Inferred from electronic annotation. Source: Ensembl

gene expression

Traceable author statement. Source: Reactome

gene silencing by RNA

Inferred from electronic annotation. Source: UniProtKB-KW

mRNA metabolic process

Traceable author statement. Source: Reactome

negative regulation of intracellular estrogen receptor signaling pathway

Inferred from mutant phenotype PubMed 16778766. Source: UniProtKB

nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

Traceable author statement. Source: Reactome

nuclear-transcribed mRNA poly(A) tail shortening

Traceable author statement. Source: Reactome

positive regulation of ligand-dependent nuclear receptor transcription coactivator activity

Inferred from direct assay Ref.5. Source: UniProtKB

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

regulation of translation

Inferred from electronic annotation. Source: UniProtKB-KW

sex differentiation

Traceable author statement Ref.1. Source: ProtInc

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentCCR4-NOT complex

Inferred from direct assay PubMed 19558367. Source: UniProtKB

cytoplasmic mRNA processing body

Inferred from sequence or structural similarity. Source: UniProtKB

cytosol

Traceable author statement. Source: Reactome

nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 299299Cell differentiation protein RCD1 homolog
PRO_0000327224

Amino acid modifications

Modified residue11N-acetylmethionine Ref.4 Ref.6

Natural variations

Natural variant1431I → T. Ref.3
Corresponds to variant rs17856204 [ dbSNP | Ensembl ].
VAR_042429

Experimental info

Mutagenesis2271R → E: Loss of DNA binding. Ref.9
Sequence conflict245 – 28036AREAL…LAQLV → FSDLTFCWSSFQR in AAH07102. Ref.3

Secondary structure

.............................................. 299
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q92600 [UniParc].

Last modified February 1, 1997. Version 1.
Checksum: CFA0E108F5E9D8F2

FASTA29933,631
        10         20         30         40         50         60 
MHSLATAAPV PTTLAQVDRE KIYQWINELS SPETRENALL ELSKKRESVP DLAPMLWHSF 

        70         80         90        100        110        120 
GTIAALLQEI VNIYPSINPP TLTAHQSNRV CNALALLQCV ASHPETRSAF LAAHIPLFLY 

       130        140        150        160        170        180 
PFLHTVSKTR PFEYLRLTSL GVIGALVKTD EQEVINFLLT TEIIPLCLRI MESGSELSKT 

       190        200        210        220        230        240 
VATFILQKIL LDDTGLAYIC QTYERFSHVA MILGKMVLQL SKEPSARLLK HVVRCYLRLS 

       250        260        270        280        290 
DNPRAREALR QCLPDQLKDT TFAQVLKDDT TTKRWLAQLV KNLQEGQVTD PRGIPLPPQ 

« Hide

References

« Hide 'large scale' references
[1]"Novel factor highly conserved among eukaryotes controls sexual development in fission yeast."
Okazaki N., Okazaki K., Watanabe Y., Kato-Hayashi M., Yamamoto M., Okayama H.
Mol. Cell. Biol. 18:887-895(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY.
Tissue: Foreskin.
[2]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"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], VARIANT THR-143.
Tissue: Brain.
[4]Bienvenut W.V., Lempens A., Norman J.C.
Submitted (OCT-2009) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 1-21; 36-44; 180-188 AND 275-292, ACETYLATION AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Ovarian carcinoma.
[5]"Components of the CCR4-NOT complex function as nuclear hormone receptor coactivators via association with the NRC-interacting Factor NIF-1."
Garapaty S., Mahajan M.A., Samuels H.H.
J. Biol. Chem. 283:6806-6816(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH ZNF335.
[6]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"C2ORF29/CNOT11 and CNOT10 form a new module of the CCR4-NOT complex."
Mauxion F., Preve B., Seraphin B.
RNA Biol. 10:267-276(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE CCR4-NOT COMPLEX.
[9]"Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties."
Garces R.G., Gillon W., Pai E.F.
Protein Sci. 16:176-188(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 18-285, DOMAIN, SUBUNIT, FUNCTION, MUTAGENESIS OF ARG-227.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D87957 Genomic DNA. Translation: BAA13508.1.
CH471063 Genomic DNA. Translation: EAW70625.1.
BC007102 mRNA. Translation: AAH07102.2. Different initiation.
BC137455 mRNA. Translation: AAI37456.1.
BC137456 mRNA. Translation: AAI37457.1.
RefSeqNP_001258564.1. NM_001271635.1.
NP_005435.1. NM_005444.2.
UniGeneHs.148767.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2FV2X-ray2.20A/B/C/D18-285[»]
ProteinModelPortalQ92600.
SMRQ92600. Positions 18-285.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114573. 18 interactions.
DIPDIP-46840N.
IntActQ92600. 7 interactions.
MINTMINT-1162783.
STRING9606.ENSP00000273064.

PTM databases

PhosphoSiteQ92600.

Polymorphism databases

DMDM74716599.

Proteomic databases

PaxDbQ92600.
PRIDEQ92600.

Protocols and materials databases

DNASU9125.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000273064; ENSP00000273064; ENSG00000144580.
ENST00000542068; ENSP00000443687; ENSG00000144580.
GeneID9125.
KEGGhsa:9125.
UCSCuc010zkh.3. human.

Organism-specific databases

CTD9125.
GeneCardsGC02P219433.
HGNCHGNC:10445. RQCD1.
HPAHPA046622.
MIM612054. gene.
neXtProtNX_Q92600.
PharmGKBPA34859.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5209.
HOGENOMHOG000192069.
HOVERGENHBG056785.
InParanoidQ92600.
KOK12606.
OrthoDBEOG7M98GN.
PhylomeDBQ92600.
TreeFamTF105734.

Enzyme and pathway databases

ReactomeREACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpressQ92600.
BgeeQ92600.
CleanExHS_RQCD1.
GenevestigatorQ92600.

Family and domain databases

Gene3D1.25.10.10. 1 hit.
InterProIPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR007216. Rcd1.
[Graphical view]
PANTHERPTHR12262. PTHR12262. 1 hit.
PfamPF04078. Rcd1. 1 hit.
[Graphical view]
SUPFAMSSF48371. SSF48371. 1 hit.
ProtoNetSearch...

Other

ChiTaRSRQCD1. human.
EvolutionaryTraceQ92600.
GenomeRNAi9125.
NextBio34205.
PROQ92600.
SOURCESearch...

Entry information

Entry nameRCD1_HUMAN
AccessionPrimary (citable) accession number: Q92600
Secondary accession number(s): B2RPI0, Q96IX4
Entry history
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: February 1, 1997
Last modified: April 16, 2014
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM