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Protein

Cell differentiation protein RCD1 homolog

Gene

RQCD1

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

Functioni

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.By similarity2 Publications

GO - Molecular functioni

  • protein domain specific binding Source: BHF-UCL
  • protein homodimerization activity Source: BHF-UCL

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Repressor

Keywords - Biological processi

RNA-mediated gene silencing, Transcription, Transcription regulation, Translation regulation

Enzyme and pathway databases

BioCyciZFISH:ENSG00000144580-MONOMER.
ReactomeiR-HSA-429947. Deadenylation of mRNA.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-6804115. TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain.

Names & Taxonomyi

Protein namesi
Recommended name:
Cell differentiation protein RCD1 homolog
Short name:
Rcd-1
Alternative name(s):
CCR4-NOT transcription complex subunit 9
Gene namesi
Name:RQCD1
Synonyms:CNOT9, RCD1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:10445. RQCD1.

Subcellular locationi

  • Nucleus By similarity
  • CytoplasmP-body By similarity

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

GO - Cellular componenti

  • CCR4-NOT complex Source: UniProtKB
  • CCR4-NOT core complex Source: GO_Central
  • cytoplasmic mRNA processing body Source: UniProtKB
  • cytosol Source: Reactome
  • membrane Source: UniProtKB
  • nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi227R → E: Loss of DNA binding. 1 Publication1

Organism-specific databases

DisGeNETi9125.
OpenTargetsiENSG00000144580.
PharmGKBiPA34859.

Polymorphism and mutation databases

DMDMi74716599.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003272241 – 299Cell differentiation protein RCD1 homologAdd BLAST299

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ92600.
MaxQBiQ92600.
PaxDbiQ92600.
PeptideAtlasiQ92600.
PRIDEiQ92600.

PTM databases

iPTMnetiQ92600.
PhosphoSitePlusiQ92600.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiENSG00000144580.
CleanExiHS_RQCD1.
ExpressionAtlasiQ92600. baseline and differential.
GenevisibleiQ92600. HS.

Organism-specific databases

HPAiHPA046622.

Interactioni

Subunit structurei

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.By similarity3 Publications

GO - Molecular functioni

  • protein domain specific binding Source: BHF-UCL
  • protein homodimerization activity Source: BHF-UCL

Protein-protein interaction databases

BioGridi114573. 47 interactors.
DIPiDIP-46840N.
IntActiQ92600. 15 interactors.
MINTiMINT-1162783.
STRINGi9606.ENSP00000273064.

Structurei

Secondary structure

1299
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi19 – 27Combined sources9
Beta strandi29 – 31Combined sources3
Helixi32 – 43Combined sources12
Turni44 – 48Combined sources5
Helixi52 – 58Combined sources7
Beta strandi59 – 61Combined sources3
Helixi62 – 71Combined sources10
Helixi72 – 76Combined sources5
Turni77 – 80Combined sources4
Helixi84 – 102Combined sources19
Turni104 – 106Combined sources3
Helixi107 – 112Combined sources6
Helixi115 – 118Combined sources4
Helixi120 – 123Combined sources4
Helixi130 – 147Combined sources18
Helixi152 – 160Combined sources9
Helixi164 – 173Combined sources10
Helixi176 – 191Combined sources16
Helixi193 – 199Combined sources7
Helixi203 – 222Combined sources20
Helixi226 – 239Combined sources14
Helixi243 – 252Combined sources10
Helixi255 – 257Combined sources3
Turni261 – 268Combined sources8
Helixi270 – 284Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FV2X-ray2.20A/B/C/D18-285[»]
4CRUX-ray1.65B19-285[»]
4CRVX-ray2.05B19-285[»]
4CT6X-ray2.10B18-285[»]
4CT7X-ray1.90B16-285[»]
ProteinModelPortaliQ92600.
SMRiQ92600.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ92600.

Family & Domainsi

Sequence similaritiesi

Belongs to the RCD1 family.Curated

Phylogenomic databases

eggNOGiKOG3036. Eukaryota.
COG5209. LUCA.
GeneTreeiENSGT00390000001225.
HOGENOMiHOG000192069.
HOVERGENiHBG056785.
InParanoidiQ92600.
KOiK12606.
OMAiEDNRRTM.
OrthoDBiEOG091G0BAM.
PhylomeDBiQ92600.
TreeFamiTF105734.

Family and domain databases

Gene3Di1.25.10.10. 1 hit.
InterProiIPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR007216. Rcd1/Caf40.
[Graphical view]
PANTHERiPTHR12262. PTHR12262. 1 hit.
SUPFAMiSSF48371. SSF48371. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q92600-1) [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
MHSLATAAPV PTTLAQVDRE KIYQWINELS SPETRENALL ELSKKRESVP
60 70 80 90 100
DLAPMLWHSF GTIAALLQEI VNIYPSINPP TLTAHQSNRV CNALALLQCV
110 120 130 140 150
ASHPETRSAF LAAHIPLFLY PFLHTVSKTR PFEYLRLTSL GVIGALVKTD
160 170 180 190 200
EQEVINFLLT TEIIPLCLRI MESGSELSKT VATFILQKIL LDDTGLAYIC
210 220 230 240 250
QTYERFSHVA MILGKMVLQL SKEPSARLLK HVVRCYLRLS DNPRAREALR
260 270 280 290
QCLPDQLKDT TFAQVLKDDT TTKRWLAQLV KNLQEGQVTD PRGIPLPPQ
Length:299
Mass (Da):33,631
Last modified:February 1, 1997 - v1
Checksum:iCFA0E108F5E9D8F2
GO
Isoform 2 (identifier: Q92600-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     143-143: I → IVETGFHHVGQADLELPTSSDLPASASQSAGIT

Note: No experimental confirmation available.
Show »
Length:331
Mass (Da):36,837
Checksum:iAD81339464CE9A5C
GO
Isoform 3 (identifier: Q92600-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     245-258: AREALRQCLPDQLK → FSDLTFCWSSFQRK
     259-299: Missing.

Show »
Length:258
Mass (Da):29,140
Checksum:iAA7F7A655A9AFD3E
GO

Sequence cautioni

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

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_042429143I → T.1 PublicationCorresponds to variant rs17856204dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_054371143I → IVETGFHHVGQADLELPTSS DLPASASQSAGIT in isoform 2. 1 Publication1
Alternative sequenceiVSP_055744245 – 258AREAL…PDQLK → FSDLTFCWSSFQRK in isoform 3. 1 PublicationAdd BLAST14
Alternative sequenceiVSP_055745259 – 299Missing in isoform 3. 1 PublicationAdd BLAST41

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D87957 Genomic DNA. Translation: BAA13508.1.
AK293281 mRNA. Translation: BAH11481.1.
AC012510 Genomic DNA. No translation available.
CH471063 Genomic DNA. Translation: EAW70625.1.
CH471063 Genomic DNA. Translation: EAW70624.1.
BC007102 mRNA. Translation: AAH07102.2. Different initiation.
BC137455 mRNA. Translation: AAI37456.1.
BC137456 mRNA. Translation: AAI37457.1.
CCDSiCCDS33379.1. [Q92600-1]
CCDS63122.1. [Q92600-2]
CCDS63123.1. [Q92600-3]
RefSeqiNP_001258563.1. NM_001271634.1. [Q92600-2]
NP_001258564.1. NM_001271635.1. [Q92600-3]
NP_005435.1. NM_005444.2. [Q92600-1]
UniGeneiHs.148767.

Genome annotation databases

EnsembliENST00000273064; ENSP00000273064; ENSG00000144580. [Q92600-1]
ENST00000295701; ENSP00000295701; ENSG00000144580. [Q92600-3]
ENST00000542068; ENSP00000443687; ENSG00000144580. [Q92600-1]
ENST00000627282; ENSP00000486540; ENSG00000144580. [Q92600-2]
GeneIDi9125.
KEGGihsa:9125.
UCSCiuc002vih.3. human. [Q92600-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D87957 Genomic DNA. Translation: BAA13508.1.
AK293281 mRNA. Translation: BAH11481.1.
AC012510 Genomic DNA. No translation available.
CH471063 Genomic DNA. Translation: EAW70625.1.
CH471063 Genomic DNA. Translation: EAW70624.1.
BC007102 mRNA. Translation: AAH07102.2. Different initiation.
BC137455 mRNA. Translation: AAI37456.1.
BC137456 mRNA. Translation: AAI37457.1.
CCDSiCCDS33379.1. [Q92600-1]
CCDS63122.1. [Q92600-2]
CCDS63123.1. [Q92600-3]
RefSeqiNP_001258563.1. NM_001271634.1. [Q92600-2]
NP_001258564.1. NM_001271635.1. [Q92600-3]
NP_005435.1. NM_005444.2. [Q92600-1]
UniGeneiHs.148767.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FV2X-ray2.20A/B/C/D18-285[»]
4CRUX-ray1.65B19-285[»]
4CRVX-ray2.05B19-285[»]
4CT6X-ray2.10B18-285[»]
4CT7X-ray1.90B16-285[»]
ProteinModelPortaliQ92600.
SMRiQ92600.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114573. 47 interactors.
DIPiDIP-46840N.
IntActiQ92600. 15 interactors.
MINTiMINT-1162783.
STRINGi9606.ENSP00000273064.

PTM databases

iPTMnetiQ92600.
PhosphoSitePlusiQ92600.

Polymorphism and mutation databases

DMDMi74716599.

Proteomic databases

EPDiQ92600.
MaxQBiQ92600.
PaxDbiQ92600.
PeptideAtlasiQ92600.
PRIDEiQ92600.

Protocols and materials databases

DNASUi9125.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000273064; ENSP00000273064; ENSG00000144580. [Q92600-1]
ENST00000295701; ENSP00000295701; ENSG00000144580. [Q92600-3]
ENST00000542068; ENSP00000443687; ENSG00000144580. [Q92600-1]
ENST00000627282; ENSP00000486540; ENSG00000144580. [Q92600-2]
GeneIDi9125.
KEGGihsa:9125.
UCSCiuc002vih.3. human. [Q92600-1]

Organism-specific databases

CTDi9125.
DisGeNETi9125.
GeneCardsiRQCD1.
HGNCiHGNC:10445. RQCD1.
HPAiHPA046622.
MIMi612054. gene.
neXtProtiNX_Q92600.
OpenTargetsiENSG00000144580.
PharmGKBiPA34859.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3036. Eukaryota.
COG5209. LUCA.
GeneTreeiENSGT00390000001225.
HOGENOMiHOG000192069.
HOVERGENiHBG056785.
InParanoidiQ92600.
KOiK12606.
OMAiEDNRRTM.
OrthoDBiEOG091G0BAM.
PhylomeDBiQ92600.
TreeFamiTF105734.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000144580-MONOMER.
ReactomeiR-HSA-429947. Deadenylation of mRNA.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
R-HSA-6804115. TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain.

Miscellaneous databases

ChiTaRSiRQCD1. human.
EvolutionaryTraceiQ92600.
GenomeRNAii9125.
PROiQ92600.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000144580.
CleanExiHS_RQCD1.
ExpressionAtlasiQ92600. baseline and differential.
GenevisibleiQ92600. HS.

Family and domain databases

Gene3Di1.25.10.10. 1 hit.
InterProiIPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR007216. Rcd1/Caf40.
[Graphical view]
PANTHERiPTHR12262. PTHR12262. 1 hit.
SUPFAMiSSF48371. SSF48371. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRCD1_HUMAN
AccessioniPrimary (citable) accession number: Q92600
Secondary accession number(s): B2RPI0
, B5MDQ4, B7Z1E5, Q96IX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: February 1, 1997
Last modified: November 2, 2016
This is version 140 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

3D-structure, Complete proteome, Direct protein sequencing, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.