Cnot6 CCR4-NOT transcription complex, subunit 6 [Rattus norvegicus (Norway rat)] - Gene - NCBI

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Cnot6 CCR4-NOT transcription complex, subunit 6 [ Rattus norvegicus (Norway rat) ]
Gene ID: 287249, updated on 9-Dec-2024

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Gene Sequences (FASTA)

Transcript sequences (FASTA)

Protein sequences(FASTA)

In addition, your package will include a detailed data report in both TSV and JSONL formats.

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Summary

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Official Symbol

Cnot6provided by RGD

Official Full Name

CCR4-NOT transcription complex, subunit 6provided by RGD

Primary source

RGD:1310783

See related

EnsemblRapid:ENSRNOG00000054891 AllianceGenome:RGD:1310783

Gene type

protein coding

RefSeq status

VALIDATED

Organism

Rattus norvegicus

Lineage

Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus

Also known as

CCR4; RGD1310783

Summary

Predicted to enable nuclear receptor coactivator activity and poly(A)-specific ribonuclease activity. Predicted to be involved in negative regulation of gene expression; positive regulation of cell population proliferation; and positive regulation of cytoplasmic mRNA processing body assembly. Predicted to be part of CCR4-NOT complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human CNOT6 (CCR4-NOT transcription complex subunit 6). [provided by Alliance of Genome Resources, Dec 2024]

Expression

Biased expression in Thymus (RPKM 393.8), Spleen (RPKM 218.6) and 9 other tissues See more

Orthologs

human mouse all

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Genomic context

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See Cnot6 in Genome Data Viewer

Location:

10q21

Exon count:

16

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Annotation release | Status | Assembly | Chr | Location
RS_2024_02 | current | GRCr8 (GCF_036323735.1) | 10 | NC_086028.1 (34479892..34532166, complement)
RS_2023_06 | previous assembly | mRatBN7.2 (GCF_015227675.2) | 10 | NC_051345.1 (33978785..34031025, complement)
106 | previous assembly | Rnor_6.0 (GCF_000001895.5) | 10 | NC_005109.4 (35144291..35195126, complement)

Items 1 - 3 of 3

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Chromosome 10 - NC_086028.1

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:
NC_086028.1 Chromosome 10 Reference GRCr8

NC_051345.1 Chromosome 10 Reference mRatBN7.2 Primary Assembly

NC_005109.4 Chromosome 10 Reference Rnor_6.0 Primary Assembly

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)

BioProject: PRJNA238328

Publication: PMID 24510058

Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

1. CCR4, a 3'-5' poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. Chen J, et al. EMBO J, 2002 Mar 15. PMID 11889047, Free PMC Article

2. The Ccr4a (CNOT6) and Ccr4b (CNOT6L) deadenylase subunits of the human Ccr4-Not complex contribute to the prevention of cell death and senescence. Mittal S, et al. Mol Biol Cell, 2011 Mar 15. PMID 21233283, Free PMC Article

3. CCR4-NOT deadenylates mRNA associated with RNA-induced silencing complexes in human cells. Piao X, et al. Mol Cell Biol, 2010 Mar. PMID 20065043, Free PMC Article

4. UNR, a new partner of poly(A)-binding protein, plays a key role in translationally coupled mRNA turnover mediated by the c-fos major coding-region determinant. Chang TC, et al. Genes Dev, 2004 Aug 15. PMID 15314026, Free PMC Article

5. Components of the CCR4-NOT complex function as nuclear hormone receptor coactivators via association with the NRC-interacting Factor NIF-1. Garapaty S, et al. J Biol Chem, 2008 Mar 14. PMID 18180299

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
Submit: New GeneRIF Correction

General gene information

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Markers

RH142065 (e-PCR)

UniSTS:224055

Homology

NCBI Orthologs
Orthologs from OrthoDB

Gene Ontology Provided by RGD

Items 1 - 11 of 11

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Function | Evidence Code | Pubs

enables 3'-5'-RNA exonuclease activity

IBA
Inferred from Biological aspect of Ancestor
more info

enables RNA binding

IEA
Inferred from Electronic Annotation
more info

enables RNA exonuclease activity

ISO
Inferred from Sequence Orthology
more info

enables RNA exonuclease activity

ISS
Inferred from Sequence or Structural Similarity
more info

enables metal ion binding

IEA
Inferred from Electronic Annotation
more info

enables nuclear receptor coactivator activity

IEA
Inferred from Electronic Annotation
more info

enables nuclear receptor coactivator activity

ISO
Inferred from Sequence Orthology
more info

enables nuclear receptor coactivator activity

ISS
Inferred from Sequence or Structural Similarity
more info

enables poly(A)-specific ribonuclease activity

IEA
Inferred from Electronic Annotation
more info

enables poly(A)-specific ribonuclease activity

ISO
Inferred from Sequence Orthology
more info

enables poly(A)-specific ribonuclease activity

ISS
Inferred from Sequence or Structural Similarity
more info

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Process | Evidence Code | Pubs

involved_in biological_process

ND
No biological Data available
more info

involved_in miRNA-mediated gene silencing by mRNA destabilization

IEA
Inferred from Electronic Annotation
more info

involved_in miRNA-mediated gene silencing by mRNA destabilization

ISO
Inferred from Sequence Orthology
more info

involved_in miRNA-mediated gene silencing by mRNA destabilization

ISS
Inferred from Sequence or Structural Similarity
more info

involved_in nuclear-transcribed mRNA catabolic process, no-go decay

IEA
Inferred from Electronic Annotation
more info

involved_in nuclear-transcribed mRNA catabolic process, no-go decay

ISO
Inferred from Sequence Orthology
more info

involved_in nuclear-transcribed mRNA catabolic process, no-go decay

ISS
Inferred from Sequence or Structural Similarity
more info

involved_in nuclear-transcribed mRNA poly(A) tail shortening

IEA
Inferred from Electronic Annotation
more info

involved_in nuclear-transcribed mRNA poly(A) tail shortening

ISO
Inferred from Sequence Orthology
more info

involved_in nuclear-transcribed mRNA poly(A) tail shortening

ISS
Inferred from Sequence or Structural Similarity
more info

involved_in positive regulation of DNA-templated transcription

IEA
Inferred from Electronic Annotation
more info

involved_in positive regulation of cell population proliferation

IEA
Inferred from Electronic Annotation
more info

involved_in positive regulation of cell population proliferation

ISO
Inferred from Sequence Orthology
more info

involved_in positive regulation of cytoplasmic mRNA processing body assembly

IEA
Inferred from Electronic Annotation
more info

involved_in positive regulation of cytoplasmic mRNA processing body assembly

ISO
Inferred from Sequence Orthology
more info

involved_in regulation of translation

IEA
Inferred from Electronic Annotation
more info

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Component | Evidence Code | Pubs

part_of CCR4-NOT complex

IEA
Inferred from Electronic Annotation
more info

part_of CCR4-NOT complex

ISO
Inferred from Sequence Orthology
more info

part_of CCR4-NOT complex

ISS
Inferred from Sequence or Structural Similarity
more info

located_in cytoplasm

IEA
Inferred from Electronic Annotation
more info

located_in nucleus

IEA
Inferred from Electronic Annotation
more info

Items 1 - 5 of 5

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General protein information

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Preferred Names

CCR4-NOT transcription complex subunit 6

Names

carbon catabolite repressor protein 4 homolog

cytoplasmic deadenylase

NP_001380807.1

EC 3.1.13.4

XP_038941302.1

EC 3.1.13.4

XP_038941304.1

EC 3.1.13.4

XP_063124645.1

EC 3.1.13.4

XP_063124646.1

EC 3.1.13.4

XP_063124647.1

EC 3.1.13.4

XP_063124648.1

EC 3.1.13.4

XP_063124650.1

EC 3.1.13.4

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

1. NM_001393878.1 → NP_001380807.1 CCR4-NOT transcription complex subunit 6

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

Q6AXU9

UniProtKB/TrEMBL

A0A0G2K816

Related

ENSRNOP00000074431.2, ENSRNOT00000084509.3

Conserved Domains (3) summary

cd10313
Location:191 → 540

Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6

COG4886
Location:52 → 159

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:53 → 75

LRR_1; leucine-rich repeat [structural motif]

RNA

1. NR_172026.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

This section includes genomic Reference Sequences (RefSeqs) from all assemblies on which this gene is annotated, such as RefSeqs for chromosomes and scaffolds (contigs) from both reference and alternate assemblies. Model RNAs and proteins are also reported here.

Reference GRCr8

Genomic

1. NC_086028.1 Reference GRCr8

Range

34479892..34532166 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

1. XM_063268576.1 → XP_063124646.1 CCR4-NOT transcription complex subunit 6 isoform X2

UniProtKB/TrEMBL

A0A0G2KA59, A6HDX6

2. XM_063268577.1 → XP_063124647.1 CCR4-NOT transcription complex subunit 6 isoform X2

UniProtKB/TrEMBL

A0A0G2KA59, A6HDX6

3. XM_063268575.1 → XP_063124645.1 CCR4-NOT transcription complex subunit 6 isoform X1

UniProtKB/Swiss-Prot

Q6AXU9

UniProtKB/TrEMBL

A0A0G2K816

4. XM_039085376.1 → XP_038941304.1 CCR4-NOT transcription complex subunit 6 isoform X2

UniProtKB/TrEMBL

A0A0G2KA59, A6HDX6

Conserved Domains (3) summary

COG4886
Location:52 → 158

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:53 → 75

LRR_1; leucine-rich repeat [structural motif]

cl00490
Location:186 → 535

EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

5. XM_039085374.1 → XP_038941302.1 CCR4-NOT transcription complex subunit 6 isoform X1

UniProtKB/Swiss-Prot

Q6AXU9

UniProtKB/TrEMBL

A0A0G2K816

Conserved Domains (3) summary

cd10313
Location:191 → 540

Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6

COG4886
Location:52 → 159

LRR; Leucine-rich repeat (LRR) protein [Transcription]

sd00031
Location:53 → 75

LRR_1; leucine-rich repeat [structural motif]

6. XM_063268578.1 → XP_063124648.1 CCR4-NOT transcription complex subunit 6 isoform X3

UniProtKB/TrEMBL

A6HDX8

7. XM_063268580.1 → XP_063124650.1 CCR4-NOT transcription complex subunit 6 isoform X3

UniProtKB/TrEMBL

A6HDX8

Related sequences

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Nucleotide | Protein | Strain
Heading | Accession and Version
genomic | CH473948.1 | EDM04230.1
| EDM04231.1
| EDM04232.1
| EDM04233.1
genomic | JAXUCZ010000010.1 (34479892..34532166) | None | BN/NHsdMcwi
mRNA | BC079308.1 | AAH79308.1
mRNA | FQ223171.1 | None | Sprague-Dawley

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Protein Accession | Links
GenPept Link | UniProtKB Link
Q6AXU9.1 | GenPept | UniProtKB/Swiss-Prot:Q6AXU9

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Additional links

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Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information

Interologous Interaction Database

Interologous Interaction Database

MilliporeSigma

CNOT6 products

Molecular Biology Databases

Bgee database

Cnot6 gene expression

BioGPS

BioGPS

CTD: Comparative Toxicogenomics Database

CTD: Comparative Toxicogenomics Database - CNOT6

GlyGen glycoinformatics resource

GlyGen glycoinformatics resource

Ingenuity Pathways Analysis

Ingenuity Pathways Analysis

Kyoto Encyclopedia of Genes and Genomes

Kyoto Encyclopedia of Genes and Genomes

OMA Browser: Orthologous MAtrix

OMA Browser: Orthologous MAtrix

OMA Browser: Orthologous MAtrix

OrthoDB catalog of orthologs

Orthologs

PhosphoSitePlus

PhosphoSitePlus® - comprehensive post-translational modification resource

Research Materials

Addgene Non-profit plasmid repository

Get Plasmids - Addgene

Creative Biogene

CCR4-NOT transcription complex, subunit 6

ExactAntigen/Labome

reagents

GenScript latest version of gene cDNA ORF Clone

GenScript latest version of gene cDNA ORF Clone

GeneCopoeia Inc.

Order TALEN/CRISPR clones

OriGene

Order Ccr4 cDNA clone/Protein/Antibody/RNAi

Order Cnot6 cDNA clone/Protein/Antibody/RNAi

Tools

GeneMANIA

GeneMANIA

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Supplemental Content

Table of contents

Summary

Genomic context

Genomic regions, transcripts, and products

Expression

Bibliography

General gene information
Markers, Homology, Gene Ontology

General protein information

NCBI Reference Sequences (RefSeq)

Related sequences

Additional links

Genome Browsers

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Related information

BioProjects
BioProjects related to a gene

BioSystems
BioSystems

Conserved Domains
Related CDD

Full text in PMC
PMC links

Full text in PMC_nucleotide
Full text in PubMedCentral identified from shared sequence links

Functional Class
Functional class of the sequence domain architecture

Gene neighbors
Overlapping genes and two nearest non-overlapping genes on either side

Genome
Related Genome

GEO Profiles
Related GEO

Nucleotide
Link to related Nucleotide entry

Probe
Related Probe entry

Protein
Link to related protein entry

PubChem Compound
PubChem Compounds

PubChem Substance
PubChem Substances

PubMed
Link to related PubMed entry

PubMed(nucleotide/PMC)
Citations in PubMed identified from shared sequence and PMC links.

RefSeq Proteins
Link to Protein RefSeqs

RefSeq RNAs
Link to Nucleotide RefSeq RNAs

Taxonomy
Link to related taxonomy entry

Links to other resources

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Cnot6 CCR4-NOT transcription complex, subunit 6 [Rattus norvegicus]
Cnot6 CCR4-NOT transcription complex, subunit 6 [Rattus norvegicus]
Gene ID:287249

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