Cnot6 CCR4-NOT transcription complex, subunit 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cnot6provided by MGI
Official Full Name: CCR4-NOT transcription complex, subunit 6provided by MGI
Primary source: MGI:MGI:2144529
See related: Ensembl:ENSMUSG00000020362 AllianceGenome:MGI:2144529
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: CCR4
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 located in cytosol. Predicted to be part of CCR4-NOT complex. Predicted to be active in cytoplasm and nucleus. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Orthologous to human CNOT6 (CCR4-NOT transcription complex subunit 6). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Broad expression in CNS E11.5 (RPKM 21.1), limb E14.5 (RPKM 17.5) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B1.2; 11 29.76 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (49562324..49604227, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (49671497..49713401, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

This study describe a third pattern of polyadenylation: mRNAs are deadenylated in growing oocytes, become polyadenylated during early maturation and then deadenylated during late maturation. The deadenylase, CNOT6, is present in cortical foci of oocytes and regulates deadenylation of these mRNAs.
Title: CNOT6 regulates a novel pattern of mRNA deadenylation during oocyte meiotic maturation.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3) 1 citation
Gene trapped (1)
Targeted (5) 1 citation

General gene information

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Markers

D20S1016 (e-PCR)
- UniSTS:1132

Cnot6 (e-PCR), detects polymorphism
- UniSTS:547199

RH124612 (e-PCR)
- UniSTS:161434

AW456442 (e-PCR)
- UniSTS:180186

Gene Ontology Provided by MGI

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	ISS Inferred from Sequence or Structural Similarity 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
enables poly(A)-specific ribonuclease activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
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	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	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

Component	Evidence Code	Pubs
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 cytosol	TAS Traceable Author Statement more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

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_001277670.1

EC 3.1.13.4

NP_001350285.1

EC 3.1.13.4

NP_001350286.1

EC 3.1.13.4

NP_997649.1

EC 3.1.13.4

XP_006532004.1

EC 3.1.13.4

XP_006532005.1

EC 3.1.13.4

XP_017169703.1

EC 3.1.13.4

XP_036012101.1

EC 3.1.13.4

XP_036012102.1

EC 3.1.13.4

NCBI Reference Sequences (RefSeq)

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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)

NM_001290741.2 → NP_001277670.1 CCR4-NOT transcription complex subunit 6 isoform 1

See identical proteins and their annotated locations for NP_001277670.1

Status: VALIDATED

Source sequence(s)

AK039164, AL606479, BB402523, BC062950, CF746424

Consensus CDS

CCDS70172.1

UniProtKB/Swiss-Prot

Q5NCL3, Q80V15, Q8K3P5

Related

ENSMUSP00000121239.2, ENSMUST00000145353.8

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]
NM_001363356.1 → NP_001350285.1 CCR4-NOT transcription complex subunit 6 isoform 4

Status: VALIDATED

Source sequence(s)

AL606479

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 → 158

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

sd00031
Location:53 → 75

LRR_1; leucine-rich repeat [structural motif]
NM_001363357.1 → NP_001350286.1 CCR4-NOT transcription complex subunit 6 isoform 3

Status: VALIDATED

Source sequence(s)

AL606479

Conserved Domains (3) summary

cd10313
Location:91 → 440

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

sd00031
Location:4 → 26

LRR_1; leucine-rich repeat [structural motif]

pfam12799
Location:3 → 44

LRR_4; Leucine Rich repeats (2 copies)
NM_212484.2 → NP_997649.1 CCR4-NOT transcription complex subunit 6 isoform 2

See identical proteins and their annotated locations for NP_997649.1

Status: VALIDATED

Source sequence(s)

AK039164, BB402523, BC062950, BY741392

Consensus CDS

CCDS24621.1

UniProtKB/Swiss-Prot

Q8K3P5

Related

ENSMUSP00000020624.7, ENSMUST00000020624.7

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

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000077.7 Reference GRCm39 C57BL/6J

Range

49562324..49604227 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006531942.3 → XP_006532005.1 CCR4-NOT transcription complex subunit 6 isoform X1

See identical proteins and their annotated locations for XP_006532005.1

UniProtKB/Swiss-Prot

Q5NCL3, Q80V15, Q8K3P5

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]
XM_017314214.3 → XP_017169703.1 CCR4-NOT transcription complex subunit 6 isoform X3

Conserved Domains (3) summary

cd10313
Location:96 → 445

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

sd00031
Location:4 → 26

LRR_1; leucine-rich repeat [structural motif]

pfam12799
Location:3 → 44

LRR_4; Leucine Rich repeats (2 copies)
XM_036156209.1 → XP_036012102.1 CCR4-NOT transcription complex subunit 6 isoform X2

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
XM_006531941.5 → XP_006532004.1 CCR4-NOT transcription complex subunit 6 isoform X1

See identical proteins and their annotated locations for XP_006532004.1

UniProtKB/Swiss-Prot

Q5NCL3, Q80V15, Q8K3P5

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]
XM_036156208.1 → XP_036012101.1 CCR4-NOT transcription complex subunit 6 isoform X1

UniProtKB/Swiss-Prot

Q5NCL3, Q80V15, Q8K3P5

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]