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CNOT6 CCR4-NOT transcription complex subunit 6 [ Homo sapiens (human) ]

Gene ID: 57472, updated on 27-Nov-2024

Summary

Official Symbol
CNOT6provided by HGNC
Official Full Name
CCR4-NOT transcription complex subunit 6provided by HGNC
Primary source
HGNC:HGNC:14099
See related
Ensembl:ENSG00000113300 MIM:608951; AllianceGenome:HGNC:14099
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CCR4; Ccr4a
Summary
This gene encodes the catalytic component of the CCR4-NOT core transcriptional regulation complex. The encoded protein has a 3'-5' RNase activity and prefers polyadenylated substrates. The CCR4-NOT complex plays a role in many cellular processes, including miRNA-mediated repression, mRNA degradation, and transcriptional regulation. [provided by RefSeq, Dec 2014]
Expression
Ubiquitous expression in testis (RPKM 8.0), urinary bladder (RPKM 6.4) and 25 other tissues See more
Orthologs
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Genomic context

See CNOT6 in Genome Data Viewer
Location:
5q35.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (180494379..180578358)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (181050244..181134238)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (179921379..180005358)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901153 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:179894063-179895262 Neighboring gene uncharacterized LOC102725231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23768 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:179901825-179902356 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:179912532-179913731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16768 Neighboring gene NANOG hESC enhancer GRCh37_chr5:179954464-179954965 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:179958359-179959013 Neighboring gene proteolipid protein 2 (colonic epithelium-enriched) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23769 Neighboring gene Sharpr-MPRA regulatory region 4663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:180016691-180017360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:180017361-180018030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:180018031-180018700 Neighboring gene uncharacterized LOC124901154 Neighboring gene secretoglobin family 3A member 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA1194

Gene Ontology Provided by GOA

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 IDA
Inferred from Direct Assay
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear receptor coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
enables poly(A)-specific ribonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
enables poly(A)-specific ribonuclease activity TAS
Traceable Author Statement
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
part_of CCR4-NOT complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of CCR4-NOT complex NAS
Non-traceable Author Statement
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in membrane HDA PubMed 

General protein information

Preferred Names
CCR4-NOT transcription complex subunit 6
Names
carbon catabolite repression 4 protein
carbon catabolite repressor protein 4 homolog
cytoplasmic deadenylase
NP_001357401.1
NP_001357402.1
NP_001357403.1
XP_016865160.1
XP_016865161.1
XP_024301904.1
XP_047273392.1
XP_047273393.1
XP_047273394.1
XP_047273395.1
XP_047273396.1
XP_047273397.1
XP_047273398.1
XP_054208966.1
XP_054208967.1
XP_054208968.1
XP_054208969.1
XP_054208970.1
XP_054208971.1
XP_054208972.1
XP_054208973.1
XP_054208974.1
XP_054208975.1

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)

  1. NM_001370472.1NP_001357401.1  CCR4-NOT transcription complex subunit 6 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC034213, AC122714
    Consensus CDS
    CCDS4455.1
    UniProtKB/Swiss-Prot
    A7MD46, D3DWR0, Q9ULM6
    Related
    ENSP00000261951.4, ENST00000261951.9
    Conserved Domains (3) summary
    cd10313
    Location:191540
    Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6
    COG4886
    Location:52159
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00031
    Location:3352
    LRR_1; leucine-rich repeat [structural motif]
  2. NM_001370473.1NP_001357402.1  CCR4-NOT transcription complex subunit 6 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC034213, AC122714
    Conserved Domains (3) summary
    cd10313
    Location:186535
    Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6
    COG4886
    Location:52158
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00031
    Location:3352
    LRR_1; leucine-rich repeat [structural motif]
  3. NM_001370474.1NP_001357403.1  CCR4-NOT transcription complex subunit 6 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC122714
    Conserved Domains (3) summary
    cd10313
    Location:96445
    Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6
    sd00033
    Location:426
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:344
    LRR_4; Leucine Rich repeats (2 copies)

RNA

  1. NR_163437.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC034213, AC122714
  2. NR_163438.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC034213, AC122714

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    180494379..180578358
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047417436.1XP_047273392.1  CCR4-NOT transcription complex subunit 6 isoform X1

    UniProtKB/Swiss-Prot
    A7MD46, D3DWR0, Q9ULM6
    Related
    ENSP00000481893.1, ENST00000618123.4
  2. XM_047417440.1XP_047273396.1  CCR4-NOT transcription complex subunit 6 isoform X4

  3. XM_047417438.1XP_047273394.1  CCR4-NOT transcription complex subunit 6 isoform X2

  4. XM_047417437.1XP_047273393.1  CCR4-NOT transcription complex subunit 6 isoform X2

  5. XM_017009672.2XP_016865161.1  CCR4-NOT transcription complex subunit 6 isoform X4

    Conserved Domains (4) summary
    sd00031
    Location:3352
    LRR_1; leucine-rich repeat [structural motif]
    pfam12799
    Location:5191
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:51109
    LRR_8; Leucine rich repeat
    cl00490
    Location:191420
    EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
  6. XM_047417439.1XP_047273395.1  CCR4-NOT transcription complex subunit 6 isoform X5

  7. XM_047417442.1XP_047273398.1  CCR4-NOT transcription complex subunit 6 isoform X7

  8. XM_017009671.3XP_016865160.1  CCR4-NOT transcription complex subunit 6 isoform X3

    Conserved Domains (3) summary
    cd10313
    Location:96445
    Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6
    sd00033
    Location:426
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:344
    LRR_4; Leucine Rich repeats (2 copies)
  9. XM_047417441.1XP_047273397.1  CCR4-NOT transcription complex subunit 6 isoform X6

  10. XM_024446136.2XP_024301904.1  CCR4-NOT transcription complex subunit 6 isoform X6

    Conserved Domains (1) summary
    cd10313
    Location:16365
    Deadenylase_CCR4a; C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    181050244..181134238
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352991.1XP_054208966.1  CCR4-NOT transcription complex subunit 6 isoform X1

    UniProtKB/Swiss-Prot
    A7MD46, D3DWR0, Q9ULM6
  2. XM_054352997.1XP_054208972.1  CCR4-NOT transcription complex subunit 6 isoform X4

  3. XM_054352993.1XP_054208968.1  CCR4-NOT transcription complex subunit 6 isoform X2

  4. XM_054352992.1XP_054208967.1  CCR4-NOT transcription complex subunit 6 isoform X2

  5. XM_054352995.1XP_054208970.1  CCR4-NOT transcription complex subunit 6 isoform X4

  6. XM_054352996.1XP_054208971.1  CCR4-NOT transcription complex subunit 6 isoform X5

  7. XM_054353000.1XP_054208975.1  CCR4-NOT transcription complex subunit 6 isoform X7

  8. XM_054352994.1XP_054208969.1  CCR4-NOT transcription complex subunit 6 isoform X3

  9. XM_054352998.1XP_054208973.1  CCR4-NOT transcription complex subunit 6 isoform X6

  10. XM_054352999.1XP_054208974.1  CCR4-NOT transcription complex subunit 6 isoform X6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001303241.2: Suppressed sequence

    Description
    NM_001303241.2: This RefSeq was removed because currently there is insufficient support for the transcript. Intron1 is not supported by transcript data and likely represented repeat copy number variation.
  2. NM_015455.3: Suppressed sequence

    Description
    NM_015455.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.