Aliases for CNOT3 Gene

Aliases for CNOT3 Gene

  • CCR4-NOT Transcription Complex Subunit 3 2 3 4 5
  • NOT3 (Negative Regulator Of Transcription 3, Yeast) Homolog 2 3
  • Leukocyte Receptor Cluster Member 2 3 4
  • CCR4-Associated Factor 3 3 4
  • LENG2 3 4
  • NOT3 3 4
  • CCR4-NOT Transcription Complex, Subunit 3 2
  • KIAA0691 4
  • IDDSADF 3
  • NOT3H 3

External Ids for CNOT3 Gene

Previous HGNC Symbols for CNOT3 Gene

  • NOT3

Previous GeneCards Identifiers for CNOT3 Gene

  • GC19P055290
  • GC19P055066
  • GC19P059318
  • GC19P059333
  • GC19P054641
  • GC19P050957
  • GC19P054138

Summaries for CNOT3 Gene

GeneCards Summary for CNOT3 Gene

CNOT3 (CCR4-NOT Transcription Complex Subunit 3) is a Protein Coding gene. Diseases associated with CNOT3 include Intellectual Developmental Disorder With Speech Delay, Autism, And Dysmorphic Facies and Precursor T-Cell Acute Lymphoblastic Leukemia. Among its related pathways are Gene Expression and TP53 Regulates Transcription of Cell Cycle Genes. An important paralog of this gene is CNOT2.

UniProtKB/Swiss-Prot Summary for CNOT3 Gene

  • 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. May be involved in metabolic regulation; may be involved in recruitment of the CCR4-NOT complex to deadenylation target mRNAs involved in energy metabolism. Involved in mitotic progression and regulation of the spindle assembly checkpoint by regulating the stability of MAD1L1 mRNA. Can repress transcription and may link the CCR4-NOT complex to transcriptional regulation; the repressive function may involve histone deacetylases. Involved in the maintenance of embryonic stem (ES) cell identity.

Gene Wiki entry for CNOT3 Gene

Additional gene information for CNOT3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CNOT3 Gene

Genomics for CNOT3 Gene

GeneHancer (GH) Regulatory Elements for CNOT3 Gene

Promoters and enhancers for CNOT3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CNOT3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CNOT3

Top Transcription factor binding sites by QIAGEN in the CNOT3 gene promoter:
  • C/EBPalpha
  • CBF(2)
  • Egr-1
  • GATA-1
  • NF-Y
  • PPAR-gamma1
  • PPAR-gamma2
  • STAT5A
  • TBP
  • TFIID

Genomic Locations for CNOT3 Gene

Genomic Locations for CNOT3 Gene
chr19:54,137,689-54,155,708
(GRCh38/hg38)
Size:
18,020 bases
Orientation:
Plus strand
chr19:54,641,436-54,659,446
(GRCh37/hg19)
Size:
18,011 bases
Orientation:
Plus strand

Genomic View for CNOT3 Gene

Genes around CNOT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CNOT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CNOT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CNOT3 Gene

Proteins for CNOT3 Gene

  • Protein details for CNOT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75175-CNOT3_HUMAN
    Recommended name:
    CCR4-NOT transcription complex subunit 3
    Protein Accession:
    O75175
    Secondary Accessions:
    • Q9NZN7
    • Q9UF76

    Protein attributes for CNOT3 Gene

    Size:
    753 amino acids
    Molecular mass:
    81872 Da
    Quaternary structure:
    • Component of the CCR4-NOT complex; distinct complexes seem to exist that differ in the participation of probably mutually exclusive catalytic subunits. In the complex interacts directly with CNOT2. Interacts with TIP120B and NANOS2.
    SequenceCaution:
    • Sequence=AAF29828.1; Type=Miscellaneous discrepancy; Note=Seems to have an artifactual loop-out at the 3'-end deleting 2 full exons and part of 2 others.; Evidence={ECO:0000305}; Sequence=BAA31666.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=CAB63766.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CNOT3 Gene

neXtProt entry for CNOT3 Gene

Post-translational modifications for CNOT3 Gene

  • Ubiquitination at Lys737
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CNOT3 Gene

Domains & Families for CNOT3 Gene

Gene Families for CNOT3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for CNOT3 Gene

Blocks:
  • NOT2/NOT3/NOT5
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CNOT3 Gene

GenScript: Design optimal peptide antigens:
  • CCR4-NOT transcription complex, subunit 3 (A9C4B1_HUMAN)
  • CCR4-NOT transcription complex, subunit 3 (B0V3I0_HUMAN)
  • Leukocyte receptor cluster member 2 (CNOT3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75175

UniProtKB/Swiss-Prot:

CNOT3_HUMAN :
  • Belongs to the CNOT2/3/5 family.
Family:
  • Belongs to the CNOT2/3/5 family.
genes like me logo Genes that share domains with CNOT3: view

Function for CNOT3 Gene

Molecular function for CNOT3 Gene

UniProtKB/Swiss-Prot 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. May be involved in metabolic regulation; may be involved in recruitment of the CCR4-NOT complex to deadenylation target mRNAs involved in energy metabolism. Involved in mitotic progression and regulation of the spindle assembly checkpoint by regulating the stability of MAD1L1 mRNA. Can repress transcription and may link the CCR4-NOT complex to transcriptional regulation; the repressive function may involve histone deacetylases. Involved in the maintenance of embryonic stem (ES) cell identity.

Phenotypes From GWAS Catalog for CNOT3 Gene

Gene Ontology (GO) - Molecular Function for CNOT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10637334
genes like me logo Genes that share ontologies with CNOT3: view
genes like me logo Genes that share phenotypes with CNOT3: view

Animal Models for CNOT3 Gene

MGI Knock Outs for CNOT3:

Animal Model Products

CRISPR Products

miRNA for CNOT3 Gene

miRTarBase miRNAs that target CNOT3

Clone Products

  • Addgene plasmids for CNOT3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CNOT3 Gene

Localization for CNOT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CNOT3 Gene

Cytoplasm. Nucleus. Cytoplasm, P-body. Note=NANOS2 promotes its localization to P-body. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CNOT3 gene
Compartment Confidence
cytosol 5
nucleus 4
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CNOT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body ISS --
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0030014 CCR4-NOT complex IDA 19558367
genes like me logo Genes that share ontologies with CNOT3: view

Pathways & Interactions for CNOT3 Gene

genes like me logo Genes that share pathways with CNOT3: view

SIGNOR curated interactions for CNOT3 Gene

Other effect:

Gene Ontology (GO) - Biological Process for CNOT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening TAS --
GO:0001829 trophectodermal cell differentiation IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006417 regulation of translation IEA --
GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest TAS --
genes like me logo Genes that share ontologies with CNOT3: view

Drugs & Compounds for CNOT3 Gene

No Compound Related Data Available

Transcripts for CNOT3 Gene

mRNA/cDNA for CNOT3 Gene

1 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for CNOT3

Alternative Splicing Database (ASD) splice patterns (SP) for CNOT3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a ·
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

ExUns: 19b ^ 20
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for CNOT3 Gene

GeneLoc Exon Structure for
CNOT3

Expression for CNOT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CNOT3 Gene

Protein differential expression in normal tissues from HIPED for CNOT3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.9) and CD8 Tcells (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CNOT3 Gene



Protein tissue co-expression partners for CNOT3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CNOT3

SOURCE GeneReport for Unigene cluster for CNOT3 Gene:

Hs.343571

mRNA Expression by UniProt/SwissProt for CNOT3 Gene:

O75175-CNOT3_HUMAN
Tissue specificity: Ubiquitous. Highly expressed in brain, heart, thymus, spleen, kidney, liver, small intestine, lung and peripheral blood leukocytes.

Evidence on tissue expression from TISSUES for CNOT3 Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Muscle(2.2)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with CNOT3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CNOT3 Gene

Orthologs for CNOT3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CNOT3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CNOT3 31 30
  • 99.51 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CNOT3 31 30
  • 91.28 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Cnot3 17 31 30
  • 90.95 (n)
rat
(Rattus norvegicus)
Mammalia Cnot3 30
  • 90.68 (n)
cow
(Bos Taurus)
Mammalia CNOT3 31 30
  • 90.64 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CNOT3 31
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CNOT3 31
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100158546 30
  • 71.22 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.33620 30
zebrafish
(Danio rerio)
Actinopterygii cnot3a 31 30
  • 70.56 (n)
OneToMany
cnot3b 31
  • 51 (a)
OneToMany
-- 30
fruit fly
(Drosophila melanogaster)
Insecta CG8426 32
  • 64 (a)
l(2)NC136 31
  • 40 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y56A3A.1 32
  • 43 (a)
ntl-3 31
  • 38 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOT3 33 31
  • 22 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.14014 30
rice
(Oryza sativa)
Liliopsida Os.8777 30
Species where no ortholog for CNOT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for CNOT3 Gene

ENSEMBL:
Gene Tree for CNOT3 (if available)
TreeFam:
Gene Tree for CNOT3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CNOT3: view image

Paralogs for CNOT3 Gene

Paralogs for CNOT3 Gene

(1) SIMAP similar genes for CNOT3 Gene using alignment to 5 proteins:

  • CNOT3_HUMAN
  • H0Y5X7_HUMAN
  • H7C148_HUMAN
  • H7C3F5_HUMAN
  • H7C5J4_HUMAN
genes like me logo Genes that share paralogs with CNOT3: view

Variants for CNOT3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CNOT3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
694669 Pathogenic: INTELLECTUAL DEVELOPMENTAL DISORDER WITH SPEECH DELAY, AUTISM, AND DYSMORPHIC FACIES 54,145,930(+) T/TC FRAMESHIFT_VARIANT
694670 Pathogenic: INTELLECTUAL DEVELOPMENTAL DISORDER WITH SPEECH DELAY, AUTISM, AND DYSMORPHIC FACIES 54,149,625(+) CAG/C FRAMESHIFT_VARIANT
694671 Pathogenic: INTELLECTUAL DEVELOPMENTAL DISORDER WITH SPEECH DELAY, AUTISM, AND DYSMORPHIC FACIES 54,152,588(+) G/A NONSENSE
694673 Pathogenic: INTELLECTUAL DEVELOPMENTAL DISORDER WITH SPEECH DELAY, AUTISM, AND DYSMORPHIC FACIES 54,153,757(+) C/T NONSENSE
rs1555806893 Likely Pathogenic: Inborn genetic diseases 54,149,592(+) C/CT FRAMESHIFT_VARIANT

Additional dbSNP identifiers (rs#s) for CNOT3 Gene

Structural Variations from Database of Genomic Variants (DGV) for CNOT3 Gene

Variant ID Type Subtype PubMed ID
esv24700 CNV loss 19812545
esv2718812 CNV deletion 23290073
esv3644782 CNV gain 21293372
esv3644783 CNV gain 21293372
nsv2545 CNV insertion 18451855
nsv515623 CNV loss 19592680
nsv953613 CNV deletion 24416366

Variation tolerance for CNOT3 Gene

Residual Variation Intolerance Score: 50.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.14; 38.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CNOT3 Gene

Human Gene Mutation Database (HGMD)
CNOT3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CNOT3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CNOT3 Gene

Disorders for CNOT3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for CNOT3 Gene - From: OMIM, ClinVar, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CNOT3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CNOT3

genes like me logo Genes that share disorders with CNOT3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CNOT3 Gene

Publications for CNOT3 Gene

  1. Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits. (PMID: 10637334) Albert TK … Timmers HT (Nucleic acids research 2000) 2 3 4 54
  2. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9734811) Ishikawa K … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 54
  3. Cnot1, Cnot2, and Cnot3 maintain mouse and human ESC identity and inhibit extraembryonic differentiation. (PMID: 22367759) Zheng X … Hu G (Stem cells (Dayton, Ohio) 2012) 3 4 54
  4. Involvement of CNOT3 in mitotic progression through inhibition of MAD1 expression. (PMID: 22342980) Takahashi A … Yamamoto T (Biochemical and biophysical research communications 2012) 3 4 54
  5. Human Ccr4-Not complexes contain variable deadenylase subunits. (PMID: 19558367) Lau NC … Timmers HT (The Biochemical journal 2009) 3 4 54

Products for CNOT3 Gene