Human Gene CNOT9 (ENST00000273064.11_4) from GENCODE V47lift37
  Description: CCR4-NOT transcription complex subunit 9, transcript variant 4 (from RefSeq NR_073390.2)
Gencode Transcript: ENST00000273064.11_4
Gencode Gene: ENSG00000144580.15_13
Transcript (Including UTRs)
   Position: hg19 chr2:219,433,562-219,461,803 Size: 28,242 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr2:219,433,678-219,458,999 Size: 25,322 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:219,433,562-219,461,803)mRNA (may differ from genome)Protein (299 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RCD1_HUMAN
DESCRIPTION: RecName: Full=Cell differentiation protein RCD1 homolog; Short=Rcd-1; AltName: Full=CCR4-NOT transcription complex subunit 9;
FUNCTION: Transcription factor that down-regulates 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.
SUBUNIT: Homodimer. 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.
SUBCELLULAR LOCATION: Nucleus (By similarity). Cytoplasm, P-body (By similarity). Note=NANOS2 promotes its localization to P-body (By similarity).
TISSUE SPECIFICITY: Detected in spleen, thymus, prostate, testis, ovary and intestine.
SIMILARITY: Belongs to the RCD1 family.
SEQUENCE CAUTION: Sequence=AAH07102.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 25.33 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 448.66 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -51.00116-0.440 Picture PostScript Text
3' UTR -916.302804-0.327 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR007216 - Cell_differentiation_Rcd1

Pfam Domains:
PF04078 - Cell differentiation family, Rcd1-like

SCOP Domains:
48371 - ARM repeat
53474 - alpha/beta-Hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2FV2 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q92600
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005154 epidermal growth factor receptor binding
GO:0005515 protein binding
GO:0019900 kinase binding
GO:0019904 protein domain specific binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006402 mRNA catabolic process
GO:0006417 regulation of translation
GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0007548 sex differentiation
GO:0017148 negative regulation of translation
GO:0019221 cytokine-mediated signaling pathway
GO:0031047 gene silencing by RNA
GO:0033138 positive regulation of peptidyl-serine phosphorylation
GO:0033147 negative regulation of intracellular estrogen receptor signaling pathway
GO:0045742 positive regulation of epidermal growth factor receptor signaling pathway
GO:2000327 positive regulation of ligand-dependent nuclear receptor transcription coactivator activity

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0030014 CCR4-NOT complex
GO:0030015 CCR4-NOT core complex
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  AK293281 - Homo sapiens cDNA FLJ58752 complete cds, highly similar to Homo sapiens RCD1 required for cell differentiation 1 homolog (RQCD1), mRNA.
AB500892 - Homo sapiens RQCD1 mRNA, complete cds.
BC137455 - Homo sapiens RCD1 required for cell differentiation1 homolog (S. pombe), mRNA (cDNA clone MGC:169078 IMAGE:9021455), complete cds.
BC137456 - Homo sapiens RCD1 required for cell differentiation1 homolog (S. pombe), mRNA (cDNA clone MGC:169079 IMAGE:9021456), complete cds.
AK316567 - Homo sapiens cDNA, FLJ93148, highly similar to Homo sapiens RCD1 required for cell differentiation1 homolog (S. pombe) (RQCD1), mRNA.
BC007102 - Homo sapiens RCD1 required for cell differentiation1 homolog (S. pombe), mRNA (cDNA clone IMAGE:4281152), partial cds.
KJ904620 - Synthetic construct Homo sapiens clone ccsbBroadEn_14014 RQCD1 gene, encodes complete protein.
AK296037 - Homo sapiens cDNA FLJ56914 complete cds, highly similar to Rattus norvegicus rcd1 (required for cell differentiation) homolog 1, mRNA.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q92600 (Reactome details) participates in the following event(s):

R-HSA-6798044 BTG2 binds CCR4-NOT complex
R-HSA-429955 CCR4-NOT complex deadenylates mRNA
R-HSA-6804115 TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
R-HSA-6791312 TP53 Regulates Transcription of Cell Cycle Genes
R-HSA-429947 Deadenylation of mRNA
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-212436 Generic Transcription Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B2RPI0, B5MDQ4, B7Z1E5, CNOT9 , CNOT9_HUMAN, ENST00000273064.1, ENST00000273064.10, ENST00000273064.2, ENST00000273064.3, ENST00000273064.4, ENST00000273064.5, ENST00000273064.6, ENST00000273064.7, ENST00000273064.8, ENST00000273064.9, NR_073390, Q92600, Q96IX4, RCD1, RQCD1, uc317jau.1, uc317jau.2
UCSC ID: ENST00000273064.11_4
RefSeq Accession: NM_005444.3
Protein: Q92600 (aka RCD1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.