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Gene: Cnot9 (CCR4-NOT transcription complex subunit 9) Rattus norvegicus

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Symbol:

Cnot9

Name:

CCR4-NOT transcription complex subunit 9

RGD ID:

1311495

Description:

Predicted to enable several functions, including epidermal growth factor receptor binding activity; protein homodimerization activity; and transcription coactivator activity. Predicted to be involved in negative regulation of intracellular estrogen receptor signaling pathway; negative regulation of translation; and positive regulation of epidermal growth factor receptor signaling pathway. Predicted to act upstream of or within cytokine-mediated signaling pathway. Predicted to be located in cytosol and nucleus. Predicted to be part of CCR4-NOT core complex. Predicted to be active in P-body. Orthologous to human CNOT9 (CCR4-NOT transcription complex subunit 9); PARTICIPATES IN microRNA pathway; RNA degradation pathway; INTERACTS WITH 2,4-dinitrotoluene; bisphenol A; dibutyl phthalate.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

cell differentiation protein RCD1 homolog; cell differentiation protein RQCD1 homolog; LOC301513; MGC95021; rcd-1; rcd1 (required for cell differentiation) homolog 1; rcd1 (required for cell differentiation) homolog 1 (S. pombe); RCD1 required for cell differentiation1 homolog; Rcd1 required for cell differentiation1 homolog (S. pombe); Rqcd1

RGD Orthologs

Alliance Orthologs

More Info

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More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CNOT9 (CCR4-NOT transcription complex subunit 9)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Cnot9 (CCR4-NOT transcription complex, subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Cnot9 (CCR4-NOT transcription complex subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CNOT9 (CCR4-NOT transcription complex subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CNOT9 (CCR4-NOT transcription complex subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cnot9 (CCR4-NOT transcription complex subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CNOT9 (CCR4-NOT transcription complex subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CNOT9 (CCR4-NOT transcription complex subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cnot9 (CCR4-NOT transcription complex subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Cnot9 (CCR4-NOT transcription complex subunit 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CNOT9 (CCR4-NOT transcription complex subunit 9)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Cnot9 (CCR4-NOT transcription complex, subunit 9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	cnot9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	CAF40	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG2053	Alliance	DIOPT (Ensembl Compara\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Rcd-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Rcd-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Rcd-1r	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Rcd-1r	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ntl-9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	cnot9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	9	83,533,369 - 83,558,207 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	9	83,533,369 - 83,558,197 (+)	Ensembl				GRCr8
mRatBN7.2	9	76,084,269 - 76,109,111 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	76,084,334 - 76,109,100 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	9	84,529,408 - 84,554,235 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	9	89,658,357 - 89,683,184 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	9	88,044,535 - 88,069,367 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	9	81,783,349 - 81,808,815 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	81,783,349 - 81,808,805 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	9	81,547,682 - 81,573,457 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	9	73,843,388 - 73,870,449 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	9	73,657,770 - 73,682,385 (+)	NCBI		Celera
RGSC_v3.1	9	73,990,369 - 74,017,421 (+)	NCBI
Cytogenetic Map	9	q33	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

cerebrotendinous xanthomatosis (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

1-chloro-2,4-dinitrobenzene (ISO)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4-dinitrotoluene (EXP)

aflatoxin B1 (ISO)

amosite asbestos (ISO)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

diarsenic trioxide (ISO)

dibutyl phthalate (EXP)

dioxygen (ISO)

doxorubicin (ISO)

ethyl methanesulfonate (ISO)

ferroheme b (ISO)

flutamide (EXP)

gentamycin (EXP)

heme b (ISO)

hydrogen cyanide (ISO)

ivermectin (ISO)

leflunomide (EXP)

methyl methanesulfonate (ISO)

nickel atom (ISO)

okadaic acid (ISO)

ozone (ISO)

perfluorooctane-1-sulfonic acid (ISO)

potassium cyanide (ISO)

quercetin (ISO)

rotenone (ISO)

sodium arsenite (ISO)

sulforaphane (ISO)

thimerosal (ISO)

thioacetamide (EXP)

thiram (ISO)

titanium dioxide (ISO)

trichostatin A (ISO)

trimellitic anhydride (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

cytokine-mediated signaling pathway (ISO)

mRNA catabolic process (IEA)

negative regulation of intracellular estrogen receptor signaling pathway (IEA,ISO,ISS)

negative regulation of translation (IBA)

positive regulation of DNA-templated transcription (IEA)

positive regulation of epidermal growth factor receptor signaling pathway (IEA,ISO)

positive regulation of peptidyl-serine phosphorylation (ISO)

regulation of translation (IEA)

regulatory ncRNA-mediated gene silencing (IEA)

Cellular Component

CCR4-NOT complex (IEA,ISO,ISS)

CCR4-NOT core complex (IBA)

cytosol (IEA)

nucleus (IEA)

P-body (IBA,IEA,ISO,ISS)

protein-containing complex (IEA,ISO)

Molecular Function

epidermal growth factor receptor binding (IEA,ISO)

kinase binding (IEA,ISO)

protein binding (IPI,ISO)

protein domain specific binding (IEA,ISO)

protein homodimerization activity (IEA,ISO)

transcription coactivator activity (IEA,ISO,ISS)

Molecular Pathway Annotations Click to see Annotation Detail View

microRNA pathway (ISO)

RNA degradation pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Components of the CCR4-NOT complex function as nuclear hormone receptor coactivators via association with the NRC-interacting Factor NIF-1.	Garapaty S, etal., J Biol Chem. 2008 Mar 14;283(11):6806-16. doi: 10.1074/jbc.M706986200. Epub 2008 Jan 7.
2.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
6.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
8.	Comprehensive gene review and curation	RGD comprehensive gene curation
9.	RNA decay machines: deadenylation by the Ccr4-not and Pan2-Pan3 complexes.	Wahle E and Winkler GS, Biochim Biophys Acta. 2013 Jun-Jul;1829(6-7):561-70. doi: 10.1016/j.bbagrm.2013.01.003. Epub 2013 Jan 19.

Additional References at PubMed

PMID:10880228	PMID:12477932	PMID:16778766	PMID:19558367	PMID:19946888	PMID:20133598	PMID:20878056	PMID:24768540

Genomics

Comparative Map Data

Cnot9
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	9	83,533,369 - 83,558,207 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	9	83,533,369 - 83,558,197 (+)	Ensembl				GRCr8
mRatBN7.2	9	76,084,269 - 76,109,111 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	9	76,084,334 - 76,109,100 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	9	84,529,408 - 84,554,235 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	9	89,658,357 - 89,683,184 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	9	88,044,535 - 88,069,367 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	9	81,783,349 - 81,808,815 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	9	81,783,349 - 81,808,805 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	9	81,547,682 - 81,573,457 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	9	73,843,388 - 73,870,449 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	9	73,657,770 - 73,682,385 (+)	NCBI		Celera
RGSC_v3.1	9	73,990,369 - 74,017,421 (+)	NCBI
Cytogenetic Map	9	q33	NCBI

CNOT9
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	218,568,839 - 218,597,080 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	218,568,580 - 218,597,080 (+)	Ensembl			hg38	GRCh38
GRCh37	2	219,433,562 - 219,461,803 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	219,141,922 - 219,167,243 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	2	219,259,182 - 219,284,504	NCBI
Celera	2	213,201,461 - 213,226,753 (+)	NCBI		Celera
Cytogenetic Map	2	q35	NCBI
HuRef	2	211,286,392 - 211,314,470 (+)	NCBI		HuRef
CHM1_1	2	219,440,299 - 219,468,136 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	219,055,409 - 219,083,622 (+)	NCBI		T2T-CHM13v2.0

Cnot9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	74,545,192 - 74,570,001 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	1	74,545,217 - 74,570,001 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	1	74,506,036 - 74,530,842 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	74,506,058 - 74,530,842 (+)	Ensembl			mm10	GRCm38
MGSCv37	1	74,552,634 - 74,577,416 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	1	74,439,265 - 74,464,048 (+)	NCBI		MGSCv36	mm8
Celera	1	75,063,648 - 75,088,335 (+)	NCBI		Celera
Cytogenetic Map	1	C4	NCBI
cM Map	1	38.54	NCBI

Cnot9
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955453	14,816,910 - 14,845,912 (-)	Ensembl
ChiLan1.0	NW_004955453	14,819,007 - 14,845,879 (-)	NCBI	ChiLan1.0	ChiLan1.0

CNOT9
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	13	121,199,746 - 121,227,266 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2B	121,214,711 - 121,242,232 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2B	105,826,633 - 105,854,415 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2B	224,422,472 - 224,450,141 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	224,422,467 - 224,450,133 (+)	Ensembl			panPan2	panpan1.1

CNOT9
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	37	25,186,928 - 25,213,255 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	37	25,187,066 - 25,212,642 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	37	26,006,559 - 26,033,165 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	37	25,202,576 - 25,229,178 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	37	25,202,854 - 25,230,708 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	37	25,107,513 - 25,134,117 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	37	25,041,698 - 25,068,291 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	37	25,061,893 - 25,088,503 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Cnot9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405303	174,680,309 - 174,706,189 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936569	1,022,979 - 1,049,136 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936569	1,023,057 - 1,048,968 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CNOT9
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	120,590,641 - 120,623,898 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	15	120,590,354 - 120,622,203 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	133,604,829 - 133,636,825 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CNOT9
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	10	104,473,215 - 104,502,321 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	10	104,473,216 - 104,503,007 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666040	94,903,347 - 94,933,564 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cnot9
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624823	6,450,656 - 6,484,578 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624823	6,449,165 - 6,484,593 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Cnot9
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	4	147,949,738 - 147,973,790 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Cnot9
97 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	582
Count of miRNA genes:	254
Interacting mature miRNAs:	330
Transcripts:	ENSRNOT00000021548
Prediction methods:	Microtar, Miranda, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2303170	Bp332	Blood pressure QTL 332	3.73	0.027	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	9	6714888	84474983	Rat
631656	Bp108	Blood pressure QTL 108	5.97	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	56047863	101047863	Rat
7411571	Bw138	Body weight QTL 138	14.3	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	9	40029925	85029925	Rat
1582203	Gluco19	Glucose level QTL 19	3.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	9	63376862	108376862	Rat
8662828	Vetf6	Vascular elastic tissue fragility QTL 6	3.9		artery integrity trait (VT:0010639)	patent ductus arteriosus score (CMO:0002566)	9	44458256	99506504	Rat
724515	Uae16	Urinary albumin excretion QTL 16	8		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	9	65657365	108376720	Rat
61352	Bp34	Blood pressure QTL 34	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	82168823	86720295	Rat
1598834	Memor11	Memory QTL 11	2.5		exploratory behavior trait (VT:0010471)	average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)	9	44458256	85262605	Rat
70186	Niddm26	Non-insulin dependent diabetes mellitus QTL 26	3.87		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	9	29567664	83835942	Rat
70218	Cm28	Cardiac mass QTL 28	8.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	9	41720295	86720295	Rat
724544	Uae9	Urinary albumin excretion QTL 9	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	9	64220169	109220169	Rat
2290450	Scl57	Serum cholesterol level QTL 57	4.15		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	9	44458256	121768150	Rat
1578760	Cm53	Cardiac mass QTL 53	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	9	64220169	109220169	Rat
1581580	Uae34	Urinary albumin excretion QTL 34			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	9	64220169	109220169	Rat
1581517	Bp284	Blood pressure QTL 284			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	39220186	84220186	Rat
1300134	Bp185	Blood pressure QTL 185	3.73		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	9	68875497	121768150	Rat
1354626	Bvd1	Brain ventricular dilatation QTL 1	3.73	0.001	brain ventricle morphology trait (VT:0000822)	hydrocephalus severity score (CMO:0001881)	9	83161999	118999486	Rat
731164	Uae25	Urinary albumin excretion QTL 25	3.5	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	9	48718864	108376862	Rat
7411656	Foco26	Food consumption QTL 26	9.8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	9	40029925	85029925	Rat
4889943	Bss90	Bone structure and strength QTL 90	4.1		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	9	54506504	99506504	Rat
1578757	Pur6	Proteinuria QTL 6	3.3	0.005	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	9	64220169	109220169	Rat

Markers in Region

BE116325

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_5.0	9	81,553,607 - 81,553,856	UniSTS	Rnor5.0
RGSC_v3.4	9	73,849,235 - 73,849,484	UniSTS	RGSC3.4
Celera	9	73,663,270 - 73,663,519	UniSTS
RH 3.4 Map	9	770.39	UniSTS
Cytogenetic Map	9	q33	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	164	91	90	59	92	59	6	356	192	11	143	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001009357	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC087134	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225078	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000009	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000021548 ⟹ ENSRNOP00000021548

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	9	83,533,369 - 83,558,197 (+)	Ensembl
mRatBN7.2 Ensembl	9	76,084,334 - 76,109,094 (+)	Ensembl
Rnor_6.0 Ensembl	9	81,783,349 - 81,808,805 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000100848 ⟹ ENSRNOP00000097848

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	9	83,538,910 - 83,558,197 (+)	Ensembl
mRatBN7.2 Ensembl	9	76,084,567 - 76,109,100 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000107071 ⟹ ENSRNOP00000076837

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	9	83,542,819 - 83,558,197 (+)	Ensembl
mRatBN7.2 Ensembl	9	76,093,719 - 76,109,100 (+)	Ensembl

RefSeq Acc Id:

NM_001009357 ⟹ NP_001009357

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	9	83,533,369 - 83,558,207 (+)	NCBI
mRatBN7.2	9	76,084,269 - 76,109,111 (+)	NCBI
Rnor_6.0	9	81,783,349 - 81,808,815 (+)	NCBI
Rnor_5.0	9	81,547,682 - 81,573,457 (+)	NCBI
RGSC_v3.4	9	73,843,388 - 73,870,449 (+)	RGD
Celera	9	73,657,770 - 73,682,385 (+)	RGD

Sequence:

show sequence

CCACCATTTTCCTCTCGCTCAGCCTGCTTGAGCATGCGCAGTTTTTGTCCTTCCAAGACTGCTG
GCCTTTTCCCGCCCTTCTCTGGCCTTAGGAGGAAAGTCAGAGTTCACGTTTCTTAGGGGATATA
CTTGCGATGCCGGGGGGATACGAGGACCAGTAGTTTGCAGACGTCATTTTGATCCTGAACCTGA
AGGTTCAAGGGACATACTTTGGGACTATTTGTTAGGCCGAGGTCCAGGAGGCGGGAAAGGGCTG
TGTGGGCGGAGGGTCGGAGGTGAGAGGTCAAAGGGCTGCGAAGAGGGAGGAGCGAGCCGGAGAC
GGATGGCGGCTCTTCATCTTCGGCTGCAGAGCCACTAAAGCTGGGACGCGGGTCCGGCGCGTCC
AGCGGAAGAAGTAGAGCGGCCCCCGCTCCCAACATGCACAGCCTGGCAACGGCAGCGCCTGTGC
CTACTGCACTGGCCCAGGTGGACAGAGAGAAGATCTATCAGTGGATCAATGAACTGTCCAGTCC
TGAAACAAGGGAAAATGCTTTGCTGGAGCTGAGCAAGAAGCGAGAGTCTGTCCCTGACCTTGCG
CCCATGCTGTGGCATTCATTCGGTACTATTGCAGCACTTTTACAGGAAATTGTAAATATTTATC
CATCTATCAACCCTCCAACCTTGACAGCACACCAATCTAACAGGGTTTGCAATGCTCTAGCATT
GCTACAGTGTGTGGCCTCACACCCAGAGACCAGGTCAGCCTTTCTTGCAGCACACATCCCACTC
TTTTTGTACCCCTTTTTGCACACAGTCAGCAAAACTCGTCCCTTTGAATATCTTCGGCTCACCA
GCCTTGGAGTTATTGGGGCCTTGGTTAAAACAGATGAGCAAGAAGTAATCAACTTTTTATTGAC
AACAGAAATCATCCCTTTGTGTTTGCGCATCATGGAATCTGGAAGTGAACTGTCTAAAACGGTT
GCCACATTCATCCTCCAGAAGATCCTCTTAGATGACACTGGTCTGGCTTATATATGTCAGACAT
ATGAGCGTTTTTCCCATGTTGCCATGATCTTGGGTAAAATGGTCCTGCAGCTATCCAAAGAACC
ATCTGCCCGTCTGCTGAAGCATGTAGTAAGATGTTACCTTCGACTCTCAGATAATCCCAGGGCA
CGTGAAGCACTCAGACAGTGCCTCCCTGACCAGCTGAAGGACACAACCTTTGCCCAGGTGCTAA
AAGATGACACCACCACCAAACGCTGGCTTGCACAACTGGTGAAGAACCTGCAGGAGGGCCAAGT
CACCGATCCCCGGGGAATTCCCCTGCCCCCTCAGTGATCCTCGACATTCCCTCTCACTACTCCC
CTACGTTGGGGAGTAAGGGTGGAACCTATGAGGAAAACAGCTCAGGTTTTATTGCCGACTGGGA
ATAGACAACCTCAATGCTGAACTGTACTGGAGAAAAGGGGCAAGGTACCCCACTGAGGTGTGTG
GGCTGACTGGAGGTCCTGGATCCCCCTACTGCTCCCAGGAATTGGGCTCCTGACAGCAGTCTGC
TACCACAGCCCCAGGAGGGTGTCAACACCAGCAAATGCTGTATTTGCAGCATGCCCAAGATGAC
CCTGCTCCCCAACCTCTGCCTAGCCACTGGTAGAGAGAGGAGAGGTGGTAATCACAGTAACACT
GTAGGCATGGAGAGCACCTGGGACCAAACCATGTGGCTTTTTTTTAAAAAAAAAAAAACAAAAA
ACAAAAAACTTTGCCTTCCTGGACGACTCAAGGTGTGTCTCTTAATTCTCTCTCACACAGTATT
TGTTTACTTTGGATTTTTGTTTTTAATCTCAAAAGAGAGAGATGTGTTTAATGGACACAAGCTG
TAGTTTTCAGCAAAACTTTGTCAGTTGGCACTGTTTACACGTCTCTTAGCTGCATAAGCTCAAT
AAAAGTTGGTCTGGGCATTGCATCCCCTCGGGCAGACCGATGGCGCTATCAGGCTGTTGGGTGG
AATGGGAGGCAGGGGAAGAGGAAAGCAAAGCCAAGCAAAAACACTACCAACCATTCCCCTCTGC
CCCTGTTGTTTCCCTCGCAAGCCTGGCTGCTGTGAGGACATTCACTTTGGCTCTGGCTTCGGCT
GCTAGCCCACCCAAATCTCAGCGCTTGCCCCTTTCCTACCACTTAGACTTAAAGCAGGCGTCTT
AATTTACCCAGCCTTCCTTAGAGAGTTGTACTGGGGTGGAGGGAGGCAGTTCTTCAGGTTCAAG
TCTTCACAGGTAGTTTCCAGGTGTCTTCTCAAATGGAACAAGCACCTAGATCCAAATGGGGCCC
TGACCCCGTTCTTCTCGTGTGGGTTTCAGTAGTGCCATCTCCTCATGATTATACTTGAAGCAGT
ATTAGCTGAATGAGTTTTTTCAGAGTTAAACAGCTGCACTCTGCTGTCTCAGTCCCCTCTCCCT
TTAACACTTTCTTTGGTCTATGGAAACTACAGGGCTACCACTGGAATGTTTTTTACTTGTTGAT
AGTGTCAGAGTTCCCTTTCCATCTCCATGGGCTTGACTTAACCTGTTACTGTAAACTGCCTTTC
TGAGATCCTTCCACTGTCAACCTTTGTTTTCTCATCCTCATCCCAAAGATGGGGTTATTAATCC
AACTCTAGAGAGAGCCCAAATCTTCAGCCCATGTCTCACACACTTGAAGGTATCTTTATTAAAT
TTGAAGAGACTATAAAGGGACAGATGCTCATAGAAACCTTTGCAGAGGCAGTTGTGCCAAACCA
AGGGCTCTTTAAGCTGACTTTCACACAGGGAGCCAGCCTTGTTTGTTGGCTTCTGTCTTCAGAG
ACAAGAAAGTGCTAATTAAGTAACCTAGATTTAGGGAGGGTAGAATAAGCATTTATTCCCCTGC
CTTCCAAATTGAAGAGGAGACCATGGCCTCAAGGCTGAAGAAGGAAAGTCTTAGAAAGCAAAGA
ACAGCATTGCCTGATAAACGTCTCGACTCACTCTGCAACTGTGATCTGGAAAGTTCACTAGGGT
ACCCTGATTTTTGAAATCCGCCTTCCTGATGAGCTGAAGTCTCTCATTCCGCCTCACTGGGGAA
GCAGCTGAGACTTGGAGCCTTGCTCCCTGGGACATTGTCTCCATCTTTCGGTGCACTGGCCATG
TTACTGTGCCAATAGTGTCTTAATTCATGTCCCATCTGTCCTCAGCTGGCCTTGGACCTACATA
GGAGTTGAATGAGGAGGAGTGCAACGGGTCTTAATTCCTGTGGTTGGTCCTGATGTTATATGTA
CTATATAAAGAGGCTCCTCCCTTTATTTTGTGTTTTCCATCCCTCACCCTCAACAGGATTAAAA
TAAAACATGCTCTGGTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001009357	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH87134	(Get FASTA)	NCBI Sequence Viewer
	EDL75357	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000021548
	ENSRNOP00000097848.1
GenBank Protein	Q5PQL2	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001009357 ⟸ NM_001009357

- UniProtKB:

Q5PQL2 (UniProtKB/Swiss-Prot), A6JVU9 (UniProtKB/TrEMBL), A0A8L2QAX2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MHSLATAAPVPTALAQVDREKIYQWINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIA
ALLQEIVNIYPSINPPTLTAHQSNRVCNALALLQCVASHPETRSAFLAAHIPLFLYPFLHTVSK
TRPFEYLRLTSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLD
DTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRLSDNPRAREALRQCLPDQ
LKDTTFAQVLKDDTTTKRWLAQLVKNLQEGQVTDPRGIPLPPQ

hide sequence

Ensembl Acc Id:

ENSRNOP00000021548 ⟸ ENSRNOT00000021548

Ensembl Acc Id:

ENSRNOP00000097848 ⟸ ENSRNOT00000100848

Ensembl Acc Id:

ENSRNOP00000076837 ⟸ ENSRNOT00000107071

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5PQL2-F1-model_v2	AlphaFold	Q5PQL2	1-299	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13696754

Promoter ID:

EPDNEW_R7278

Type:

initiation region

Name:

Cnot9_1

Description:

CCR4-NOT transcription complex subunit 9

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	9	81,783,386 - 81,783,446	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311495	AgrOrtholog
BioCyc Gene	G2FUF-27129	BioCyc
Ensembl Genes	ENSRNOG00000016034	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000021548	ENTREZGENE
	ENSRNOT00000100848.1	UniProtKB/Swiss-Prot
Gene3D-CATH	1.25.10.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7122272	IMAGE-MGC_LOAD
InterPro	ARM-like	UniProtKB/Swiss-Prot
	ARM-type_fold	UniProtKB/Swiss-Prot
	CNOT9	UniProtKB/Swiss-Prot
KEGG Report	rno:301513	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:95021	IMAGE-MGC_LOAD
NCBI Gene	301513	ENTREZGENE
PANTHER	UNCHARACTERIZED	UniProtKB/Swiss-Prot
Pfam	Rcd1	UniProtKB/Swiss-Prot
PhenoGen	Cnot9	PhenoGen
RatGTEx	ENSRNOG00000016034	RatGTEx
Superfamily-SCOP	SSF48371	UniProtKB/Swiss-Prot
UniProt	A0A8I5Y955_RAT	UniProtKB/TrEMBL
	A0A8L2QAX2	ENTREZGENE, UniProtKB/TrEMBL
	A6JVU9	ENTREZGENE, UniProtKB/TrEMBL
	CNOT9_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-04-20	Cnot9	CCR4-NOT transcription complex subunit 9	Rqcd1	Rcd1 required for cell differentiation1 homolog (S. pombe)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-02-27	Rqcd1	Rcd1 required for cell differentiation1 homolog (S. pombe)	Rqcd1	rcd1 (required for cell differentiation) homolog 1 (S. pombe)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Rqcd1	rcd1 (required for cell differentiation) homolog 1 (S. pombe)	Rqcd1_predicted	rcd1 (required for cell differentiation) homolog 1 (S. pombe) (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Rqcd1_predicted	rcd1 (required for cell differentiation) homolog 1 (S. pombe) (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)