Cnot1 (CCR4-NOT transcription complex, subunit 1) - Rat Genome Database

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Gene: Cnot1 (CCR4-NOT transcription complex, subunit 1) Rattus norvegicus
Analyze
Symbol: Cnot1
Name: CCR4-NOT transcription complex, subunit 1
RGD ID: 1308009
Description: Is predicted to contribute to poly(A)-specific ribonuclease activity. Predicted to be involved in several processes, including negative regulation of signal transduction; positive regulation of cytoplasmic mRNA processing body assembly; and regulation of gene expression. Predicted to localize to CCR4-NOT core complex; P-body; and cytosol. Human ortholog(s) of this gene implicated in holoprosencephaly. Orthologous to human CNOT1 (CCR4-NOT transcription complex subunit 1); PARTICIPATES IN microRNA pathway; RNA degradation pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: adrenal gland protein AD-005; CCR4-NOT transcription complex subunit 1; hypothetical protein LOC291841; LOC291841; MGC116302; RGD1308009; similar to KIAA1007 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
Rnor_6.0 Ensembl199,668,186 - 9,761,605 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0199,668,186 - 9,761,605 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0199,652,472 - 9,746,683 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4199,712,024 - 9,803,182 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1199,788,162 - 9,807,989 (+)NCBI
Celera199,151,859 - 9,241,563 (+)NCBICelera
Cytogenetic Map19p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:16778766   PMID:19558367   PMID:19946888   PMID:20133598   PMID:21278420   PMID:21525035   PMID:21976065   PMID:22367759   PMID:22658674   PMID:22664934   PMID:22681889  
PMID:22977175   PMID:23172285   PMID:23644599   PMID:24736845   PMID:24768540  


Genomics

Comparative Map Data
Cnot1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
Rnor_6.0 Ensembl199,668,186 - 9,761,605 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0199,668,186 - 9,761,605 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0199,652,472 - 9,746,683 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4199,712,024 - 9,803,182 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1199,788,162 - 9,807,989 (+)NCBI
Celera199,151,859 - 9,241,563 (+)NCBICelera
Cytogenetic Map19p13NCBI
CNOT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1658,519,951 - 58,629,885 (-)EnsemblGRCh38hg38GRCh38
GRCh381658,519,951 - 58,629,826 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371658,553,855 - 58,663,730 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361657,111,356 - 57,221,251 (-)NCBINCBI36hg18NCBI36
Celera1643,052,843 - 43,163,048 (-)NCBI
Cytogenetic Map16q21NCBI
HuRef1644,421,846 - 44,532,633 (-)NCBIHuRef
CHM1_11659,961,044 - 60,070,690 (-)NCBICHM1_1
Cnot1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39896,445,559 - 96,534,741 (-)NCBIGRCm39mm39
GRCm39 Ensembl896,446,079 - 96,534,092 (-)Ensembl
GRCm38895,718,931 - 95,808,113 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl895,719,451 - 95,807,464 (-)EnsemblGRCm38mm10GRCm38
MGSCv37898,243,351 - 98,331,366 (-)NCBIGRCm37mm9NCBIm37
MGSCv36898,608,580 - 98,696,595 (-)NCBImm8
Celera8100,030,369 - 100,118,172 (-)NCBICelera
Cytogenetic Map8D1NCBI
Cnot1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543315,938,791 - 16,027,545 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543315,938,791 - 16,027,547 (-)NCBIChiLan1.0ChiLan1.0
CNOT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11657,919,276 - 58,027,472 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1657,919,283 - 58,027,472 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01638,793,212 - 38,902,686 (-)NCBIMhudiblu_PPA_v0panPan3
CNOT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1258,038,456 - 58,138,364 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl258,038,483 - 58,137,622 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha254,668,858 - 54,768,748 (+)NCBI
ROS_Cfam_1.0258,576,260 - 58,677,212 (+)NCBI
UMICH_Zoey_3.1255,405,764 - 55,506,839 (+)NCBI
UNSW_CanFamBas_1.0256,410,286 - 56,514,088 (+)NCBI
UU_Cfam_GSD_1.0257,308,231 - 57,409,115 (+)NCBI
Cnot1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934949,204,138 - 49,286,987 (+)NCBI
SpeTri2.0NW_00493647510,302,091 - 10,384,945 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CNOT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl620,271,596 - 20,372,280 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1620,271,593 - 20,372,300 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2618,405,850 - 18,474,575 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CNOT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1544,460,025 - 44,567,843 (-)NCBI
ChlSab1.1 Ensembl544,455,311 - 44,567,815 (-)Ensembl
Vero_WHO_p1.0NW_02366604731,603,098 - 31,711,911 (+)NCBI
Cnot1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474627,659,424 - 27,757,024 (+)NCBI

Position Markers
BF387398  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,337,425 - 9,337,576 (+)MAPPER
Rnor_6.0199,752,463 - 9,752,613NCBIRnor6.0
Rnor_5.0199,737,541 - 9,737,691UniSTSRnor5.0
RGSC_v3.4199,794,040 - 9,794,190UniSTSRGSC3.4
Celera199,232,690 - 9,232,840UniSTS
RH 3.4 Map1976.92UniSTS
Cytogenetic Map19p13UniSTS
AU047625  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,292,337 - 9,292,532 (+)MAPPER
Rnor_6.0199,705,315 - 9,705,509NCBIRnor6.0
Rnor_5.0199,690,498 - 9,690,692UniSTSRnor5.0
RGSC_v3.4199,749,153 - 9,749,347UniSTSRGSC3.4
Celera199,188,982 - 9,189,176UniSTS
Cytogenetic Map19p13UniSTS
MARC_16903-16904:1022861972:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2199,295,865 - 9,296,372 (+)MAPPER
Rnor_6.0199,708,842 - 9,709,348NCBIRnor6.0
Rnor_5.0199,694,025 - 9,694,531UniSTSRnor5.0
RGSC_v3.4199,752,680 - 9,753,186UniSTSRGSC3.4
Celera199,192,509 - 9,193,015UniSTS
Cytogenetic Map19p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124933090Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127635288Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19129558305Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19129558305Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:42
Interacting mature miRNAs:51
Transcripts:ENSRNOT00000016563
Prediction methods:Miranda, Rnahybrid, 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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 42 57 41 19 41 8 11 74 35 41 11 8
Low 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001134840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097549 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC086325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC099150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC168171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000303 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000016563   ⟹   ENSRNOP00000016563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl199,668,186 - 9,761,605 (+)Ensembl
RefSeq Acc Id: NM_001134840   ⟹   NP_001128312
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,194 - 9,346,574 (+)NCBI
Rnor_6.0199,668,186 - 9,761,605 (+)NCBI
Rnor_5.0199,652,472 - 9,746,683 (+)NCBI
RGSC_v3.4199,712,024 - 9,803,182 (+)RGD
Celera199,151,859 - 9,241,563 (+)RGD
Sequence:
RefSeq Acc Id: XM_039097540   ⟹   XP_038953468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097541   ⟹   XP_038953469
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,951 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097542   ⟹   XP_038953470
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,205 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097543   ⟹   XP_038953471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097544   ⟹   XP_038953472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097545   ⟹   XP_038953473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097546   ⟹   XP_038953474
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097547   ⟹   XP_038953475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097548   ⟹   XP_038953476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
RefSeq Acc Id: XM_039097549   ⟹   XP_038953477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,255,190 - 9,346,574 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001128312   ⟸   NM_001134840
- UniProtKB: G3V7M0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016563   ⟸   ENSRNOT00000016563
RefSeq Acc Id: XP_038953468   ⟸   XM_039097540
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953474   ⟸   XM_039097546
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038953473   ⟸   XM_039097545
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038953471   ⟸   XM_039097543
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038953472   ⟸   XM_039097544
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038953477   ⟸   XM_039097549
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038953476   ⟸   XM_039097548
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038953475   ⟸   XM_039097547
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038953470   ⟸   XM_039097542
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953469   ⟸   XM_039097541
- Peptide Label: isoform X1
Protein Domains
CNOT1_CAF1_bind   CNOT1_HEAT   CNOT1_TTP_bind   DUF3819   Not1

Transcriptome

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

Promoters
RGD ID:13700922
Promoter ID:EPDNEW_R11446
Type:multiple initiation site
Name:Cnot1_1
Description:CCR4-NOT transcription complex, subunit 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0199,668,219 - 9,668,279EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308009 AgrOrtholog
Ensembl Genes ENSRNOG00000012271 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016563 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016563 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.180 UniProtKB/TrEMBL
  1.25.40.840 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7107420 IMAGE-MGC_LOAD
InterPro CCR4-Not_Not1_C UniProtKB/TrEMBL
  CCR4-Not_Not1su_DUF3819 UniProtKB/TrEMBL
  CNOT1 UniProtKB/TrEMBL
  CNOT1_CAF1_bind UniProtKB/TrEMBL
  CNOT1_HEAT UniProtKB/TrEMBL
  CNOT1_TTP_bind UniProtKB/TrEMBL
  CNOT1_TTP_bind_sf UniProtKB/TrEMBL
  MIF4-like_sf UniProtKB/TrEMBL
KEGG Report rno:291841 UniProtKB/TrEMBL
MGC_CLONE MGC:105825 IMAGE-MGC_LOAD
NCBI Gene 291841 ENTREZGENE
PANTHER PTHR13162 UniProtKB/TrEMBL
Pfam CNOT1_CAF1_bind UniProtKB/TrEMBL
  CNOT1_HEAT UniProtKB/TrEMBL
  CNOT1_TTP_bind UniProtKB/TrEMBL
  DUF3819 UniProtKB/TrEMBL
  Not1 UniProtKB/TrEMBL
PhenoGen Cnot1 PhenoGen
UniProt G3V7M0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Cnot1  CCR4-NOT transcription complex, subunit 1  RGD1308009  similar to KIAA1007 protein; adrenal gland protein AD-005  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1308009  similar to KIAA1007 protein; adrenal gland protein AD-005  RGD1308009_predicted  similar to KIAA1007 protein; adrenal gland protein AD-005 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1308009_predicted  similar to KIAA1007 protein; adrenal gland protein AD-005 (predicted)  LOC291841_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC291841_predicted  similar to KIAA1007 protein; adrenal gland protein AD-005 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL