Cul4a (cullin 4A) - Rat Genome Database
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Gene: Cul4a (cullin 4A) Rattus norvegicus
Analyze
Symbol: Cul4a
Name: cullin 4A
RGD ID: 1563853
Description: Predicted to have ubiquitin protein ligase binding activity and ubiquitin-protein transferase activity. Predicted to be involved in several processes, including cellular protein metabolic process; positive regulation of G1/S transition of mitotic cell cycle; and regulation of response to DNA damage stimulus. Predicted to localize to Cul4A-RING E3 ubiquitin ligase complex and SCF ubiquitin ligase complex. Orthologous to human CUL4A (cullin 4A); PARTICIPATES IN nucleotide excision repair pathway; ubiquitin/proteasome degradation pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cullin-4A; hypothetical protein LOC361181; LOC361181; RGD1563853; similar to cullin 4A
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
Rnor_6.01681,718,784 - 81,756,653 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,719,028 - 81,756,654 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01681,204,989 - 81,242,020 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41681,242,293 - 81,279,498 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1674,191,398 - 74,228,350 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12077329   PMID:12393421   PMID:12477932   PMID:12732143   PMID:14739464   PMID:16467204   PMID:16949367   PMID:17085480   PMID:17616641   PMID:18339895   PMID:18381890   PMID:18794347  
PMID:19056892   PMID:19481525   PMID:20129063   PMID:20223979   PMID:22871113   PMID:26431207   PMID:26711351   PMID:28437394   PMID:31178959  


Genomics

Comparative Map Data
Cul4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01681,718,784 - 81,756,653 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,719,028 - 81,756,654 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01681,204,989 - 81,242,020 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41681,242,293 - 81,279,498 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1674,191,398 - 74,228,350 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
CUL4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13113,208,193 - 113,267,108 (+)EnsemblGRCh38hg38GRCh38
GRCh3813113,208,193 - 113,267,108 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713113,862,507 - 113,919,392 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613112,911,087 - 112,967,393 (+)NCBINCBI36hg18NCBI36
Build 3413112,911,086 - 112,967,392NCBI
Celera1394,689,332 - 94,746,025 (+)NCBI
Cytogenetic Map13q34NCBI
HuRef1394,301,391 - 94,358,301 (+)NCBIHuRef
CHM1_113113,831,366 - 113,888,434 (+)NCBICHM1_1
Cul4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39813,155,623 - 13,197,940 (+)NCBIGRCm39mm39
GRCm38813,105,623 - 13,147,940 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl813,105,621 - 13,147,940 (+)EnsemblGRCm38mm10GRCm38
MGSCv37813,105,721 - 13,147,940 (+)NCBIGRCm37mm9NCBIm37
MGSCv36813,105,720 - 13,147,753 (+)NCBImm8
Celera813,272,636 - 13,315,964 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
Cul4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955404583,261 - 617,914 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955404583,261 - 617,914 (-)NCBIChiLan1.0ChiLan1.0
CUL4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113113,428,215 - 113,474,194 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13113,428,271 - 113,472,701 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01394,350,484 - 94,409,183 (+)NCBIMhudiblu_PPA_v0panPan3
CUL4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2260,624,241 - 60,666,616 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12260,624,215 - 60,667,844 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cul4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936472409,083 - 432,442 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CUL4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1178,557,070 - 78,589,194 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11178,557,030 - 78,588,964 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21186,146,594 - 86,178,480 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CUL4A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl391,212,193 - 91,268,838 (+)Ensembl
ChlSab1.1391,211,238 - 91,267,236 (+)NCBI
Cul4a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624793686,720 - 722,516 (-)NCBI

Position Markers
AA866392  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01681,719,038 - 81,719,253NCBIRnor6.0
Rnor_5.01681,204,475 - 81,204,690UniSTSRnor5.0
RGSC_v3.41681,241,779 - 81,241,994UniSTSRGSC3.4
Celera1674,190,884 - 74,191,099UniSTS
Cytogenetic Map16q12.5UniSTS
RH 3.4 Map16743.9UniSTS
AI228118  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01681,719,363 - 81,719,556NCBIRnor6.0
Rnor_5.01681,204,800 - 81,204,993UniSTSRnor5.0
RGSC_v3.41681,242,104 - 81,242,297UniSTSRGSC3.4
Celera1674,191,209 - 74,191,402UniSTS
Cytogenetic Map16q12.5UniSTS
RH 3.4 Map16762.2UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163900002184000021Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165781635790668790Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165781635790668790Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165781635790668790Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165928577589248943Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:515
Count of miRNA genes:252
Interacting mature miRNAs:305
Transcripts:ENSRNOT00000026653
Prediction methods:Microtar, 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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026653   ⟹   ENSRNOP00000026653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1681,719,028 - 81,756,654 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092421   ⟹   ENSRNOP00000075917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1681,733,602 - 81,740,562 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092551   ⟹   ENSRNOP00000075804
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1681,740,889 - 81,756,631 (-)Ensembl
RefSeq Acc Id: NM_001127301   ⟹   NP_001120773
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01681,719,552 - 81,756,653 (-)NCBI
Rnor_5.01681,204,989 - 81,242,020 (-)NCBI
RGSC_v3.41681,242,293 - 81,279,498 (-)RGD
Celera1674,191,398 - 74,228,350 (-)RGD
Sequence:
RefSeq Acc Id: XM_008771401   ⟹   XP_008769623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01681,718,784 - 81,756,057 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001120773 (Get FASTA)   NCBI Sequence Viewer  
  XP_008769623 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66799 (Get FASTA)   NCBI Sequence Viewer  
  EDM08875 (Get FASTA)   NCBI Sequence Viewer  
  EDM08876 (Get FASTA)   NCBI Sequence Viewer  
  EDM08877 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001120773   ⟸   NM_001127301
- UniProtKB: B2RYJ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769623   ⟸   XM_008771401
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075917   ⟸   ENSRNOT00000092421
RefSeq Acc Id: ENSRNOP00000075804   ⟸   ENSRNOT00000092551
RefSeq Acc Id: ENSRNOP00000026653   ⟸   ENSRNOT00000026653
Protein Domains
CULLIN_2

Transcriptome

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

Promoters
RGD ID:13700239
Promoter ID:EPDNEW_R10757
Type:multiple initiation site
Name:Cul4a_1
Description:cullin 4A
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_6.01681,756,652 - 81,756,712EPDNEW

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)
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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: 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)
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: SBN/Ygl sequenced by MCW
SBN/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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 81733505 81733506 G T snv F344/NCrl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563853 AgrOrtholog
Ensembl Genes ENSRNOG00000019649 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000026653 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075804 UniProtKB/TrEMBL
  ENSRNOP00000075917 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026653 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092421 UniProtKB/TrEMBL
  ENSRNOT00000092551 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7938235 IMAGE-MGC_LOAD
InterPro Cullin_CS UniProtKB/TrEMBL
  Cullin_homology UniProtKB/TrEMBL
  Cullin_homology_sf UniProtKB/TrEMBL
  Cullin_N UniProtKB/TrEMBL
  Cullin_neddylation_domain UniProtKB/TrEMBL
  Cullin_repeat-like_dom UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:361181 UniProtKB/TrEMBL
MGC_CLONE MGC:188598 IMAGE-MGC_LOAD
NCBI Gene 361181 ENTREZGENE
Pfam Cullin UniProtKB/TrEMBL
  Cullin_Nedd8 UniProtKB/TrEMBL
PhenoGen Cul4a PhenoGen
PROSITE CULLIN_1 UniProtKB/TrEMBL
  CULLIN_2 UniProtKB/TrEMBL
SMART CULLIN UniProtKB/TrEMBL
  Cullin_Nedd8 UniProtKB/TrEMBL
Superfamily-SCOP Cullin_homology UniProtKB/TrEMBL
  Cullin_repeat-like UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
UniGene Rn.1987 ENTREZGENE
UniProt A0A0U1RRT3_RAT UniProtKB/TrEMBL
  A0A0U1RS34_RAT UniProtKB/TrEMBL
  B2RYJ3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-05-05 Cul4a  cullin 4A  RGD1563853  similar to cullin 4A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563853  similar to cullin 4A   RGD1563853_predicted  similar to cullin 4A (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563853_predicted  similar to cullin 4A (predicted)  LOC361181  similar to cullin 4A  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC361181  similar to cullin 4A      Symbol and Name status set to provisional 70820 PROVISIONAL