Dennd3 (DENN domain containing 3) - Rat Genome Database

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Gene: Dennd3 (DENN domain containing 3) Rattus norvegicus
Analyze
Symbol: Dennd3
Name: DENN domain containing 3
RGD ID: 1311559
Description: Predicted to have guanyl-nucleotide exchange factor activity. Predicted to be involved in cellular protein catabolic process; endosome to lysosome transport; and regulation of Rab protein signal transduction. Predicted to localize to cytoplasmic vesicle. Orthologous to human DENND3 (DENN domain containing 3); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: DENN domain-containing protein 3; DENN/MADD domain containing 3; hypothetical LOC315055; LOC315055; RGD1311559
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
mRatBN7.27105,415,870 - 105,473,583 (+)NCBI
Rnor_6.0 Ensembl7114,724,610 - 114,812,708 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07114,724,644 - 114,812,471 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07114,657,996 - 114,736,407 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47111,218,116 - 111,275,479 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17111,225,832 - 111,309,709 (+)NCBI
Celera7101,823,319 - 101,881,083 (+)NCBICelera
Cytogenetic Map7q34NCBI
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

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:20937701   PMID:21718402  


Genomics

Comparative Map Data
Dennd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27105,415,870 - 105,473,583 (+)NCBI
Rnor_6.0 Ensembl7114,724,610 - 114,812,708 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07114,724,644 - 114,812,471 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07114,657,996 - 114,736,407 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47111,218,116 - 111,275,479 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17111,225,832 - 111,309,709 (+)NCBI
Celera7101,823,319 - 101,881,083 (+)NCBICelera
Cytogenetic Map7q34NCBI
DENND3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8141,117,278 - 141,195,808 (+)EnsemblGRCh38hg38GRCh38
GRCh388141,128,562 - 141,195,804 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378142,138,688 - 142,205,903 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 368142,207,902 - 142,275,083 (+)NCBINCBI36hg18NCBI36
Celera8138,306,916 - 138,374,104 (+)NCBI
Cytogenetic Map8q24.3NCBI
HuRef8137,450,378 - 137,517,552 (+)NCBIHuRef
CHM1_18142,178,995 - 142,246,171 (+)NCBICHM1_1
Dennd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391573,384,333 - 73,444,091 (+)NCBIGRCm39mm39
GRCm39 Ensembl1573,384,409 - 73,444,091 (+)Ensembl
GRCm381573,512,560 - 73,572,242 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1573,512,560 - 73,572,242 (+)EnsemblGRCm38mm10GRCm38
MGSCv371573,342,990 - 73,402,672 (+)NCBIGRCm37mm9NCBIm37
MGSCv361573,339,816 - 73,399,498 (+)NCBImm8
Celera1575,014,224 - 75,076,612 (+)NCBICelera
Cytogenetic Map15D3NCBI
Dennd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955454185,299 - 253,428 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955454185,299 - 253,935 (+)NCBIChiLan1.0ChiLan1.0
DENND3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.18140,889,347 - 140,956,973 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl8140,889,343 - 140,956,967 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v08137,805,456 - 137,873,492 (+)NCBIMhudiblu_PPA_v0panPan3
DENND3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11335,649,797 - 35,696,149 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1335,685,829 - 35,694,800 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1335,505,304 - 35,555,435 (+)NCBI
ROS_Cfam_1.01336,031,571 - 36,081,695 (+)NCBI
UMICH_Zoey_3.11335,751,650 - 35,801,765 (+)NCBI
UNSW_CanFamBas_1.01335,841,295 - 35,891,529 (+)NCBI
UU_Cfam_GSD_1.01336,261,339 - 36,311,719 (+)NCBI
Dennd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244053032,793,039 - 2,838,863 (-)NCBI
SpeTri2.0NW_00493647010,217,404 - 10,264,911 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DENND3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl42,530,644 - 2,578,099 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.142,530,640 - 2,578,104 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.242,284,519 - 2,300,731 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DENND3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18135,367,847 - 135,437,434 (+)NCBI
ChlSab1.1 Ensembl8135,368,076 - 135,437,559 (+)Ensembl
Vero_WHO_p1.0NW_0236660394,695,279 - 4,765,143 (-)NCBI
Dennd3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473515,158,892 - 15,224,895 (-)NCBI

Position Markers
BI303224  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27105,473,372 - 105,473,540 (+)MAPPER
Rnor_6.07114,812,261 - 114,812,428NCBIRnor6.0
Rnor_5.07114,736,197 - 114,736,364UniSTSRnor5.0
RGSC_v3.47111,275,269 - 111,275,436UniSTSRGSC3.4
Celera7101,880,873 - 101,881,040UniSTS
RH 3.4 Map7753.51UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)770421228115421228Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)777428105127748511Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)777428234122421148Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)788365265119318087Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)788365265121986709Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)7102588256116249643Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)7103815550126525386Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)7103867802126080176Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7112429186126525386Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:61
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000014541
Prediction methods:Miranda, Rnahybrid
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 2 8 19 29 9 11
Low 1 43 49 41 41 8 11 74 6 32 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014541   ⟹   ENSRNOP00000014542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7114,724,610 - 114,812,708 (+)Ensembl
RefSeq Acc Id: XM_001072997   ⟹   XP_001072997
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera7101,823,320 - 101,881,083 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006226093   ⟹   XP_006226155
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera7101,823,319 - 101,881,083 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241738   ⟹   XP_006241800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27105,415,871 - 105,473,583 (+)NCBI
Rnor_6.07114,724,644 - 114,812,471 (+)NCBI
Rnor_5.07114,657,996 - 114,736,407 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765603   ⟹   XP_008763825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07114,724,644 - 114,808,133 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008776480   ⟹   XP_008774702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera7101,823,319 - 101,876,745 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595246   ⟹   XP_017450735
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27105,415,870 - 105,469,261 (+)NCBI
Rnor_6.07114,724,644 - 114,808,134 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603446   ⟹   XP_017458935
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera7101,823,319 - 101,876,746 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039080223   ⟹   XP_038936151
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27105,426,488 - 105,473,583 (+)NCBI
RefSeq Acc Id: XM_039080224   ⟹   XP_038936152
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27105,433,544 - 105,473,583 (+)NCBI
RefSeq Acc Id: XM_039080225   ⟹   XP_038936153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27105,441,761 - 105,473,583 (+)NCBI
RefSeq Acc Id: XM_235398   ⟹   XP_235398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27105,415,873 - 105,473,583 (+)NCBI
Rnor_6.07114,724,646 - 114,812,471 (+)NCBI
Rnor_5.07114,657,996 - 114,736,407 (+)NCBI
RGSC_v3.47111,218,116 - 111,275,479 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: XP_001072997   ⟸   XM_001072997
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_235398   ⟸   XM_235398
- Peptide Label: isoform X1
- UniProtKB: D4A2H4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006226155   ⟸   XM_006226093
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006241800   ⟸   XM_006241738
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008774702   ⟸   XM_008776480
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008763825   ⟸   XM_008765603
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017458935   ⟸   XM_017603446
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017450735   ⟸   XM_017595246
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000014542   ⟸   ENSRNOT00000014541
RefSeq Acc Id: XP_038936151   ⟸   XM_039080223
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038936152   ⟸   XM_039080224
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038936153   ⟸   XM_039080225
- Peptide Label: isoform X6
Protein Domains
uDENN   WD_REPEATS_REGION

Transcriptome

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


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)
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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)
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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
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:1311559 AgrOrtholog
Ensembl Genes ENSRNOG00000010794 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014542 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014541 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  3.40.50.11500 UniProtKB/TrEMBL
InterPro dDENN UniProtKB/TrEMBL
  DENN UniProtKB/TrEMBL
  DENN_C UniProtKB/TrEMBL
  Tripartite_DENN UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_CS UniProtKB/TrEMBL
  WD40_repeat_dom UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:315055 UniProtKB/TrEMBL
NCBI Gene 315055 ENTREZGENE
Pfam DENN UniProtKB/TrEMBL
PhenoGen Dennd3 PhenoGen
PROSITE DENN UniProtKB/TrEMBL
  WD_REPEATS_1 UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/TrEMBL
SMART dDENN UniProtKB/TrEMBL
  DENN UniProtKB/TrEMBL
  WD40 UniProtKB/TrEMBL
Superfamily-SCOP WD40_like UniProtKB/TrEMBL
UniProt D4A2H4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Dennd3  DENN domain containing 3  Dennd3  DENN/MADD domain containing 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-27 Dennd3  DENN/MADD domain containing 3  RGD1311559_predicted  hypothetical LOC315055 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1311559_predicted  hypothetical LOC315055 (predicted)  LOC315055_predicted    Symbol and Name status set to approved 1331353 APPROVED