Depdc1 (DEP domain containing 1) - Rat Genome Database

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Gene: Depdc1 (DEP domain containing 1) Rattus norvegicus
Analyze
Symbol: Depdc1
Name: DEP domain containing 1
RGD ID: 1306987
Description: Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Orthologous to human DEPDC1 (DEP domain containing 1); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DEP domain containing 1a; DEP domain-containing protein 1A; Depdc1a; LOC295538
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22248,684,508 - 248,717,951 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2248,684,523 - 248,717,951 (+)Ensembl
Rnor_6.02264,704,738 - 264,738,265 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2264,704,769 - 264,738,257 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02283,373,918 - 283,407,440 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42257,763,301 - 257,796,571 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12257,722,336 - 257,811,979 (+)NCBI
Celera2240,433,308 - 240,466,751 (+)NCBICelera
Cytogenetic Map2q45NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
all-trans-retinoic acid  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
azoxystrobin  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
dimethylarsinous acid  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
gentamycin  (EXP)
indometacin  (ISO)
leflunomide  (ISO)
lucanthone  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
N-Nitrosopyrrolidine  (ISO)
nobiletin  (EXP,ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
pentanal  (ISO)
perfluorononanoic acid  (ISO)
phenformin  (EXP)
progesterone  (ISO)
propanal  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20587513  


Genomics

Comparative Map Data
Depdc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22248,684,508 - 248,717,951 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2248,684,523 - 248,717,951 (+)Ensembl
Rnor_6.02264,704,738 - 264,738,265 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2264,704,769 - 264,738,257 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02283,373,918 - 283,407,440 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42257,763,301 - 257,796,571 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12257,722,336 - 257,811,979 (+)NCBI
Celera2240,433,308 - 240,466,751 (+)NCBICelera
Cytogenetic Map2q45NCBI
DEPDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38168,474,152 - 68,497,082 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl168,474,152 - 68,497,221 (-)EnsemblGRCh38hg38GRCh38
GRCh37168,939,835 - 68,962,765 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36168,713,526 - 68,735,295 (-)NCBINCBI36hg18NCBI36
Build 34168,652,959 - 68,674,728NCBI
Celera167,230,053 - 67,253,019 (-)NCBI
Cytogenetic Map1p31.3NCBI
HuRef167,049,654 - 67,072,558 (-)NCBIHuRef
CHM1_1169,055,195 - 69,078,161 (-)NCBICHM1_1
T2T-CHM13v2.0168,351,536 - 68,374,468 (-)NCBI
Depdc1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393159,201,042 - 159,235,690 (+)NCBIGRCm39mm39
GRCm39 Ensembl3159,201,070 - 159,235,592 (+)Ensembl
GRCm383159,495,414 - 159,529,955 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3159,495,433 - 159,529,955 (+)EnsemblGRCm38mm10GRCm38
MGSCv373159,158,397 - 159,192,919 (+)NCBIGRCm37mm9NCBIm37
MGSCv363159,430,744 - 159,464,869 (+)NCBImm8
Celera3165,936,145 - 165,970,664 (+)NCBICelera
Cytogenetic Map3H4NCBI
Depdc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542323,137,835 - 23,159,385 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542323,137,841 - 23,157,548 (+)NCBIChiLan1.0ChiLan1.0
DEPDC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1169,668,934 - 69,692,143 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl169,668,899 - 69,692,143 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0167,711,907 - 67,734,986 (-)NCBIMhudiblu_PPA_v0panPan3
DEPDC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1676,848,586 - 76,867,888 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl676,847,715 - 76,865,413 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha679,456,476 - 79,478,640 (+)NCBI
ROS_Cfam_1.0677,438,007 - 77,460,456 (+)NCBI
ROS_Cfam_1.0 Ensembl677,437,719 - 77,457,981 (+)Ensembl
UMICH_Zoey_3.1676,988,860 - 77,011,249 (+)NCBI
UNSW_CanFamBas_1.0676,891,831 - 76,914,611 (+)NCBI
UU_Cfam_GSD_1.0677,379,331 - 77,401,692 (+)NCBI
Depdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505881,153,752 - 81,185,722 (-)NCBI
SpeTri2.0NW_0049365913,303,915 - 3,323,462 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DEPDC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6144,157,588 - 144,185,963 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16144,157,569 - 144,183,977 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
DEPDC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12064,615,693 - 64,639,088 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2064,615,866 - 64,636,294 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603352,974,266 - 52,997,660 (-)NCBIVero_WHO_p1.0
Depdc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474227,240,342 - 27,258,681 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462474227,240,906 - 27,288,872 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH131980  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22248,717,766 - 248,717,936 (+)MAPPERmRatBN7.2
Rnor_6.02264,738,081 - 264,738,250NCBIRnor6.0
Rnor_5.02283,407,256 - 283,407,425UniSTSRnor5.0
RGSC_v3.42257,797,188 - 257,797,357UniSTSRGSC3.4
Celera2240,466,567 - 240,466,736UniSTS
RH 3.4 Map21660.41UniSTS
Cytogenetic Map2q45UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
631563Hcuc3Hepatic copper content QTL 33.87hepatic copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:182
Count of miRNA genes:79
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000012667, ENSRNOT00000031544
Prediction methods:Microtar, 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 1 26 29 22 13 22 28 18 29
Low 2 8 16 11 6 11 4 4 29 9 12 11 4
Below cutoff 9 10 6 6 4 6 12 7 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012667   ⟹   ENSRNOP00000012667
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2248,684,523 - 248,717,951 (+)Ensembl
Rnor_6.0 Ensembl2264,704,769 - 264,738,257 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118417   ⟹   ENSRNOP00000090441
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2248,684,534 - 248,717,942 (+)Ensembl
RefSeq Acc Id: NM_001305205   ⟹   NP_001292134
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22248,684,523 - 248,717,951 (+)NCBI
Rnor_6.02264,704,751 - 264,738,265 (+)NCBI
Celera2240,433,308 - 240,466,751 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233537   ⟹   XP_006233599
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22248,684,508 - 248,717,150 (+)NCBI
Rnor_6.02264,704,738 - 264,738,265 (+)NCBI
Rnor_5.02283,373,918 - 283,407,440 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001292134 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233599 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82580 (Get FASTA)   NCBI Sequence Viewer  
  EDL82581 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006233599   ⟸   XM_006233537
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001292134   ⟸   NM_001305205
- UniProtKB: D3ZGJ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012667   ⟸   ENSRNOT00000012667
RefSeq Acc Id: ENSRNOP00000090441   ⟸   ENSRNOT00000118417
Protein Domains
DEP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZGJ9-F1-model_v2 AlphaFold D3ZGJ9 1-809 view protein structure

Transcriptome

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

Promoters
RGD ID:13691839
Promoter ID:EPDNEW_R2364
Type:initiation region
Name:Depdc1_1
Description:DEP domain containing 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_6.02264,704,779 - 264,704,839EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 264715725 264715726 A T snv CDR, WKY/N (MCW), LEW/Crl (RGD), LEW/NCrlBR (RGD), WKY/N (2020), WKY/NHsd (RGD), LEW/Crl (2019), WKY/NCrl (2019), WKY/NCrl (RGD)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 283384900 283384901 A T snv LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), WKY/NHsd (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), LEW/NCrl (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 248695497 248695498 A T snv LEW/Crl (2019), WKY/N (2020), WKY/NCrl (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306987 AgrOrtholog
BioCyc Gene G2FUF-50687 BioCyc
Ensembl Genes ENSRNOG00000009503 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012667 ENTREZGENE
  ENSRNOP00000012667.6 UniProtKB/TrEMBL
  ENSRNOP00000090441 ENTREZGENE
  ENSRNOP00000090441.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012667 ENTREZGENE
  ENSRNOT00000012667.9 UniProtKB/TrEMBL
  ENSRNOT00000118417 ENTREZGENE
  ENSRNOT00000118417.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
  1.10.555.10 UniProtKB/TrEMBL
InterPro DEP_dom UniProtKB/TrEMBL
  Rho_GTPase_activation_prot UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:295538 UniProtKB/TrEMBL
NCBI Gene 295538 ENTREZGENE
Pfam DEP UniProtKB/TrEMBL
PhenoGen Depdc1 PhenoGen
PROSITE DEP UniProtKB/TrEMBL
SMART DEP UniProtKB/TrEMBL
Superfamily-SCOP Rho_GAP UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
UniProt A0A8I6AEC2_RAT UniProtKB/TrEMBL
  D3ZGJ9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-26 Depdc1  DEP domain containing 1  Depdc1a  DEP domain containing 1a   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Depdc1a  DEP domain containing 1a   Depdc1a_predicted  DEP domain containing 1a (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Depdc1a_predicted  DEP domain containing 1a (predicted)  Depdc1_predicted  DEP domain containing 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Depdc1_predicted  DEP domain containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED