Depdc5 (DEP domain containing 5, GATOR1 subcomplex subunit) - Rat Genome Database

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Gene: Depdc5 (DEP domain containing 5, GATOR1 subcomplex subunit) Rattus norvegicus
Analyze
Symbol: Depdc5
Name: DEP domain containing 5, GATOR1 subcomplex subunit
RGD ID: 1311535
Description: Predicted to contribute to GTPase activator activity. Predicted to be involved in cellular response to amino acid starvation; negative regulation of TORC1 signaling; and positive regulation of autophagy. Predicted to be located in cytosol; lysosome; and perinuclear region of cytoplasm. Predicted to be part of GATOR1 complex. Predicted to be active in lysosomal membrane. Human ortholog(s) of this gene implicated in focal epilepsy. Orthologous to human DEPDC5 (DEP domain containing 5, GATOR1 subcomplex subunit); PARTICIPATES IN mTOR signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DEP domain containing 5; DEP domain-containing protein 5; GATOR complex protein DEPDC5; LOC305464
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Depdc5em1Kyo   Depdc5em2Kyo  
Genetic Models: F344-Depdc5em1Kyo+/- F344-Depdc5em2Kyo+/-
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21477,732,297 - 77,862,924 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1477,732,297 - 77,862,794 (-)Ensembl
Rnor_6.01483,089,000 - 83,219,576 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1483,089,000 - 83,219,464 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01483,775,510 - 83,906,381 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41483,484,354 - 83,614,818 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11483,494,440 - 83,629,671 (-)NCBI
Celera1476,647,953 - 76,778,356 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:17897319   PMID:23542697   PMID:23723238   PMID:25457612   PMID:28199306   PMID:29769719  


Genomics

Comparative Map Data
Depdc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21477,732,297 - 77,862,924 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1477,732,297 - 77,862,794 (-)Ensembl
Rnor_6.01483,089,000 - 83,219,576 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1483,089,000 - 83,219,464 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01483,775,510 - 83,906,381 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41483,484,354 - 83,614,818 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11483,494,440 - 83,629,671 (-)NCBI
Celera1476,647,953 - 76,778,356 (-)NCBICelera
Cytogenetic Map14q21NCBI
DEPDC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2231,753,867 - 31,908,033 (+)EnsemblGRCh38hg38GRCh38
GRCh382231,753,968 - 31,908,033 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372232,149,954 - 32,304,019 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362230,480,069 - 30,633,001 (+)NCBINCBI36hg18NCBI36
Build 342230,474,622 - 30,627,554NCBI
Celera2215,950,512 - 16,103,452 (+)NCBI
Cytogenetic Map22q12.2-q12.3NCBI
HuRef2215,105,131 - 15,259,327 (+)NCBIHuRef
CHM1_12232,109,512 - 32,262,422 (+)NCBICHM1_1
Depdc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39533,020,989 - 33,151,577 (+)NCBIGRCm39mm39
GRCm39 Ensembl533,021,045 - 33,151,580 (+)Ensembl
GRCm38532,863,646 - 32,994,233 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl532,863,701 - 32,994,236 (+)EnsemblGRCm38mm10GRCm38
MGSCv37533,206,370 - 33,336,882 (+)NCBIGRCm37mm9NCBIm37
MGSCv36533,180,578 - 33,308,417 (+)NCBImm8
Celera530,326,971 - 30,470,736 (+)NCBICelera
Cytogenetic Map5B1NCBI
cM Map517.35NCBI
Depdc5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554555,881,631 - 6,005,514 (+)NCBIChiLan1.0ChiLan1.0
DEPDC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12230,630,110 - 30,781,591 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2230,630,110 - 30,781,578 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02212,774,147 - 12,929,261 (+)NCBIMhudiblu_PPA_v0panPan3
DEPDC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12624,629,369 - 24,754,728 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2624,630,295 - 24,754,256 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2624,497,751 - 24,623,053 (+)NCBI
ROS_Cfam_1.02625,014,159 - 25,140,999 (+)NCBI
ROS_Cfam_1.0 Ensembl2625,015,075 - 25,140,995 (+)Ensembl
UMICH_Zoey_3.12624,715,227 - 24,840,522 (+)NCBI
UNSW_CanFamBas_1.02624,977,065 - 25,102,363 (+)NCBI
UU_Cfam_GSD_1.02625,039,161 - 25,164,511 (+)NCBI
Depdc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118117,614,267 - 117,770,284 (+)NCBI
SpeTri2.0NW_004936755871,935 - 1,024,538 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DEPDC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11448,421,788 - 48,523,530 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21451,687,092 - 51,788,759 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DEPDC5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11914,634,836 - 14,798,050 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1914,635,947 - 14,787,591 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666045111,310,353 - 111,477,738 (-)NCBIVero_WHO_p1.0
Depdc5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247478,169,035 - 8,310,945 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
BI280365  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23163,259,116 - 163,260,557 (+)MAPPERmRatBN7.2
mRatBN7.21477,863,644 - 77,863,825 (+)MAPPERmRatBN7.2
Rnor_6.01483,220,339 - 83,220,519NCBIRnor6.0
Rnor_6.03172,563,150 - 172,564,590NCBIRnor6.0
Rnor_5.03178,609,156 - 178,610,596UniSTSRnor5.0
Rnor_5.01483,907,181 - 83,907,361UniSTSRnor5.0
RGSC_v3.41483,615,693 - 83,615,873UniSTSRGSC3.4
Celera1476,779,231 - 76,779,411UniSTS
Celera3162,432,501 - 162,433,941UniSTS
RH 3.4 Map14514.17UniSTS
Cytogenetic Map14q21UniSTS
RH143825  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21477,804,834 - 77,805,022 (+)MAPPERmRatBN7.2
Rnor_6.01483,161,532 - 83,161,719NCBIRnor6.0
Rnor_5.01483,848,142 - 83,848,329UniSTSRnor5.0
RGSC_v3.41483,556,886 - 83,557,073UniSTSRGSC3.4
Celera1476,720,439 - 76,720,626UniSTS
RH 3.4 Map14520.3UniSTS
Cytogenetic Map14q21UniSTS
BF413401  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21477,748,454 - 77,748,613 (+)MAPPERmRatBN7.2
Rnor_6.01483,105,155 - 83,105,313NCBIRnor6.0
Rnor_5.01483,791,665 - 83,791,823UniSTSRnor5.0
RGSC_v3.41483,500,509 - 83,500,667UniSTSRGSC3.4
Celera1476,664,108 - 76,664,266UniSTS
RH 3.4 Map14517.1UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat


Genetic Models
This gene Depdc5 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:600
Count of miRNA genes:278
Interacting mature miRNAs:334
Transcripts:ENSRNOT00000067694
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 2 10 17 4 17 4 66 14 36
Low 1 33 40 37 2 37 8 11 8 21 5 11 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001107229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770289 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599213 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091998 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC105515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC109660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000067694   ⟹   ENSRNOP00000061924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1477,732,297 - 77,862,770 (-)Ensembl
Rnor_6.0 Ensembl1483,089,000 - 83,219,464 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085788   ⟹   ENSRNOP00000073874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1477,771,278 - 77,862,794 (-)Ensembl
Rnor_6.0 Ensembl1483,091,779 - 83,219,071 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101652   ⟹   ENSRNOP00000086876
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1477,732,297 - 77,862,770 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112043   ⟹   ENSRNOP00000086641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1477,732,297 - 77,859,010 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113787   ⟹   ENSRNOP00000076509
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1477,732,297 - 77,862,770 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116122   ⟹   ENSRNOP00000078180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1477,732,297 - 77,840,810 (-)Ensembl
RefSeq Acc Id: NM_001107229   ⟹   NP_001100699
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,732,297 - 77,862,770 (-)NCBI
Rnor_6.01483,089,000 - 83,219,464 (-)NCBI
Rnor_5.01483,775,510 - 83,906,381 (-)NCBI
RGSC_v3.41483,484,354 - 83,614,818 (-)RGD
Celera1476,647,953 - 76,778,356 (-)RGD
Sequence:
RefSeq Acc Id: XM_008770289   ⟹   XP_008768511
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
Rnor_6.01483,091,783 - 83,219,479 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599211   ⟹   XP_017454700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
Rnor_6.01483,091,783 - 83,219,479 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599212   ⟹   XP_017454701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
Rnor_6.01483,091,783 - 83,219,479 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599213   ⟹   XP_017454702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
Rnor_6.01483,091,783 - 83,219,479 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599214   ⟹   XP_017454703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
Rnor_6.01483,091,783 - 83,219,479 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091986   ⟹   XP_038947914
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
RefSeq Acc Id: XM_039091987   ⟹   XP_038947915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,830 (-)NCBI
RefSeq Acc Id: XM_039091988   ⟹   XP_038947916
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,924 (-)NCBI
RefSeq Acc Id: XM_039091989   ⟹   XP_038947917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,792 (-)NCBI
RefSeq Acc Id: XM_039091990   ⟹   XP_038947918
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,904 (-)NCBI
RefSeq Acc Id: XM_039091991   ⟹   XP_038947919
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,823 (-)NCBI
RefSeq Acc Id: XM_039091992   ⟹   XP_038947920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
RefSeq Acc Id: XM_039091993   ⟹   XP_038947921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
RefSeq Acc Id: XM_039091994   ⟹   XP_038947922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
RefSeq Acc Id: XM_039091995   ⟹   XP_038947923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
RefSeq Acc Id: XM_039091996   ⟹   XP_038947924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,862,855 (-)NCBI
RefSeq Acc Id: XM_039091998   ⟹   XP_038947926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21477,735,078 - 77,850,707 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100699   ⟸   NM_001107229
- UniProtKB: D4A362 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768511   ⟸   XM_008770289
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017454702   ⟸   XM_017599213
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017454700   ⟸   XM_017599211
- Peptide Label: isoform X5
- UniProtKB: A0A0G2K6M8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454701   ⟸   XM_017599212
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017454703   ⟸   XM_017599214
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: ENSRNOP00000061924   ⟸   ENSRNOT00000067694
RefSeq Acc Id: ENSRNOP00000073874   ⟸   ENSRNOT00000085788
RefSeq Acc Id: XP_038947916   ⟸   XM_039091988
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947918   ⟸   XM_039091990
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947923   ⟸   XM_039091995
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038947921   ⟸   XM_039091993
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038947922   ⟸   XM_039091994
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038947920   ⟸   XM_039091992
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947924   ⟸   XM_039091996
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038947914   ⟸   XM_039091986
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947915   ⟸   XM_039091987
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947919   ⟸   XM_039091991
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947917   ⟸   XM_039091989
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947926   ⟸   XM_039091998
- Peptide Label: isoform X12
RefSeq Acc Id: ENSRNOP00000078180   ⟸   ENSRNOT00000116122
RefSeq Acc Id: ENSRNOP00000086641   ⟸   ENSRNOT00000112043
RefSeq Acc Id: ENSRNOP00000086876   ⟸   ENSRNOT00000101652
RefSeq Acc Id: ENSRNOP00000076509   ⟸   ENSRNOT00000113787
Protein Domains
DEP

Transcriptome

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

Promoters
RGD ID:13699416
Promoter ID:EPDNEW_R9941
Type:initiation region
Name:Depdc5_1
Description:DEP domain containing 5
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_6.01483,219,509 - 83,219,569EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
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/EurMcwi (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)
ACI/EurMcwi (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
ACI/N (2020)
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Sequenced By: MCW
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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/SsN (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
BUF/N (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
FXLE16/Stm (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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
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/FarMcwi (2019)
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Sequenced By: MCW
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
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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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Sequenced By: MCW
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/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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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/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/MavRrrcAek (2020)
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Sequenced By: MCW
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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Sequenced By: MCW
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/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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
MWF/Hsd (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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)
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)
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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/OlalpcvMcwi (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
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 (2020)
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Sequenced By: MCW
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
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 (2019)
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Sequenced By: MCW
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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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/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 (2019)
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Sequenced By: MCW
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/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 (2020)
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Sequenced By: MCW
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
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: mRatBN7.2
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 77781549 77781550 G A snv HXB31/IpcvMcwi (2019)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 83138246 83138247 G A snv HXB31/IpcvMcwi (2019)
14 83180561 83180562 C G snv SR/JrHsd (MCW)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 83498858 83498859 T C snv LCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311535 AgrOrtholog
Ensembl Genes ENSRNOG00000018144 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061924 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073874 UniProtKB/TrEMBL
  ENSRNOP00000076509 ENTREZGENE
  ENSRNOP00000078180 ENTREZGENE
  ENSRNOP00000086876 ENTREZGENE
Ensembl Transcript ENSRNOT00000067694 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085788 UniProtKB/TrEMBL
  ENSRNOT00000101652 ENTREZGENE
  ENSRNOT00000113787 ENTREZGENE
  ENSRNOT00000116122 ENTREZGENE
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro DEP_dom UniProtKB/TrEMBL
  IML1 UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:305464 UniProtKB/TrEMBL
NCBI Gene 305464 ENTREZGENE
PANTHER PTHR13179 UniProtKB/TrEMBL
Pfam DEP UniProtKB/TrEMBL
  DUF3608 UniProtKB/TrEMBL
PhenoGen Depdc5 PhenoGen
PROSITE DEP UniProtKB/TrEMBL
SMART DEP UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A0A0G2K6M8 ENTREZGENE, UniProtKB/TrEMBL
  D4A362 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-09-13 Depdc5  DEP domain containing 5, GATOR1 subcomplex subunit  Depdc5  DEP domain containing 5, GATOR1 subcomplex subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2019-09-13 Depdc5  DEP domain containing 5, GATOR1 subcomplex subunit  Depdc5  DEP domain containing 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Depdc5  DEP domain containing 5   Depdc5_predicted  DEP domain containing 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Depdc5_predicted  DEP domain containing 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED