Ino80d (INO80 complex subunit D) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Ino80d (INO80 complex subunit D) Rattus norvegicus
Analyze
Symbol: Ino80d
Name: INO80 complex subunit D
RGD ID: 1304808
Description: Predicted to localize to nucleus. Orthologous to human INO80D (INO80 complex subunit D); PARTICIPATES IN INO80 family mediated chromatin remodeling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-Tetrachlorodibenzofuran; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC316440; RGD1304808; similar to hypothetical protein FLJ20309
Orthologs:
Homo sapiens (human) : INO80D (INO80 complex subunit D)  HGNC  Alliance
Mus musculus (house mouse) : Ino80d (INO80 complex subunit D)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Ino80d (INO80 complex subunit D)
Pan paniscus (bonobo/pygmy chimpanzee) : INO80D (INO80 complex subunit D)
Canis lupus familiaris (dog) : INO80D (INO80 complex subunit D)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Ino80d (INO80 complex subunit D)
Sus scrofa (pig) : INO80D (INO80 complex subunit D)
Chlorocebus sabaeus (African green monkey) : INO80D (INO80 complex subunit D)
Heterocephalus glaber (naked mole-rat) : Ino80d (INO80 complex subunit D)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0969,820,520 - 69,887,475 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl969,830,424 - 69,878,706 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0969,629,390 - 69,696,566 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4961,708,910 - 61,746,437 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1961,855,901 - 61,912,107 (-)NCBI
Celera961,875,183 - 61,912,560 (-)NCBICelera
Cytogenetic Map9q32NCBI
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References


Genomics

Comparative Map Data
Ino80d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0969,820,520 - 69,887,475 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl969,830,424 - 69,878,706 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0969,629,390 - 69,696,566 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4961,708,910 - 61,746,437 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1961,855,901 - 61,912,107 (-)NCBI
Celera961,875,183 - 61,912,560 (-)NCBICelera
Cytogenetic Map9q32NCBI
INO80D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2205,993,721 - 206,086,303 (-)EnsemblGRCh38hg38GRCh38
GRCh382205,993,721 - 206,086,174 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372206,858,445 - 206,950,906 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362206,566,690 - 206,659,151 (-)NCBINCBI36hg18NCBI36
Celera2200,615,842 - 200,708,300 (-)NCBI
Cytogenetic Map2q33.3NCBI
HuRef2198,706,439 - 198,799,527 (-)NCBIHuRef
CHM1_12206,864,927 - 206,957,389 (-)NCBICHM1_1
Ino80d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39163,086,960 - 63,153,426 (-)NCBI
GRCm38163,047,801 - 63,114,267 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl162,958,418 - 63,114,667 (-)EnsemblGRCm38mm10GRCm38
MGSCv37163,094,375 - 63,160,841 (-)NCBIGRCm37mm9NCBIm37
MGSCv36162,992,456 - 63,048,605 (-)NCBImm8
Celera163,558,373 - 63,624,725 (-)NCBICelera
Cytogenetic Map1C2NCBI
Ino80d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554578,924,615 - 8,973,274 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554578,913,625 - 8,983,859 (+)NCBIChiLan1.0ChiLan1.0
INO80D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B211,363,367 - 211,433,124 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B211,373,993 - 211,433,124 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B93,233,672 - 93,325,871 (-)NCBIMhudiblu_PPA_v0panPan3
INO80D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3714,591,055 - 14,647,936 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13714,581,531 - 14,647,930 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ino80d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366312,405,056 - 2,474,798 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
INO80D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15109,307,166 - 109,376,463 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115109,301,753 - 109,376,614 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215120,860,998 - 120,926,506 (-)NCBISscrofa10.2Sscrofa10.2susScr3
INO80D
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1091,781,563 - 91,843,787 (-)Ensembl
ChlSab1.11091,770,873 - 91,864,797 (-)NCBI
Ino80d
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476510,040,259 - 10,127,449 (+)NCBI

Position Markers
D9Rat65  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0969,881,257 - 69,881,454NCBIRnor6.0
Rnor_5.0969,690,312 - 69,690,509UniSTSRnor5.0
RGSC_v3.4961,759,520 - 61,759,718RGDRGSC3.4
RGSC_v3.4961,759,521 - 61,759,718UniSTSRGSC3.4
RGSC_v3.1961,906,503 - 61,906,700RGD
Celera961,925,699 - 61,925,896UniSTS
Cytogenetic Map9q31UniSTS
RH 3.4 Map9530.1UniSTS
RH 3.4 Map9530.1RGD
RH 2.0 Map9598.5RGD
SHRSP x BN Map944.3798RGD
FHH x ACI Map942.32RGD
D9Got69  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0969,870,152 - 69,870,311NCBIRnor6.0
Rnor_5.0969,679,207 - 69,679,366UniSTSRnor5.0
RGSC_v3.4961,748,416 - 61,748,575RGDRGSC3.4
RGSC_v3.4961,748,416 - 61,748,575UniSTSRGSC3.4
RGSC_v3.1961,895,398 - 61,895,557RGD
Celera961,914,539 - 61,914,698UniSTS
Cytogenetic Map9q31UniSTS
RH 3.4 Map9530.0UniSTS
RH 3.4 Map9530.0RGD
RH 2.0 Map9598.6RGD
BF413441  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0969,888,032 - 69,888,343NCBIRnor6.0
Rnor_5.0969,697,087 - 69,697,398UniSTSRnor5.0
RGSC_v3.4961,766,296 - 61,766,607UniSTSRGSC3.4
Celera961,932,532 - 61,932,843UniSTS
Cytogenetic Map9q31UniSTS
RH 3.4 Map9532.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
1598849Memor17Memory QTL 172.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)95488504176677636Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1578659Tspe1Trichinella spiralis expulsion QTL 14.8parasite quantity (VT:0010441)logarithm of the intestinal adult Trichinella spiralis count (CMO:0002024)96675744471010122Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:126
Count of miRNA genes:102
Interacting mature miRNAs:111
Transcripts:ENSRNOT00000035879
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 17 2 16 2 23 9 10 8
Low 3 43 39 38 3 38 8 11 51 26 31 3 8
Below cutoff 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035879   ⟹   ENSRNOP00000037428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl969,830,424 - 69,878,706 (-)Ensembl
RefSeq Acc Id: NM_001191809   ⟹   NP_001178738
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,830,610 - 69,868,173 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Celera961,875,183 - 61,912,560 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245023   ⟹   XP_006245085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,820,520 - 69,887,475 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245025   ⟹   XP_006245087
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,820,520 - 69,887,475 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245026   ⟹   XP_006245088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,820,520 - 69,887,318 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245029   ⟹   XP_006245091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,820,520 - 69,886,930 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245031   ⟹   XP_006245093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,820,520 - 69,886,930 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245032   ⟹   XP_006245094
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,820,520 - 69,887,318 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245033   ⟹   XP_006245095
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,820,520 - 69,886,930 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245034   ⟹   XP_006245096
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0969,820,520 - 69,887,475 (-)NCBI
Rnor_5.0969,629,390 - 69,696,566 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001178738   ⟸   NM_001191809
- UniProtKB: D3ZTM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245087   ⟸   XM_006245025
- Peptide Label: isoform X1
- UniProtKB: D3ZTM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245085   ⟸   XM_006245023
- Peptide Label: isoform X1
- UniProtKB: D3ZTM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245096   ⟸   XM_006245034
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006245094   ⟸   XM_006245032
- Peptide Label: isoform X1
- UniProtKB: D3ZTM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245088   ⟸   XM_006245026
- Peptide Label: isoform X1
- UniProtKB: D3ZTM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245095   ⟸   XM_006245033
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006245093   ⟸   XM_006245031
- Peptide Label: isoform X1
- UniProtKB: D3ZTM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245091   ⟸   XM_006245029
- Peptide Label: isoform X1
- UniProtKB: D3ZTM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000037428   ⟸   ENSRNOT00000035879
Protein Domains
zf-C3Hc3H

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304808 AgrOrtholog
Ensembl Genes ENSRNOG00000024272 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037428 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035879 ENTREZGENE, UniProtKB/TrEMBL
InterPro Potential_DNA-bd UniProtKB/TrEMBL
KEGG Report rno:316440 UniProtKB/TrEMBL
NCBI Gene 316440 ENTREZGENE
Pfam zf-C3Hc3H UniProtKB/TrEMBL
PhenoGen Ino80d PhenoGen
UniGene Rn.9388 ENTREZGENE
UniProt D3ZTM2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Ino80d  INO80 complex subunit D  RGD1304808  similar to hypothetical protein FLJ20309   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1304808  similar to hypothetical protein FLJ20309   RGD1304808_predicted  similar to hypothetical protein FLJ20309 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1304808_predicted  similar to hypothetical protein FLJ20309 (predicted)  LOC316440_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC316440_predicted  similar to hypothetical protein FLJ20309 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL