Chd5 (chromodomain helicase DNA binding protein 5) - Rat Genome Database

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Gene: Chd5 (chromodomain helicase DNA binding protein 5) Rattus norvegicus
Analyze
Symbol: Chd5
Name: chromodomain helicase DNA binding protein 5
RGD ID: 1582725
Description: Enables chromatin binding activity. Involved in transcription by RNA polymerase II. Located in nucleus. Colocalizes with chromatin. Orthologous to human CHD5 (chromodomain helicase DNA binding protein 5); PARTICIPATES IN CHD family mediated chromatin remodeling pathway; INTERACTS WITH bisphenol A; cadmium dichloride; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ATP-dependent helicase CHD5; CHD-5; chromodomain-helicase-DNA-binding protein 5; LOC691589; similar to chromodomain helicase DNA binding protein 5
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
mRatBN7.25162,848,273 - 162,898,997 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5162,848,394 - 162,896,291 (+)Ensembl
Rnor_6.05169,519,212 - 169,572,059 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5169,519,212 - 169,567,107 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05173,072,537 - 173,124,329 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45169,570,804 - 169,616,812 (+)NCBIRGSC3.4rn4RGSC3.4
Celera5161,089,207 - 161,126,951 (+)NCBICelera
Cytogenetic Map5q36NCBI
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
Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:17289567   PMID:19946888   PMID:23318260   PMID:23948251   PMID:24252660  


Genomics

Comparative Map Data
Chd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25162,848,273 - 162,898,997 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5162,848,394 - 162,896,291 (+)Ensembl
Rnor_6.05169,519,212 - 169,572,059 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5169,519,212 - 169,567,107 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05173,072,537 - 173,124,329 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45169,570,804 - 169,616,812 (+)NCBIRGSC3.4rn4RGSC3.4
Celera5161,089,207 - 161,126,951 (+)NCBICelera
Cytogenetic Map5q36NCBI
CHD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl16,101,787 - 6,180,321 (-)EnsemblGRCh38hg38GRCh38
GRCh3816,101,787 - 6,180,321 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3716,161,847 - 6,240,381 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3616,084,440 - 6,162,770 (-)NCBINCBI36hg18NCBI36
Build 3416,096,118 - 6,174,449NCBI
Celera15,276,664 - 5,354,707 (-)NCBI
Cytogenetic Map1p36.31NCBI
HuRef15,310,665 - 5,388,563 (-)NCBIHuRef
CHM1_116,150,226 - 6,228,570 (-)NCBICHM1_1
Chd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394152,423,103 - 152,474,651 (+)NCBIGRCm39mm39
GRCm39 Ensembl4152,423,108 - 152,474,651 (+)Ensembl
GRCm384152,338,646 - 152,390,194 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4152,338,651 - 152,390,194 (+)EnsemblGRCm38mm10GRCm38
MGSCv374151,712,760 - 151,764,303 (+)NCBIGRCm37mm9NCBIm37
MGSCv364151,182,451 - 151,233,994 (+)NCBImm8
Celera4154,635,153 - 154,677,359 (+)NCBICelera
Cytogenetic Map4E2NCBI
Chd5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554866,320,380 - 6,369,065 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554866,320,380 - 6,369,020 (+)NCBIChiLan1.0ChiLan1.0
CHD5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.116,121,040 - 6,190,367 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl16,125,525 - 6,191,991 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v014,867,636 - 4,947,401 (-)NCBIMhudiblu_PPA_v0panPan3
CHD5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1560,022,451 - 60,080,663 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl560,025,602 - 60,081,148 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha560,035,909 - 60,094,034 (-)NCBI
ROS_Cfam_1.0560,241,590 - 60,299,755 (-)NCBI
UMICH_Zoey_3.1560,241,294 - 60,299,358 (-)NCBI
UNSW_CanFamBas_1.0560,107,975 - 60,166,057 (-)NCBI
UU_Cfam_GSD_1.0560,509,416 - 60,567,561 (-)NCBI
Chd5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505830,503,185 - 30,559,221 (-)NCBI
SpeTri2.0NW_004936623988,423 - 1,046,969 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHD5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl667,017,425 - 67,087,043 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1667,017,410 - 67,086,685 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2661,940,486 - 62,084,194 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHD5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120125,558,640 - 125,635,748 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl20125,558,713 - 125,631,277 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605429,664,099 - 29,783,593 (+)NCBIVero_WHO_p1.0
Chd5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248185,203,200 - 5,251,057 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D5S619  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.05173,086,343 - 173,086,624NCBIRnor5.0
Rnor_5.01014,056,298 - 14,056,408NCBIRnor5.0
RGSC_v3.41014,127,391 - 14,127,500UniSTSRGSC3.4
RGSC_v3.45169,584,067 - 169,584,347UniSTSRGSC3.4
Celera1013,578,514 - 13,578,623UniSTS
Celera5161,092,523 - 161,092,803UniSTS
Cytogenetic Map10q12UniSTS
Cytogenetic Map5q36UniSTS
AU046936  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25162,882,670 - 162,882,847 (+)MAPPERmRatBN7.2
Rnor_6.05169,553,487 - 169,553,663NCBIRnor6.0
Rnor_5.05173,107,150 - 173,107,326UniSTSRnor5.0
RGSC_v3.45169,604,873 - 169,605,049UniSTSRGSC3.4
Celera5161,113,329 - 161,113,505UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5151113452164465185Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:241
Count of miRNA genes:141
Interacting mature miRNAs:150
Transcripts:ENSRNOT00000024732, ENSRNOT00000067364, ENSRNOT00000067892
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 64 7
Low 3 9 26 10 19 10 8 8 4 11 25 11 8
Below cutoff 10 9 9 9 3 6 24 9

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001271226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC097926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC135674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000024732   ⟹   ENSRNOP00000024732
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5162,848,394 - 162,896,291 (+)Ensembl
Rnor_6.0 Ensembl5169,519,212 - 169,567,107 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000067892   ⟹   ENSRNOP00000060241
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5162,858,339 - 162,894,691 (+)Ensembl
Rnor_6.0 Ensembl5169,521,179 - 169,565,421 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101697   ⟹   ENSRNOP00000086830
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5162,848,394 - 162,896,291 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112715   ⟹   ENSRNOP00000087017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5162,848,394 - 162,896,291 (+)Ensembl
RefSeq Acc Id: NM_001271226   ⟹   NP_001258155
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,394 - 162,896,291 (+)NCBI
Rnor_6.05169,519,212 - 169,567,107 (+)NCBI
Rnor_5.05173,072,537 - 173,124,329 (+)NCBI
Celera5161,089,207 - 161,126,951 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593639   ⟹   XP_017449128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,218 - 169,572,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593640   ⟹   XP_017449129
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,234 - 169,572,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593641   ⟹   XP_017449130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,218 - 169,572,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593642   ⟹   XP_017449131
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,234 - 169,572,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593643   ⟹   XP_017449132
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,234 - 169,572,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593644   ⟹   XP_017449133
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,851,073 - 162,898,997 (+)NCBI
Rnor_6.05169,521,976 - 169,572,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593645   ⟹   XP_017449134
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,895,816 (+)NCBI
Rnor_6.05169,519,234 - 169,566,582 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593646   ⟹   XP_017449135
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,234 - 169,572,059 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593647   ⟹   XP_017449136
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,234 - 169,566,640 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593648   ⟹   XP_017449137
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,234 - 169,566,640 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593649   ⟹   XP_017449138
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
Rnor_6.05169,519,234 - 169,566,640 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039110813   ⟹   XP_038966741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,898,997 (+)NCBI
RefSeq Acc Id: XM_039110814   ⟹   XP_038966742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,274 - 162,894,185 (+)NCBI
RefSeq Acc Id: XM_039110815   ⟹   XP_038966743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25162,848,273 - 162,888,642 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001258155   ⟸   NM_001271226
- UniProtKB: A0A0H2UHP5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017449128   ⟸   XM_017593639
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017449130   ⟸   XM_017593641
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017449135   ⟸   XM_017593646
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017449129   ⟸   XM_017593640
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017449131   ⟸   XM_017593642
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017449132   ⟸   XM_017593643
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017449136   ⟸   XM_017593647
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017449137   ⟸   XM_017593648
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017449138   ⟸   XM_017593649
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017449134   ⟸   XM_017593645
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017449133   ⟸   XM_017593644
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: ENSRNOP00000060241   ⟸   ENSRNOT00000067892
RefSeq Acc Id: ENSRNOP00000024732   ⟸   ENSRNOT00000024732
RefSeq Acc Id: XP_038966743   ⟸   XM_039110815
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038966741   ⟸   XM_039110813
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038966742   ⟸   XM_039110814
- Peptide Label: isoform X12
RefSeq Acc Id: ENSRNOP00000086830   ⟸   ENSRNOT00000101697
RefSeq Acc Id: ENSRNOP00000087017   ⟸   ENSRNOT00000112715
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 (2019)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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)
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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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)
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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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
F344/Stm (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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/FarMcwi (2019)
Visual CSV TAB Printer
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)
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2019)
Visual CSV TAB Printer
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)
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
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 (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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 (2019)
Visual CSV TAB Printer
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)
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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)
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 (2019)
Visual CSV TAB Printer
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)
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 (2020)
Visual CSV TAB Printer
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: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 173111459 173111460 T G snv F344/Jcl (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 169564941 169564942 C T snv FHH/EurMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1582725 AgrOrtholog
Ensembl Genes ENSRNOG00000011268 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024732 UniProtKB/TrEMBL
  ENSRNOP00000060241 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024732 UniProtKB/TrEMBL
  ENSRNOT00000067892 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.10810 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CHD5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHD_C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHD_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo/chromo_shadow_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA/RNA_helicase_DEAH_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF1086 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF1087 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:691589 UniProtKB/TrEMBL
NCBI Gene 691589 ENTREZGENE
PANTHER PTHR45623:SF6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CHDCT2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHDNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chromo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF1086 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF1087 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chd5 PhenoGen
PROSITE CHROMO_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEAH_ATP_HELICASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CHROMO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DEXDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF1086 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DUF1087 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54160 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57903 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHP5 ENTREZGENE, UniProtKB/TrEMBL
  CHD5_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  D3ZR50_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Chd5  chromodomain helicase DNA binding protein 5  LOC691589  similar to chromodomain helicase DNA binding protein 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691589  similar to chromodomain helicase DNA binding protein 5  LOC686986  similar to chromodomain helicase DNA binding protein 5  Data Merged 1643240 APPROVED
2006-11-20 LOC686986  similar to chromodomain helicase DNA binding protein 5      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC691589  similar to chromodomain helicase DNA binding protein 5      Symbol and Name status set to provisional 70820 PROVISIONAL