Hmgb3 (high mobility group box 3) - Rat Genome Database
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Gene: Hmgb3 (high mobility group box 3) Rattus norvegicus
Analyze
Symbol: Hmgb3
Name: high mobility group box 3
RGD ID: 1564407
Description: Predicted to have DNA binding activity, bending; RNA binding activity; and four-way junction DNA binding activity. Predicted to be involved in DNA geometric change; negative regulation of hemopoiesis; and regulation of transcription by RNA polymerase II. Predicted to localize to nuclear chromatin. Human ortholog(s) of this gene implicated in syndromic microphthalmia 13. Orthologous to human HMGB3 (high mobility group box 3); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; chlorpyrifos.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: high mobility group protein B3; LOC305373; RGD1564407; similar to high mobility group protein homolog HMG4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X149,296,309 - 149,301,294 (+)NCBI
Rnor_6.0 Ensembl1451,458,443 - 51,462,721 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1736,690,249 - 36,694,325 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01736,690,190 - 36,694,329 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01451,617,771 - 51,622,052 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X157,027,845 - 157,033,080 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic Map17p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IBA)
chromosome  (IEA)
nucleus  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:12714519   PMID:19890330   PMID:22681889   PMID:30166860  


Genomics

Comparative Map Data
Hmgb3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X149,296,309 - 149,301,294 (+)NCBI
Rnor_6.0 Ensembl1451,458,443 - 51,462,721 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1736,690,249 - 36,694,325 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01736,690,190 - 36,694,329 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01451,617,771 - 51,622,052 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X157,027,845 - 157,033,080 (+)NCBIRGSC3.4rn4RGSC3.4
Cytogenetic Map17p12NCBI
HMGB3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX150,980,509 - 150,990,771 (+)EnsemblGRCh38hg38GRCh38
GRCh38X150,980,507 - 150,990,773 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X150,148,980 - 150,159,244 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37X150,149,056 - 150,159,248 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X149,902,421 - 149,909,906 (+)NCBINCBI36hg18NCBI36
Build 34X149,822,336 - 149,827,902NCBI
CeleraX150,399,636 - 150,407,102 (+)NCBI
Cytogenetic MapXq28NCBI
HuRefX139,013,654 - 139,018,732 (+)NCBIHuRef
CHM1_1X150,023,365 - 150,033,552 (+)NCBICHM1_1
Hmgb3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X70,599,523 - 70,604,279 (+)NCBIGRCm39mm39
GRCm38X71,555,917 - 71,560,673 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX71,555,918 - 71,560,676 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X68,809,168 - 68,813,829 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X67,816,549 - 67,821,210 (+)NCBImm8
CeleraX62,536,255 - 62,540,916 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
Hmgb3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554986,633,540 - 6,640,393 (+)NCBIChiLan1.0ChiLan1.0
HMGB3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X150,565,153 - 150,570,752 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0X140,632,163 - 140,639,774 (+)NCBIMhudiblu_PPA_v0panPan3
HMGB3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX119,155,786 - 119,159,814 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X119,152,166 - 119,159,803 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hmgb3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367141,523,016 - 1,527,301 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMGB3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX122,592,936 - 122,599,493 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X122,591,413 - 122,599,496 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X140,189,835 - 140,193,015 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HMGB3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X125,568,622 - 125,572,184 (+)NCBI
Hmgb3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249231,245,898 - 1,250,571 (+)NCBI

Position Markers
UniSTS:256978  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01737,997,594 - 37,997,937NCBIRnor5.0
Rnor_5.01451,618,739 - 51,619,082NCBIRnor5.0
Rnor_5.01451,331,169 - 51,331,360NCBIRnor5.0
RGSC_v3.4X157,031,769 - 157,032,111UniSTSRGSC3.4
RGSC_v3.4413,292,046 - 13,292,236UniSTSRGSC3.4
Celera1448,406,068 - 48,406,258UniSTS
Cytogenetic Map4q11UniSTS
Cytogenetic MapXq37UniSTS
Hmgb3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01737,997,594 - 37,997,937NCBIRnor5.0
Rnor_5.01451,618,739 - 51,619,082NCBIRnor5.0
Rnor_5.01451,331,169 - 51,331,360NCBIRnor5.0
RGSC_v3.4X157,031,769 - 157,032,111UniSTSRGSC3.4
RGSC_v3.4413,292,046 - 13,292,236UniSTSRGSC3.4
Celera1448,406,068 - 48,406,258UniSTS
Cytogenetic Map4q11UniSTS
Cytogenetic MapXq37UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138243814Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17163676140Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17333697237790462Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17333697263676140Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17519104750191047Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17519104750191047Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17982730454827304Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)171052970942542027Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171574375561036897Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171867614063676140Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171867614063676140Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095062195822Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095066490950Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172149095066490950Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172149095066490950Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172149095066490950Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172149095066490950Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172149095074823273Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172213681453475276Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172277506564946194Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172403061863676140Rat
4889891Eae32Experimental allergic encephalomyelitis QTL 324.80.0002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)172769095938110914Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172769095961794615Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172769095963994435Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172807358956207236Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172841314873413148Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)173097522875975228Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)173097522875975228Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173205588258468016Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173205588277922655Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173330362753475276Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173330362778303627Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173628324577922655Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:88
Count of miRNA genes:83
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000015044
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 1 18 15 10 7 10 100 26 44 1
Below cutoff 4 38 55 42 23 42 1 3 32 24 22 9 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015044   ⟹   ENSRNOP00000015044
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1451,458,443 - 51,462,721 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000074314   ⟹   ENSRNOP00000066102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1736,691,875 - 36,693,476 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082140   ⟹   ENSRNOP00000069465
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1736,690,249 - 36,694,325 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089476   ⟹   ENSRNOP00000070959
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1736,690,249 - 36,693,499 (+)Ensembl
RefSeq Acc Id: NM_001173341   ⟹   NP_001166812
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X149,296,309 - 149,301,290 (+)NCBI
Rnor_6.01736,690,190 - 36,694,325 (+)NCBI
Rnor_5.01451,617,771 - 51,622,052 (-)NCBI
Sequence:
RefSeq Acc Id: XM_003751682   ⟹   XP_003751730
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X149,296,374 - 149,301,294 (+)NCBI
Rnor_6.01736,690,255 - 36,694,329 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099681   ⟹   XP_038955609
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X149,297,398 - 149,301,294 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001166812 (Get FASTA)   NCBI Sequence Viewer  
  XP_003751730 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955609 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58740 (Get FASTA)   NCBI Sequence Viewer  
  EDL82825 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001166812   ⟸   NM_001173341
- UniProtKB: B0BN99 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_003751730   ⟸   XM_003751682
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000069465   ⟸   ENSRNOT00000082140
RefSeq Acc Id: ENSRNOP00000070959   ⟸   ENSRNOT00000089476
RefSeq Acc Id: ENSRNOP00000066102   ⟸   ENSRNOT00000074314
RefSeq Acc Id: ENSRNOP00000015044   ⟸   ENSRNOT00000015044
RefSeq Acc Id: XP_038955609   ⟸   XM_039099681
- Peptide Label: isoform X2
Protein Domains
HMG box

Transcriptome

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

Promoters
RGD ID:13700435
Promoter ID:EPDNEW_R10957
Type:initiation region
Name:Hmgb3_1
Description:high mobility group box 3
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_6.01736,690,181 - 36,690,241EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564407 AgrOrtholog
Ensembl Genes ENSRNOG00000011096 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000050910 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015044 UniProtKB/TrEMBL
  ENSRNOP00000066102 UniProtKB/TrEMBL
  ENSRNOP00000069465 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070959 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015044 UniProtKB/TrEMBL
  ENSRNOT00000074314 UniProtKB/TrEMBL
  ENSRNOT00000082140 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089476 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9099241 IMAGE-MGC_LOAD
InterPro HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_boxA_CS UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
  HMGB3 UniProtKB/TrEMBL
KEGG Report rno:305373 UniProtKB/TrEMBL
MGC_CLONE MGC:187907 IMAGE-MGC_LOAD
NCBI Gene 305373 ENTREZGENE
PANTHER PTHR48112:SF14 UniProtKB/TrEMBL
Pfam DUF1898 UniProtKB/TrEMBL
  HMG_box UniProtKB/TrEMBL
PhenoGen Hmgb3 PhenoGen
PROSITE HMG_BOX_1 UniProtKB/TrEMBL
  HMG_BOX_2 UniProtKB/TrEMBL
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL
UniProt B0BN99 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Hmgb3  high mobility group box 3  RGD1564407_predicted  similar to high mobility group protein homolog HMG4 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564407_predicted  similar to high mobility group protein homolog HMG4 (predicted)  LOC305373  similar to high mobility group protein homolog HMG4  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC305373  similar to high mobility group protein homolog HMG4      Symbol and Name status set to provisional 70820 PROVISIONAL