HMGB1 (high mobility group box 1) - Rat Genome Database

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Gene: HMGB1 (high mobility group box 1) Canis lupus familiaris
Analyze
Symbol: HMGB1
Name: high mobility group box 1
RGD ID: 12060047
Description: ENCODES a protein that exhibits 5S rRNA binding (ortholog); bent DNA binding (ortholog); bubble DNA binding (ortholog); INVOLVED IN actin cytoskeleton reorganization (ortholog); apoptotic cell clearance (ortholog); base-excision repair (ortholog); PARTICIPATES IN cisplatin drug pathway; mismatch repair pathway; pro-inflammatory cytokine mediated pathway; ASSOCIATED WITH Acute Experimental Pancreatitis (ortholog); Acute Lung Injury (ortholog); Acute-On-Chronic Liver Failure (ortholog); FOUND IN chromatin (ortholog); cytoplasm (ortholog); cytosol (ortholog)
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: high mobility group protein B1; HMG1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1259,431,223 - 9,558,167 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl259,431,218 - 9,558,165 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha259,596,948 - 9,603,279 (+)NCBI
ROS_Cfam_1.0259,542,952 - 9,670,011 (+)NCBI
UMICH_Zoey_3.1259,558,389 - 9,564,743 (+)NCBI
UNSW_CanFamBas_1.0259,566,227 - 9,572,605 (+)NCBI
UU_Cfam_GSD_1.0259,608,257 - 9,614,621 (+)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Experimental Pancreatitis  (ISO)
Acute Lung Injury  (ISO)
Acute-On-Chronic Liver Failure  (ISO)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis  (ISO)
atherosclerosis  (ISO)
Brain Injuries  (ISO)
Burns  (ISO)
Cardiomegaly  (ISO)
cerebral infarction  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
Chronic Allograft Dysfunction  (ISO)
colon adenocarcinoma  (ISO)
congestive heart failure  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
Endotoxemia  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Arthritis  (ISO)
Experimental Autoimmune Myocarditis  (ISO)
Experimental Diabetes Mellitus  (ISO)
extrahepatic cholestasis  (ISO)
Fever  (ISO)
Heat Stroke  (ISO)
high grade glioma  (ISO)
hydrocephalus  (ISO)
Hyperalgesia  (ISO)
hypertension  (ISO)
Inflammation  (ISO)
Intestinal Reperfusion Injury  (ISO)
Kawasaki disease  (ISO)
Knee Osteoarthritis  (ISO)
leukostasis  (ISO)
Liver Reperfusion Injury  (ISO)
Lung Reperfusion Injury  (ISO)
Lymphatic Metastasis  (ISO)
middle cerebral artery infarction  (ISO)
Multiple Organ Failure  (ISO)
myocardial infarction  (ISO)
Myocardial Ischemia  (ISO)
Myocardial Reperfusion Injury  (ISO)
Necrosis  (ISO)
Neuralgia  (ISO)
obstructive jaundice  (ISO)
osteoarthritis  (ISO)
Oxygen-Induced Retinopathy  (ISO)
Painful Neuropathy  (ISO)
periodontitis  (ISO)
Premature Aging  (ISO)
pulmonary fibrosis  (ISO)
pulmonary hypertension  (ISO)
Reperfusion Injury  (ISO)
Retina Reperfusion Injury  (ISO)
sciatic neuropathy  (ISO)
Sepsis  (ISO)
Spinal Cord Injuries  (ISO)
systemic scleroderma  (ISO)
Systemic Vasculitis  (ISO)
transient cerebral ischemia  (ISO)
Ventilator-Induced Lung Injury  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin cytoskeleton reorganization  (ISO)
activation of innate immune response  (IEA)
apoptotic cell clearance  (ISS)
autophagy  (IEA)
base-excision repair  (ISO)
cell morphogenesis  (ISO)
cellular response to interleukin-1  (ISO)
cellular response to interleukin-7  (ISO)
cellular response to lipopolysaccharide  (ISO)
chemotaxis  (IEA,ISO)
chromatin assembly  (ISO)
circadian rhythm  (ISO)
DNA geometric change  (ISO,ISS)
DNA repair  (IEA)
double-strand break repair via nonhomologous end joining  (ISO)
endothelial cell chemotaxis  (ISO)
endothelial cell proliferation  (ISO)
eye development  (ISO)
induction of positive chemotaxis  (ISO)
inflammatory response  (ISO)
inflammatory response to antigenic stimulus  (IEA)
innate immune response  (IEA)
lung development  (ISO)
macrophage activation involved in immune response  (ISO)
male-specific defense response to bacterium  (ISO)
MyD88-dependent toll-like receptor signaling pathway  (ISO)
myeloid dendritic cell activation  (ISO)
myoblast proliferation  (ISO)
negative regulation of apoptotic cell clearance  (IEA)
negative regulation of blood vessel endothelial cell migration  (IEA)
negative regulation of CD4-positive, alpha-beta T cell differentiation  (IEA)
negative regulation of DNA replication  (ISO)
negative regulation of interferon-gamma production  (IEA)
negative regulation of RNA polymerase II transcription preinitiation complex assembly  (IEA)
negative regulation of transcription by RNA polymerase II  (ISO)
nervous system development  (ISO)
neuron projection development  (ISO)
neutrophil clearance  (ISS)
nucleosome assembly  (ISO)
plasmacytoid dendritic cell activation  (ISO)
positive regulation of activated T cell proliferation  (IEA)
positive regulation of apoptotic process  (IEA,ISO)
positive regulation of autophagy  (IEA,ISO)
positive regulation of blood vessel endothelial cell migration  (IEA)
positive regulation of cell death  (ISO)
positive regulation of cell migration  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of chemokine (C-X-C motif) ligand 2 production  (IEA)
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  (IEA)
positive regulation of cytosolic calcium ion concentration  (IEA)
positive regulation of dendritic cell differentiation  (IEA)
positive regulation of DNA binding  (IEA)
positive regulation of DNA ligase activity  (ISO)
positive regulation of DNA ligation  (ISS)
positive regulation of ERK1 and ERK2 cascade  (IEA)
positive regulation of glycogen catabolic process  (ISO)
positive regulation of innate immune response  (ISO)
positive regulation of interferon-alpha production  (ISO)
positive regulation of interferon-beta production  (ISO)
positive regulation of interleukin-1 beta production  (ISO)
positive regulation of interleukin-1 production  (IEA)
positive regulation of interleukin-10 production  (IEA)
positive regulation of interleukin-12 production  (IEA)
positive regulation of interleukin-6 production  (IEA,ISO)
positive regulation of interleukin-8 production  (IEA)
positive regulation of JNK cascade  (IEA)
positive regulation of macrophage inflammatory protein 1 alpha production  (ISO)
positive regulation of MAPK cascade  (ISO)
positive regulation of mesenchymal cell proliferation  (ISO)
positive regulation of mismatch repair  (IEA)
positive regulation of mitotic cell cycle  (ISO)
positive regulation of monocyte chemotactic protein-1 production  (ISO)
positive regulation of monocyte chemotaxis  (IEA)
positive regulation of myeloid cell apoptotic process  (ISO)
positive regulation of myeloid cell differentiation  (ISO)
positive regulation of myoblast differentiation  (ISO)
positive regulation of neuron projection development  (ISO)
positive regulation of NIK/NF-kappaB signaling  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of smooth muscle cell migration  (ISO)
positive regulation of sprouting angiogenesis  (ISO)
positive regulation of toll-like receptor 2 signaling pathway  (ISO)
positive regulation of toll-like receptor 4 signaling pathway  (ISO)
positive regulation of toll-like receptor 9 signaling pathway  (ISS)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of tumor necrosis factor production  (IEA,ISO)
positive regulation of vascular endothelial cell proliferation  (IEA)
positive regulation of wound healing  (ISO)
protein-containing complex assembly  (ISO)
regulation of inflammatory response  (ISO)
regulation of nucleotide-excision repair  (ISO)
regulation of restriction endodeoxyribonuclease activity  (IEA)
regulation of T cell mediated immune response to tumor cell  (ISS)
regulation of tolerance induction  (IEA)
regulation of transcription by RNA polymerase II  (IBA)
response to glucocorticoid  (ISO)
response to glucose  (ISO)
response to heat  (ISO)
response to insulin  (ISO)
response to interferon-gamma  (ISO)
response to lipopolysaccharide  (ISO)
response to xenobiotic stimulus  (ISO)
T-helper 1 cell activation  (IEA)
T-helper 1 cell differentiation  (IEA)
toll-like receptor 2 signaling pathway  (ISO)
toll-like receptor 4 signaling pathway  (ISO)
V(D)J recombination  (IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:14571134   PMID:21617208   PMID:22154216  


Genomics

Comparative Map Data
HMGB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1259,431,223 - 9,558,167 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl259,431,218 - 9,558,165 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha259,596,948 - 9,603,279 (+)NCBI
ROS_Cfam_1.0259,542,952 - 9,670,011 (+)NCBI
UMICH_Zoey_3.1259,558,389 - 9,564,743 (+)NCBI
UNSW_CanFamBas_1.0259,566,227 - 9,572,605 (+)NCBI
UU_Cfam_GSD_1.0259,608,257 - 9,614,621 (+)NCBI
HMGB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1330,456,704 - 30,617,597 (-)EnsemblGRCh38hg38GRCh38
GRCh381330,456,704 - 30,617,597 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371331,030,841 - 31,191,734 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361329,930,877 - 29,938,081 (-)NCBINCBI36hg18NCBI36
Celera1312,102,423 - 12,109,630 (-)NCBI
Cytogenetic Map13q12.3NCBI
HuRef1311,850,667 - 11,857,904 (-)NCBIHuRef
CHM1_11331,000,434 - 31,007,630 (-)NCBICHM1_1
Hmgb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395148,983,512 - 148,989,867 (-)NCBIGRCm39mm39
GRCm39 Ensembl5148,983,512 - 149,121,299 (-)Ensembl
GRCm385149,046,702 - 149,053,057 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5149,046,702 - 149,184,489 (-)EnsemblGRCm38mm10GRCm38
MGSCv375149,858,803 - 149,864,613 (-)NCBIGRCm37mm9NCBIm37
MGSCv365149,357,579 - 149,363,386 (-)NCBImm8
Celera5147,061,615 - 147,067,633 (-)NCBICelera
Cytogenetic Map5G3NCBI
cM Map589.18NCBI
Hmgb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2125,973,062 - 5,978,565 (+)NCBImRatBN7.2
Rnor_6.0127,082,529 - 7,090,246 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1637,500,017 - 37,502,237 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0129,177,615 - 9,178,878 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.11637,462,230 - 37,464,451 (+)NCBI
Celera127,732,744 - 7,737,689 (+)NCBICelera
Cytogenetic Map12p11NCBI
Hmgb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543115,373,207 - 15,377,339 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543115,373,207 - 15,377,339 (+)NCBIChiLan1.0ChiLan1.0
HMGB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11330,173,875 - 30,179,527 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1330,174,899 - 30,179,527 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01311,737,942 - 11,894,923 (-)NCBIMhudiblu_PPA_v0panPan3
Hmgb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945170,705,559 - 170,715,427 (+)NCBI
SpeTri2.0NW_00493647225,236,728 - 25,246,585 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMGB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1117,195,556 - 7,321,071 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2117,006,105 - 7,131,947 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HMGB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.139,353,333 - 9,357,765 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605735,008,842 - 35,015,311 (+)NCBIVero_WHO_p1.0
Hmgb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247767,858,400 - 7,862,716 (+)NCBIHetGla_female_1.0hetGla2


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 reproductive system respiratory system adipose tissue
High
Medium 5 5 22 6 6 6 6 6 12 8 10 6
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000010639   ⟹   ENSCAFP00000009862
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl259,551,857 - 9,558,165 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000046727   ⟹   ENSCAFP00000041181
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl259,431,218 - 9,556,677 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000093577   ⟹   ENSCAFP00000048788
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl259,431,218 - 9,556,677 (+)Ensembl
RefSeq Acc Id: NM_001002937   ⟹   NP_001002937
RefSeq Status: VALIDATED
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1259,551,857 - 9,558,165 (+)NCBI
Dog10K_Boxer_Tasha259,596,948 - 9,603,279 (+)NCBI
ROS_Cfam_1.0259,663,670 - 9,670,009 (+)NCBI
UMICH_Zoey_3.1259,558,389 - 9,564,743 (+)NCBI
UNSW_CanFamBas_1.0259,566,227 - 9,572,605 (+)NCBI
UU_Cfam_GSD_1.0259,608,257 - 9,614,621 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038434506   ⟹   XP_038290434
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0259,660,449 - 9,670,011 (+)NCBI
RefSeq Acc Id: XM_038434508   ⟹   XP_038290436
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0259,542,952 - 9,670,011 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001002937 (Get FASTA)   NCBI Sequence Viewer  
  XP_038290434 (Get FASTA)   NCBI Sequence Viewer  
  XP_038290436 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAN11296 (Get FASTA)   NCBI Sequence Viewer  
  AAN11319 (Get FASTA)   NCBI Sequence Viewer  
  Q6YKA4 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001002937   ⟸   NM_001002937
- UniProtKB: Q6YKA4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSCAFP00000009862   ⟸   ENSCAFT00000010639
RefSeq Acc Id: ENSCAFP00000048788   ⟸   ENSCAFT00000093577
RefSeq Acc Id: ENSCAFP00000041181   ⟸   ENSCAFT00000046727
RefSeq Acc Id: XP_038290436   ⟸   XM_038434508
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038290434   ⟸   XM_038434506
- Peptide Label: isoform X1

Promoters
RGD ID:13687719
Promoter ID:EPDNEW_C5787
Type:initiation region
Name:HMGB1_1
Description:High mobility group protein B1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1259,551,922 - 9,551,982EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000006597 Ensembl
NCBI Gene HMGB1 ENTREZGENE
UniProt Q6YKA4 ENTREZGENE
VGNC ID VGNC:59082 ENTREZGENE