Hmgb4 (high-mobility group box 4) - Rat Genome Database

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Gene: Hmgb4 (high-mobility group box 4) Rattus norvegicus
Analyze
Symbol: Hmgb4
Name: high-mobility group box 4
RGD ID: 1596426
Description: Predicted to enable DNA binding activity, bending. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Orthologous to human HMGB4 (high mobility group box 4); INTERACTS WITH bisphenol A; furan; lead nitrate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: high mobility group protein B4; LOC685271; similar to RIKEN cDNA 1700001F22
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Hmgb4-ps3   Hmgb4-ps5  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85145,900,465 - 145,901,147 (-)NCBIGRCr8
mRatBN7.25140,616,040 - 140,616,722 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5140,615,197 - 140,616,770 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5143,311,996 - 143,312,678 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05145,081,823 - 145,082,505 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05145,082,744 - 145,083,426 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05146,445,545 - 146,446,227 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5146,445,545 - 146,446,227 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05150,186,040 - 150,186,722 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45147,486,501 - 147,487,183 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5139,102,413 - 139,103,095 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Hmgb4RatCharcot-Marie-Tooth disease dominant intermediate C  ISOHMGB4 (Homo sapiens)8554872ClinVar Annotator: match by term: Charcot-Marie-Tooth disease dominant intermediate CClinVarPMID:28492532


  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Hmgb4Rat1,2-dichloroethane decreases expressionISOHmgb4 (Mus musculus)6480464ethylene dichloride results in decreased expression of HMGB4 mRNACTDPMID:28960355
Hmgb4Ratbenzo[a]pyrene affects methylationISOHMGB4 (Homo sapiens)6480464Benzo(a)pyrene affects the methylation of HMGB4 5' UTRCTDPMID:27901495
Hmgb4Ratbisphenol A decreases expressionEXP 6480464bisphenol A results in decreased expression of HMGB4 mRNACTDPMID:25181051
Hmgb4RatCGP 52608 multiple interactionsISOHMGB4 (Homo sapiens)6480464CGP 52608 promotes the reaction [RORA protein binds to HMGB4 gene]CTDPMID:28238834
Hmgb4Ratfuran increases methylationEXP 6480464furan results in increased methylation of HMGB4 geneCTDPMID:22079235
Hmgb4Ratlead nitrate decreases expressionEXP 6480464lead nitrate results in decreased expression of HMGB4 mRNACTDPMID:21628963
Hmgb4Ratparacetamol decreases expressionISOHMGB4 (Homo sapiens)6480464Acetaminophen results in decreased expression of HMGB4 mRNACTDPMID:26690555


Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Hmgb4Ratregulation of transcription by RNA polymerase II involved_inIBAMGI:96113 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Hmgb4Ratnucleus located_inIEAUniRule:UR0004008111600115GO_REF:0000104UniProtGO_REF:0000104
Hmgb4Ratnucleus located_inIEAUniProtKB-KW:KW-05391600115GO_REF:0000043UniProtGO_REF:0000043

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Hmgb4RatDNA binding enablesIEAUniProtKB-KW:KW-02381600115GO_REF:0000043UniProtGO_REF:0000043
Hmgb4RatDNA binding enablesIEAUniRule:UR0004008111600115GO_REF:0000104UniProtGO_REF:0000104
Hmgb4RatDNA binding, bending enablesIBAFB:FBgn0004362 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Hmgb4Ratprotein binding enablesISOHMGB4 (Homo sapiens)1624291UniProtKB:P60329 more ...RGDPMID:25416956 and PMID:32296183


#
Reference Title
Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:21630459  



Hmgb4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85145,900,465 - 145,901,147 (-)NCBIGRCr8
mRatBN7.25140,616,040 - 140,616,722 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5140,615,197 - 140,616,770 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5143,311,996 - 143,312,678 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05145,081,823 - 145,082,505 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05145,082,744 - 145,083,426 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05146,445,545 - 146,446,227 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5146,445,545 - 146,446,227 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05150,186,040 - 150,186,722 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45147,486,501 - 147,487,183 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5139,102,413 - 139,103,095 (-)NCBICelera
Cytogenetic Map5q36NCBI
HMGB4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38133,860,475 - 33,864,791 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl133,860,475 - 33,864,791 (+)EnsemblGRCh38hg38GRCh38
GRCh37134,326,076 - 34,330,392 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36134,098,663 - 34,102,979 (+)NCBINCBI36Build 36hg18NCBI36
Celera132,597,828 - 32,602,145 (+)NCBICelera
Cytogenetic Map1p35.1NCBI
HuRef132,442,269 - 32,444,888 (+)NCBIHuRef
CHM1_1134,441,465 - 34,445,784 (+)NCBICHM1_1
T2T-CHM13v2.0133,722,055 - 33,726,370 (+)NCBIT2T-CHM13v2.0
Hmgb4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394128,154,005 - 128,154,688 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4128,154,005 - 128,154,750 (-)EnsemblGRCm39 Ensembl
GRCm384128,260,212 - 128,260,895 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4128,260,212 - 128,260,957 (-)EnsemblGRCm38mm10GRCm38
MGSCv374127,937,456 - 127,938,139 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364127,762,517 - 127,763,197 (-)NCBIMGSCv36mm8
Celera4126,598,050 - 126,598,733 (-)NCBICelera
Cytogenetic Map4D2.2NCBI
cM Map461.97NCBI
Hmgb4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545212,013,456 - 12,014,041 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545212,013,304 - 12,014,058 (+)NCBIChiLan1.0ChiLan1.0
HMGB4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21192,961,899 - 192,966,213 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11192,083,989 - 192,088,311 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0133,146,630 - 33,150,947 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1134,329,708 - 34,334,020 (+)NCBIpanpan1.1PanPan1.1panPan2
HMGB4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1157,915,066 - 7,915,803 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl157,915,096 - 7,915,920 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha158,158,414 - 8,159,156 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0158,061,106 - 8,061,848 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1157,890,761 - 7,891,503 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0157,970,955 - 7,971,697 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0157,986,253 - 7,986,995 (-)NCBIUU_Cfam_GSD_1.0
Hmgb4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505850,804,281 - 50,805,038 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493647416,629,225 - 16,629,803 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMGB4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl690,135,806 - 90,136,396 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1690,133,911 - 90,136,413 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HMGB4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12099,018,137 - 99,018,867 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2099,018,176 - 99,018,745 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603317,682,238 - 17,697,240 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hmgb4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476416,921,101 - 16,924,955 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

.

.
Variants in Hmgb4
1 total Variants

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:45
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000044868
Prediction methods: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.


1 to 10 of 43 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
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
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5129132428143070159Rat

1 to 10 of 43 rows



alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
3 10 6 35 20 30 8 12 8 3 45 23 29 3 33 22


RefSeq Transcripts NM_001109463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000044868   ⟹   ENSRNOP00000041856
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5140,615,197 - 140,616,770 (-)Ensembl
Rnor_6.0 Ensembl5146,445,545 - 146,446,227 (-)Ensembl
RefSeq Acc Id: NM_001109463   ⟹   NP_001102933
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85145,900,465 - 145,901,147 (-)NCBI
mRatBN7.25140,616,040 - 140,616,722 (-)NCBI
Rnor_6.05146,445,545 - 146,446,227 (-)NCBI
Rnor_5.05150,186,040 - 150,186,722 (-)NCBI
RGSC_v3.45147,486,501 - 147,487,183 (-)RGD
Celera5139,102,413 - 139,103,095 (-)RGD
Sequence:
Protein RefSeqs NP_001102933 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL80494 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000041856.2
  ENSRNOP00000098702
RefSeq Acc Id: NP_001102933   ⟸   NM_001109463
- UniProtKB: D3ZMW8 (UniProtKB/TrEMBL),   A6ISE2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000041856   ⟸   ENSRNOT00000044868
HMG box

Name Modeler Protein Id AA Range Protein Structure
AF-D3ZMW8-F1-model_v2 AlphaFold D3ZMW8 1-181 view protein structure


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

RGD ID:13694051
Promoter ID:EPDNEW_R4576
Type:multiple initiation site
Name:Hmgb4_1
Description:high-mobility group box 4
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_6.05146,446,226 - 146,446,286EPDNEW


1 to 24 of 24 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-39842 BioCyc
Ensembl Genes ENSRNOG00000032889 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000071968 ENTREZGENE
Ensembl Transcript ENSRNOT00000044868.4 UniProtKB/TrEMBL
  ENSRNOT00000148475 ENTREZGENE
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
  HMGB UniProtKB/TrEMBL
KEGG Report rno:685271 UniProtKB/TrEMBL
NCBI Gene 685271 ENTREZGENE
PANTHER HIGH MOBILITY GROUP PROTEIN B4 UniProtKB/TrEMBL
  HIGH MOBILITY GROUP PROTEIN DSP1 UniProtKB/TrEMBL
Pfam DUF1898 UniProtKB/TrEMBL
  HMG_box UniProtKB/TrEMBL
PhenoGen Hmgb4 PhenoGen
PRINTS HIGHMOBLTY12 UniProtKB/TrEMBL
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032889 RatGTEx
  ENSRNOG00000071968 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL
UniProt A6ISE2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZMW8 ENTREZGENE, UniProtKB/TrEMBL
1 to 24 of 24 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Hmgb4  high-mobility group box 4  LOC685271  similar to RIKEN cDNA 1700001F22  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC685271  similar to RIKEN cDNA 1700001F22  LOC682086  similar to RIKEN cDNA 1700001F22  Data merged from RGD:1588082 1643240 APPROVED
2006-11-20 LOC685271  similar to RIKEN cDNA 1700001F22      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC682086  similar to RIKEN cDNA 1700001F22      Symbol and Name status set to provisional 70820 PROVISIONAL