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

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Gene: Hmgb4 (high-mobility group box 4) Mus musculus
Analyze
Symbol: Hmgb4
Name: high-mobility group box 4
RGD ID: 1323371
MGI Page MGI
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 chromosome and nucleus. Orthologous to human HMGB4 (high mobility group box 4).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1700001F22Rik; AI326135; high mobility group protein B4; MGC107306; RP23-284L15.1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromosome  (IEA)
nucleus  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, etal., Science 2004 Dec 24;306(5705):2255-7.
2. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:12477932   PMID:14681479   PMID:15489334   PMID:16141072   PMID:16141073   PMID:17609113   PMID:18987332   PMID:20059953   PMID:20932939  
PMID:21267068   PMID:21384471   PMID:21873635   PMID:22901013   PMID:24952961   PMID:27608812   PMID:31201419   PMID:38355793  


Genomics

Comparative Map Data
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
(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
(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
(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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:81
Count of miRNA genes:78
Interacting mature miRNAs:79
Transcripts:ENSMUST00000053830
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142139Adip12_madiposity 12 (mouse)Not determined4124621281156860686Mouse
10047132Albq19_malbuminuria QTL 19 (mouse)Not determined4112824389146824389Mouse
1301525Lmb1_mlupus in MRL and B6 F2 cross (mouse)Not determined4124264957150676858Mouse
14746982Manh56_mmandible shape 56 (mouse)4117815917151815917Mouse
4141623W6q13_mweight 6 weeks QTL 13 (mouse)Not determined88982069140468203Mouse
12910797Pwgrq4_mpre-weaning growth rate QTL 4 (mouse)4105835310141433838Mouse
25314312Syncl2_msynaptonemal complex length 2 (mouse)465718237146584457Mouse
12910794Pwbwq8_mpost-weaning body weight QTL 8 (mouse)4105835310141433838Mouse
1300743Skull6_mskull morphology 6 (mouse)Not determined4111009051145009280Mouse
1301382Arvm2_mautoimmune renal vasculitis 2 (mouse)Not determined4107791564141791756Mouse
1302149Tlsr2_mthymic lymphoma suppressor region 2 (mouse)Not determined4124264957142230960Mouse
12910813Pwbwq4_mpre-weaning body weight QTL 4 (mouse)4105835310141433838Mouse
4141093W3q17_mweight 3 weeks QTL 17 (mouse)Not determined88982069140468203Mouse
27226757Femd1_mfemur midshaft diameter 1, 5 week (mouse)4123993793144326570Mouse
12910808Pwbwq9_mpost-weaning body weight QTL 9 (mouse)4105835310141433838Mouse
1300621Tpnr1_mthermal pain response 1 (mouse)Not determined4125230872156860686Mouse
11567249Elorr3_methanol induced loss of righting response 3 (mouse)43722677156268235Mouse
4142493Femwf13_mfemur work to failure 13 (mouse)Not determined116154678150154782Mouse
1301815Sles2_msystemic lupus erythmatosus suppressor 2 (mouse)Not determined494957579150676858Mouse
1300663Start2_mstartle response 2 (mouse)Not determined4107264957141265153Mouse
1300917Gasa1_mgastritis type A susceptibility locus 1 (mouse)Not determined4124055093142438020Mouse
1301823Bmd7_mbone mineral density 7 (mouse)Not determined488982069151654550Mouse
10412210Cypr6_mcytokine production 6 (mouse)Not determined4120617848154617995Mouse
1302078Sluc21_msusceptibility to lung cancer 21 (mouse)Not determined4117401141151401275Mouse
10045620Heal22_mwound healing/regeneration 22 (mouse)Not determined4125230872156860686Mouse
4142481Gct1_mgranulosa cell tumorigenesis 1 (mouse)Not determined4127784226156860686Mouse
4141065Shali2_msurvival time to hyperoxic acute lung injury 2 (mouse)Not determined124055093141572792Mouse
10412072Ssen1_msuseptibility to Sendai virus 1 (mouse)Not determined4109658132133154782Mouse
13503348Bntq18_mbone traits QTL 18 (mouse)4120617848154617995Mouse
13208562Wght7_mweight 7 (mouse)490888237148084457Mouse
1300655Nidds_mnon-insulin-dependent diabetes mellitus in SJL (mouse)Not determined4115030777129465915Mouse
1300781Lith8_mlithogenic gene 8 (mouse)Not determined4107264957141265153Mouse
39128212Lwq21_mliver weight QTL 21 (mouse)488982069140468203Mouse
4141180Ssic1_msusceptibility to small intestinal cancer 1 (mouse)Not determined120674005154674151Mouse
1301847Fecq2_mfecundity QTL 2 (mouse)Not determined4100071971134072206Mouse
1302102Bis1_mbeta-carboline-induced seizures 1 (mouse)Not determined4119864433153864536Mouse
10043996Gct5_mgranulosa cell tumorigenesis 5 (mouse)Not determined4127784226156860686Mouse
26884445Sklq7_mskull length QTL 7, 10 week (mouse)468018237150884457Mouse
10043985Stheal12_msoft tissue heal 12 (mouse)Not determined4121342649155342753Mouse
1301982Pltiq1_mphospholipid transfer protein inducibility QTL 1 (mouse)Not determined4124621281156860686Mouse
26884437Sklq13_mskull length QTL 13, 16 week (mouse)457700000155684457Mouse
1300803Sluc6_msusceptibility to lung cancer 6 (mouse)Not determined4120674005154674151Mouse
4141549W10q10_mweight 10 weeks QTL 10 (mouse)Not determined88982069140468203Mouse
4142061Chlq16_mcirculating hormone level QTL 16 (mouse)Not determined4121342649155342753Mouse
1357895Ctrcts_mcataract severity (mouse)Not determined445709925138342753Mouse
1300933Cdcs9_mcytokine deficiency colitis susceptibility 9 (mouse)Not determined4125230872156860686Mouse
1300809Ccrs2_mcorpus callosum hemisphere surface size 2 (mouse)Not determined4107264957141265153Mouse
1301452Elsgp1_melevated serum gp70 1 (mouse)Not determined4121342649155342753Mouse
1301964Bw8q2_mbody weight at 8 weeks QTL 2 (mouse)Not determined4119864433153864536Mouse
1301106Skts7_mskin tumor susceptibility 7 (mouse)Not determined4100071971134072206Mouse
10755520Rbc1_mred blood cell count 1 (mouse)4108477692142477692Mouse
10755521Hct1_mhematocrit 1 (mouse)4108477692142477692Mouse
10755522Hgb1_mhemoglobin 1 (mouse)4108477692142477692Mouse
1300858Tafat_mtally ho associated mesenteric fat pad weight (mouse)Not determined4124621281156860686Mouse
27095924Pglq2_mpelvic girdle length QTL 2, 5 week (mouse)469118237130727311Mouse
10755531Lymph3_mlymphocyte differential 3 (mouse)4124553483156860686Mouse
1301731Cafq2_mcaffeine metabolism QTL 2 (mouse)Not determined494732255128732454Mouse
27095917Scvln14_msacral vertebrae length 2, 16 week (mouse)468018237130277062Mouse
15039382Ltgq7_mliver triglyceride QTL 7 (mouse)4105705794139705794Mouse
11533916Mts1_mmammary tumor susceptibility 1 (mouse)4125289325156860686Mouse
1300839Dyscalc2_mdystrophic cardiac calcinosis 2 (mouse)Not determined4111009051145009280Mouse
15039377Bw45_mbody weight QTL 45 (mouse)4105705794139705794Mouse
12880433Fgf23lq1_mFGF23 serum level QTL 1 (mouse)4101157197135157197Mouse
4141001Tgq17_mtriglyceride QTL 17 (mouse)Not determined112523489146523489Mouse
15039378Adip30_madiposity 30 (mouse)4105705794139705794Mouse
26884449Sklq2_mskull length QTL 2, 5 week (mouse)436700000128993793Mouse
1357800Tgq3_mtriglyceride QTL 3 (mouse)Not determined4107055093141055180Mouse
27095905Scvln3_msacral vertebrae length 2, 5 week (mouse)455600000128993793Mouse
15039385Mvlq3_mmacrovesicular liver lesion QTL 3 (mouse)4112182386146182386Mouse

Markers in Region
AI326135  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm384128,260,234 - 128,260,325UniSTSGRCm38
MGSCv374127,937,478 - 127,937,569UniSTSGRCm37
Celera4126,598,072 - 126,598,163UniSTS
Cytogenetic Map4D2.2UniSTS
Whitehead/MRC_RH41663.74UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000053830   ⟹   ENSMUSP00000059625
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4128,154,005 - 128,154,750 (-)Ensembl
GRCm38.p6 Ensembl4128,260,212 - 128,260,957 (-)Ensembl
RefSeq Acc Id: NM_027036   ⟹   NP_081312
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394128,154,005 - 128,154,688 (-)NCBI
GRCm384128,260,212 - 128,260,895 (-)ENTREZGENE
MGSCv374127,937,456 - 127,938,139 (-)RGD
Celera4126,598,050 - 126,598,733 (-)RGD
cM Map4 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_081312 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH61030 (Get FASTA)   NCBI Sequence Viewer  
  BAB24141 (Get FASTA)   NCBI Sequence Viewer  
  EDL30242 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000059625
  ENSMUSP00000059625.4
GenBank Protein Q6P8W9 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_081312   ⟸   NM_027036
- UniProtKB: Q9DAR4 (UniProtKB/Swiss-Prot),   Q6P8W9 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000059625   ⟸   ENSMUST00000053830

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P8W9-F1-model_v2 AlphaFold Q6P8W9 1-181 view protein structure

Promoters
RGD ID:6884708
Promoter ID:EPDNEW_M5805
Type:multiple initiation site
Name:Hmgb4_1
Description:Mus musculus high-mobility group box 4 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm384128,260,893 - 128,260,953EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1916567 AgrOrtholog
Ensembl Genes ENSMUSG00000048686 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000053830 ENTREZGENE
  ENSMUST00000053830.5 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot
InterPro HMG_box_dom UniProtKB/Swiss-Prot
  HMG_box_dom_sf UniProtKB/Swiss-Prot
  HMGB UniProtKB/Swiss-Prot
KEGG Report mmu:69317 UniProtKB/Swiss-Prot
MGD MGI:1916567 ENTREZGENE
NCBI Gene 69317 ENTREZGENE
PANTHER HIGH MOBILITY GROUP PROTEIN B4 UniProtKB/Swiss-Prot
  HIGH MOBILITY GROUP PROTEIN DSP1 UniProtKB/Swiss-Prot
Pfam HMG_box UniProtKB/Swiss-Prot
  HMG_box_2 UniProtKB/Swiss-Prot
PhenoGen Hmgb4 PhenoGen
PRINTS HIGHMOBLTY12 UniProtKB/Swiss-Prot
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot
SMART HMG UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot
UniProt HMGB4_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q9DAR4 ENTREZGENE
UniProt Secondary Q9DAR4 UniProtKB/Swiss-Prot