Hmg20b (high mobility group 20 B) - Rat Genome Database

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Gene: Hmg20b (high mobility group 20 B) Rattus norvegicus
Analyze
Symbol: Hmg20b
Name: high mobility group 20 B
RGD ID: 1309235
Description: Predicted to enable DNA binding activity. Predicted to be involved in regulation of gene expression. Predicted to act upstream of or within negative regulation of protein sumoylation; positive regulation of neuron differentiation; and skeletal muscle cell differentiation. Predicted to be located in nuclear body. Predicted to be active in nucleus. Orthologous to human HMG20B (high mobility group 20B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC362825; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,019,670 - 9,024,382 (+)NCBIGRCr8
mRatBN7.278,368,934 - 8,373,650 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,368,990 - 8,373,640 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,254,569 - 11,259,228 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,130,054 - 13,134,714 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0710,997,679 - 11,002,358 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,238,594 - 11,243,312 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,238,630 - 11,243,310 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0711,405,476 - 11,410,192 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.479,853,290 - 9,857,970 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.179,837,939 - 9,857,556 (+)NCBI
Celera76,558,025 - 6,562,701 (+)NCBICelera
Cytogenetic Map7q11NCBI
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

Cellular Component
nuclear body  (IEA,ISO)
nucleoplasm  (ISO)
nucleus  (IBA)

Molecular Function

References

References - curated
# 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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20530487   PMID:22147266   PMID:22570500  


Genomics

Comparative Map Data
Hmg20b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,019,670 - 9,024,382 (+)NCBIGRCr8
mRatBN7.278,368,934 - 8,373,650 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,368,990 - 8,373,640 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,254,569 - 11,259,228 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,130,054 - 13,134,714 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0710,997,679 - 11,002,358 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,238,594 - 11,243,312 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,238,630 - 11,243,310 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0711,405,476 - 11,410,192 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.479,853,290 - 9,857,970 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.179,837,939 - 9,857,556 (+)NCBI
Celera76,558,025 - 6,562,701 (+)NCBICelera
Cytogenetic Map7q11NCBI
HMG20B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38193,572,944 - 3,579,083 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl193,572,777 - 3,579,088 (+)EnsemblGRCh38hg38GRCh38
GRCh37193,572,942 - 3,579,081 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36193,523,943 - 3,530,081 (+)NCBINCBI36Build 36hg18NCBI36
Build 34193,525,521 - 3,530,079NCBI
Celera193,509,760 - 3,515,897 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef193,338,210 - 3,344,475 (+)NCBIHuRef
CHM1_1193,572,606 - 3,578,717 (+)NCBICHM1_1
T2T-CHM13v2.0193,551,100 - 3,557,239 (+)NCBIT2T-CHM13v2.0
Hmg20b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391081,181,880 - 81,186,777 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1081,181,882 - 81,186,314 (-)EnsemblGRCm39 Ensembl
GRCm381081,346,046 - 81,350,943 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1081,346,048 - 81,350,480 (-)EnsemblGRCm38mm10GRCm38
MGSCv371080,808,791 - 80,813,202 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361080,749,181 - 80,753,539 (-)NCBIMGSCv36mm8
Celera1082,366,836 - 82,371,247 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Hmg20b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554955,524,874 - 5,529,926 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554955,515,996 - 5,530,424 (+)NCBIChiLan1.0ChiLan1.0
HMG20B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2207,970,098 - 7,976,304 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1197,202,040 - 7,208,250 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0192,598,588 - 2,604,799 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1193,548,451 - 3,554,725 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl193,548,451 - 3,554,725 (+)Ensemblpanpan1.1panPan2
HMG20B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,840,192 - 55,844,949 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,841,959 - 55,844,862 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2055,565,327 - 55,570,345 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02056,500,142 - 56,505,157 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2056,500,137 - 56,505,529 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12055,555,796 - 55,560,811 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02056,039,212 - 56,044,218 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02056,237,958 - 56,242,974 (-)NCBIUU_Cfam_GSD_1.0
Hmg20b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,802,182 - 215,807,432 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,027,317 - 2,032,834 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,027,360 - 2,032,601 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMG20B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl275,093,075 - 75,098,536 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1275,093,071 - 75,098,566 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HMG20B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.163,333,731 - 3,340,033 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl63,333,885 - 3,340,138 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660815,148,505 - 5,155,151 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hmg20b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248286,278,111 - 6,283,244 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248286,277,743 - 6,283,154 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hmg20b
14 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:49
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000028002
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat

Markers in Region
RH130154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.278,373,403 - 8,373,604 (+)MAPPERmRatBN7.2
Rnor_6.0711,243,066 - 11,243,266NCBIRnor6.0
Rnor_5.0711,409,946 - 11,410,146UniSTSRnor5.0
RGSC_v3.479,857,726 - 9,857,926UniSTSRGSC3.4
Celera76,562,457 - 6,562,657UniSTS
Cytogenetic Map7q11UniSTS


Expression

RNA-SEQ Expression

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
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000028002   ⟹   ENSRNOP00000028002
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl78,369,039 - 8,373,637 (+)Ensembl
Rnor_6.0 Ensembl711,238,630 - 11,243,310 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000086194   ⟹   ENSRNOP00000074794
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl78,368,990 - 8,373,640 (+)Ensembl
Rnor_6.0 Ensembl711,238,644 - 11,243,305 (+)Ensembl
RefSeq Acc Id: NM_001108731   ⟹   NP_001102201
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,702 - 9,024,382 (+)NCBI
mRatBN7.278,368,967 - 8,373,648 (+)NCBI
Rnor_6.0711,238,630 - 11,243,310 (+)NCBI
Rnor_5.0711,405,476 - 11,410,192 (+)NCBI
RGSC_v3.479,853,290 - 9,857,970 (+)RGD
Celera76,558,025 - 6,562,701 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240944   ⟹   XP_006241006
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,671 - 9,024,379 (+)NCBI
mRatBN7.278,368,934 - 8,373,650 (+)NCBI
Rnor_6.0711,238,594 - 11,243,312 (+)NCBI
Rnor_5.0711,405,476 - 11,410,192 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006240946   ⟹   XP_006241008
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,671 - 9,024,379 (+)NCBI
mRatBN7.278,368,934 - 8,373,650 (+)NCBI
Rnor_6.0711,238,594 - 11,243,312 (+)NCBI
Rnor_5.0711,405,476 - 11,410,192 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063263714   ⟹   XP_063119784
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,670 - 9,024,379 (+)NCBI
RefSeq Acc Id: XM_063263716   ⟹   XP_063119786
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,670 - 9,024,379 (+)NCBI
RefSeq Acc Id: XM_063263717   ⟹   XP_063119787
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,670 - 9,024,379 (+)NCBI
RefSeq Acc Id: XM_063263718   ⟹   XP_063119788
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,671 - 9,024,379 (+)NCBI
RefSeq Acc Id: XM_063263719   ⟹   XP_063119789
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,671 - 9,024,379 (+)NCBI
RefSeq Acc Id: XM_063263720   ⟹   XP_063119790
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,019,909 - 9,024,379 (+)NCBI
RefSeq Acc Id: NP_001102201   ⟸   NM_001108731
- UniProtKB: A6K887 (UniProtKB/TrEMBL),   A6K890 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241006   ⟸   XM_006240944
- Peptide Label: isoform X6
- UniProtKB: A6K890 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241008   ⟸   XM_006240946
- Peptide Label: isoform X8
- UniProtKB: A6K887 (UniProtKB/TrEMBL),   A6K890 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000028002   ⟸   ENSRNOT00000028002
Ensembl Acc Id: ENSRNOP00000074794   ⟸   ENSRNOT00000086194
RefSeq Acc Id: XP_063119784   ⟸   XM_063263714
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063119786   ⟸   XM_063263716
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063119787   ⟸   XM_063263717
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K8Z5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063119789   ⟸   XM_063263719
- Peptide Label: isoform X5
- UniProtKB: A0A0G2K8Z5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063119788   ⟸   XM_063263718
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K8Z5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063119790   ⟸   XM_063263720
- Peptide Label: isoform X7
- UniProtKB: A6K890 (UniProtKB/TrEMBL)
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A586-F1-model_v2 AlphaFold D4A586 1-318 view protein structure

Transcriptome

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

Promoters
RGD ID:13694983
Promoter ID:EPDNEW_R5501
Type:initiation region
Name:Hmg20b_1
Description:high mobility group 20 B
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_6.0711,238,649 - 11,238,709EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309235 AgrOrtholog
BioCyc Gene G2FUF-35019 BioCyc
Ensembl Genes ENSRNOG00000020601 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028002.7 UniProtKB/TrEMBL
  ENSRNOT00000086194.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro ChromReg_NeuronalGeneExpr UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
KEGG Report rno:362825 UniProtKB/TrEMBL
NCBI Gene 362825 ENTREZGENE
PANTHER HIGH MOBILITY GROUP PROTEIN 2 UniProtKB/TrEMBL
  SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY E MEMBER 1-RELATED UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
PhenoGen Hmg20b PhenoGen
PRINTS HIGHMOBLTY12 UniProtKB/TrEMBL
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020601 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL
UniProt A0A0G2K8Z5 ENTREZGENE, UniProtKB/TrEMBL
  A6K887 ENTREZGENE, UniProtKB/TrEMBL
  A6K890 ENTREZGENE, UniProtKB/TrEMBL
  D4A586_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Hmg20b  high mobility group 20 B   Hmg20b_predicted  high mobility group 20 B (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Hmg20b_predicted  high mobility group 20 B (predicted)      Symbol and Name status set to approved 70820 APPROVED