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 have DNA binding activity. Predicted to be involved in several processes, including negative regulation of protein sumoylation; positive regulation of neuron differentiation; and skeletal muscle cell differentiation. Predicted to localize to nuclear body. Orthologous to human HMG20B (high mobility group 20B); INTERACTS WITH bisphenol A; cadmium dichloride; pregnenolone 16alpha-carbonitrile.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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 Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.278,368,934 - 8,373,650 (+)NCBI
Rnor_6.0 Ensembl711,238,630 - 11,243,310 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0711,238,594 - 11,243,312 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0711,405,476 - 11,410,192 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.479,853,290 - 9,857,970 (+)NCBIRGSC3.4rn4RGSC3.4
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

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
mRatBN7.278,368,934 - 8,373,650 (+)NCBI
Rnor_6.0 Ensembl711,238,630 - 11,243,310 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0711,238,594 - 11,243,312 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0711,405,476 - 11,410,192 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.479,853,290 - 9,857,970 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl193,572,777 - 3,579,088 (+)EnsemblGRCh38hg38GRCh38
GRCh38193,572,916 - 3,579,083 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37193,572,942 - 3,579,081 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37193,572,936 - 3,579,081 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36193,523,943 - 3,530,081 (+)NCBINCBI36hg18NCBI36
Build 34193,525,521 - 3,530,079NCBI
Celera193,509,760 - 3,515,897 (+)NCBI
Cytogenetic Map19p13.3NCBI
HuRef193,338,210 - 3,344,475 (+)NCBIHuRef
CHM1_1193,572,606 - 3,578,717 (+)NCBICHM1_1
Hmg20b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391081,181,880 - 81,186,777 (-)NCBIGRCm39mm39
GRCm381081,346,046 - 81,350,943 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1081,346,048 - 81,350,480 (-)EnsemblGRCm38mm10GRCm38
MGSCv371080,808,791 - 80,813,202 (-)NCBIGRCm37mm9NCBIm37
MGSCv361080,749,181 - 80,753,539 (-)NCBImm8
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
PanPan1.1193,548,451 - 3,554,725 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl193,548,451 - 3,554,725 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0192,598,588 - 2,604,799 (+)NCBIMhudiblu_PPA_v0panPan3
HMG20B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2055,841,959 - 55,844,862 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12055,840,192 - 55,844,949 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hmg20b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - 75,098,557 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1275,093,071 - 75,098,566 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HMG20B
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.163,333,731 - 3,340,033 (+)NCBI
ChlSab1.1 Ensembl63,333,885 - 3,340,138 (+)Ensembl
Hmg20b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248286,277,743 - 6,283,154 (+)NCBI

Position Markers
RH130154  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat

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.


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 3 37 56 40 17 40 2 60 35 39 11
Low 6 1 1 2 1 8 9 14 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028002   ⟹   ENSRNOP00000028002
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl711,238,630 - 11,243,310 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086194   ⟹   ENSRNOP00000074794
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_039079382   ⟹   XP_038935310
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,369,043 - 8,373,650 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102201   ⟸   NM_001108731
- UniProtKB: D4A586 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241006   ⟸   XM_006240944
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006241008   ⟸   XM_006240946
- Peptide Label: isoform X2
- UniProtKB: D4A586 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000028002   ⟸   ENSRNOT00000028002
RefSeq Acc Id: ENSRNOP00000074794   ⟸   ENSRNOT00000086194
RefSeq Acc Id: XP_038935310   ⟸   XM_039079382
- Peptide Label: isoform X1
Protein Domains
HMG box

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

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)
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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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:1309235 AgrOrtholog
Ensembl Genes ENSRNOG00000020601 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000028002 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074794 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028002 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000086194 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
KEGG Report rno:362825 UniProtKB/TrEMBL
NCBI Gene 362825 ENTREZGENE
Pfam HMG_box UniProtKB/TrEMBL
PhenoGen Hmg20b PhenoGen
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL
UniProt D4A586 ENTREZGENE, 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