Hbp1 (HMG-box transcription factor 1) - Rat Genome Database
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Gene: Hbp1 (HMG-box transcription factor 1) Rattus norvegicus
Analyze
Symbol: Hbp1
Name: HMG-box transcription factor 1
RGD ID: 620444
Description: Exhibits DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of potassium ion transport. Predicted to localize to nuclear speck. Orthologous to human HBP1 (HMG-box transcription factor 1); INTERACTS WITH 1,2,4-trimethylbenzene; 17alpha-ethynylestradiol; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: high mobility group box transcription factor 1; high mobility group protein 1; HMG box transcription factor 1; HMG box-containing protein 1; HMG-box containing protein 1; Hmgb1
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
mRatBN7.2648,529,633 - 48,555,775 (-)NCBI
Rnor_6.0 Ensembl651,231,480 - 51,257,625 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0651,231,479 - 51,257,699 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0659,902,128 - 59,929,303 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4650,201,281 - 50,227,095 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1650,204,414 - 50,230,207 (-)NCBI
Celera647,731,479 - 47,757,413 (-)NCBICelera
Cytogenetic Map6q16NCBI
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
(+)-catechin  (ISO)
(-)-demecolcine  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxynon-2-enal  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
leflunomide  (ISO)
menadione  (ISO)
methyl methanesulfonate  (ISO)
methylphenidate  (ISO)
mitomycin C  (ISO)
motexafin gadolinium  (ISO)
N-methylformamide  (ISO)
nickel atom  (ISO)
niclosamide  (ISO)
paracetamol  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
pyrvinium  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
rotenone  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
tauroursodeoxycholic acid  (EXP)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tunicamycin  (ISO)
uranium atom  (ISO)
urethane  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
vorinostat  (ISO)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

References

Additional References at PubMed
PMID:8889548   PMID:9178770   PMID:12477932   PMID:15489334   PMID:24675724   PMID:31139836  


Genomics

Comparative Map Data
Hbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2648,529,633 - 48,555,775 (-)NCBI
Rnor_6.0 Ensembl651,231,480 - 51,257,625 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0651,231,479 - 51,257,699 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0659,902,128 - 59,929,303 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4650,201,281 - 50,227,095 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1650,204,414 - 50,230,207 (-)NCBI
Celera647,731,479 - 47,757,413 (-)NCBICelera
Cytogenetic Map6q16NCBI
HBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7107,168,961 - 107,202,522 (+)EnsemblGRCh38hg38GRCh38
GRCh387107,168,987 - 107,202,523 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh377106,809,448 - 106,842,967 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367106,596,696 - 106,630,210 (+)NCBINCBI36hg18NCBI36
Build 347106,403,410 - 106,436,924NCBI
Celera7101,614,757 - 101,648,271 (+)NCBI
Cytogenetic Map7q22.3NCBI
HuRef7101,169,955 - 101,203,527 (+)NCBIHuRef
CHM1_17106,742,977 - 106,776,953 (+)NCBICHM1_1
CRA_TCAGchr7v27106,170,493 - 106,204,061 (+)NCBI
Hbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391231,976,449 - 32,000,529 (-)NCBIGRCm39mm39
GRCm39 Ensembl1231,976,253 - 32,000,534 (-)Ensembl
GRCm381231,926,452 - 31,950,530 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1231,926,254 - 31,950,535 (-)EnsemblGRCm38mm10GRCm38
MGSCv371232,611,320 - 32,635,400 (-)NCBIGRCm37mm9NCBIm37
MGSCv361232,511,722 - 32,535,470 (-)NCBImm8
Celera1233,380,824 - 33,404,870 (-)NCBICelera
Cytogenetic Map12A3NCBI
Hbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541011,626,743 - 11,652,343 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541011,626,743 - 11,652,343 (+)NCBIChiLan1.0ChiLan1.0
HBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17111,873,196 - 111,906,437 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7111,873,874 - 111,906,437 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0799,147,813 - 99,181,335 (+)NCBIMhudiblu_PPA_v0panPan3
HBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1813,340,287 - 13,367,915 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11813,339,359 - 13,368,105 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647916,855,368 - 16,886,210 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9106,965,947 - 106,996,048 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19106,966,060 - 106,993,915 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HBP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12176,088,411 - 76,121,884 (+)NCBI
ChlSab1.1 Ensembl2176,088,542 - 76,124,610 (+)Ensembl
Hbp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473922,504,766 - 22,531,718 (-)NCBI

Position Markers
RH143729  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0651,248,908 - 51,249,073NCBIRnor6.0
Rnor_5.0659,919,502 - 59,919,667UniSTSRnor5.0
RGSC_v3.4650,218,433 - 50,218,598UniSTSRGSC3.4
Celera647,748,924 - 47,749,089UniSTS
RH 3.4 Map6302.4UniSTS
Cytogenetic Map6q16UniSTS
RH144560  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0651,233,775 - 51,233,947NCBIRnor6.0
Rnor_5.0659,904,424 - 59,904,596UniSTSRnor5.0
RGSC_v3.4650,203,577 - 50,203,749UniSTSRGSC3.4
Celera647,733,775 - 47,733,947UniSTS
RH 3.4 Map6300.8UniSTS
Cytogenetic Map6q16UniSTS
MARC_4117-4118:991938388:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01620,294,454 - 20,294,655NCBIRnor6.0
Rnor_6.0651,246,027 - 51,246,137NCBIRnor6.0
Rnor_5.01620,151,998 - 20,152,199UniSTSRnor5.0
Rnor_5.0659,916,676 - 59,916,786UniSTSRnor5.0
RGSC_v3.41619,043,240 - 19,043,441UniSTSRGSC3.4
RGSC_v3.4650,215,830 - 50,215,940UniSTSRGSC3.4
Celera1618,736,389 - 18,736,590UniSTS
Celera647,746,028 - 47,746,138UniSTS
Cytogenetic Map16p14UniSTS
Cytogenetic Map6q16UniSTS
RH69992  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0651,246,044 - 51,246,174NCBIRnor6.0
Rnor_5.0659,916,693 - 59,916,823UniSTSRnor5.0
RGSC_v3.4650,215,847 - 50,215,977UniSTSRGSC3.4
Celera647,746,045 - 47,746,175UniSTS
Cytogenetic Map6q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)63425776653855198Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63626028860606186Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63760898075023446Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63810630883106308Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63819641260606431Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64167904686679046Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:173
Count of miRNA genes:120
Interacting mature miRNAs:139
Transcripts:ENSRNOT00000012004
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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012004   ⟹   ENSRNOP00000012004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl651,231,480 - 51,257,625 (-)Ensembl
RefSeq Acc Id: NM_013221   ⟹   NP_037353
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2648,529,633 - 48,555,775 (-)NCBI
Rnor_6.0651,231,479 - 51,257,625 (-)NCBI
Rnor_5.0659,902,128 - 59,929,303 (-)NCBI
RGSC_v3.4650,201,281 - 50,227,095 (-)RGD
Celera647,731,479 - 47,757,413 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239975   ⟹   XP_006240037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0651,231,486 - 51,257,699 (-)NCBI
Rnor_5.0659,902,128 - 59,929,303 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_037353 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA53240 (Get FASTA)   NCBI Sequence Viewer  
  AAH91165 (Get FASTA)   NCBI Sequence Viewer  
  EDM03261 (Get FASTA)   NCBI Sequence Viewer  
  Q62661 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037353   ⟸   NM_013221
- UniProtKB: Q62661 (UniProtKB/Swiss-Prot),   Z4YNI2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240037   ⟸   XM_006239975
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000012004   ⟸   ENSRNOT00000012004
Protein Domains
AXH   HMG box

Transcriptome

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

Promoters
RGD ID:13694547
Promoter ID:EPDNEW_R5071
Type:multiple initiation site
Name:Hbp1_1
Description:HMG-box transcription factor 1
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_6.0651,257,619 - 51,257,679EPDNEW

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)
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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)
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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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (MCW)
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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)
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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
SBN/Ygl (MCW)
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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)
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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
SHR/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
SHRSP/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
SR/JrHsd (MCW)
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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)
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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
SS/Jr (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
SS/JrHsdMcwi (MCW)
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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)
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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
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:620444 AgrOrtholog
Ensembl Genes ENSRNOG00000008927 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012004 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012004 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7097013 IMAGE-MGC_LOAD
InterPro Ataxin_AXH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ataxin_AXH_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HBP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:27080 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:108754 IMAGE-MGC_LOAD
NCBI Gene 27080 ENTREZGENE
PANTHER PTHR15499 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam AXH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hbp1 PhenoGen
PROSITE AXH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART AXH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF102031 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47095 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt HBP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Z4YNI2 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q5BK86 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-17 Hbp1  HMG-box transcription factor 1  Hbp1  high mobility group box transcription factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Hbp1  high mobility group box transcription factor 1    HMG-box containing protein 1  Name updated 1299863 APPROVED
2002-08-07 Hbp1  HMG-box containing protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains two HMG box domains plus a highly acidic C-terminal domain 632908