Dbx1 (developing brain homeobox 1) - Rat Genome Database

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Gene: Dbx1 (developing brain homeobox 1) Rattus norvegicus
Analyze
Symbol: Dbx1
Name: developing brain homeobox 1
RGD ID: 1308896
Description: Predicted to enable DNA binding activity and DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in cell differentiation in spinal cord and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within ventral spinal cord interneuron specification. Predicted to be located in nucleus. Orthologous to human DBX1 (developing brain homeobox 1); INTERACTS WITH bisphenol A; (-)-alpha-phellandrene (ortholog); 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: developing brain homeobox protein 1; homeobox protein DBX1; LOC292934
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
GRCr81108,484,846 - 108,490,381 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1108,484,863 - 108,490,381 (-)EnsemblGRCr8
mRatBN7.2199,348,638 - 99,354,173 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl199,349,608 - 99,354,038 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1104,703,682 - 104,708,112 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01113,175,603 - 113,180,033 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01106,497,856 - 106,502,286 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01104,969,218 - 104,973,648 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1104,969,218 - 104,973,648 (-)Ensemblrn6Rnor6.0
Rnor_5.01106,021,689 - 106,026,119 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4199,437,189 - 99,441,619 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera193,549,691 - 93,554,121 (-)NCBICelera
RGSC_v3.1199,515,299 - 99,519,730 (-)NCBI
Cytogenetic Map1q22NCBI
JBrowse:




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
nucleus  (IEA)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11239429   PMID:20081190  


Genomics

Comparative Map Data
Dbx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81108,484,846 - 108,490,381 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1108,484,863 - 108,490,381 (-)EnsemblGRCr8
mRatBN7.2199,348,638 - 99,354,173 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl199,349,608 - 99,354,038 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1104,703,682 - 104,708,112 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01113,175,603 - 113,180,033 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01106,497,856 - 106,502,286 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01104,969,218 - 104,973,648 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1104,969,218 - 104,973,648 (-)Ensemblrn6Rnor6.0
Rnor_5.01106,021,689 - 106,026,119 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4199,437,189 - 99,441,619 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera193,549,691 - 93,554,121 (-)NCBICelera
RGSC_v3.1199,515,299 - 99,519,730 (-)NCBI
Cytogenetic Map1q22NCBI
DBX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381120,156,155 - 20,160,475 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1120,156,155 - 20,160,475 (-)Ensemblhg38GRCh38
GRCh371120,177,701 - 20,182,021 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361120,134,336 - 20,138,446 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1120,310,390 - 20,314,496 (-)NCBICelera
Cytogenetic Map11p15.1NCBI
HuRef1119,861,122 - 19,865,226 (-)NCBIHuRef
CHM1_11120,177,693 - 20,181,798 (-)NCBICHM1_1
T2T-CHM13v2.01120,276,786 - 20,281,102 (-)NCBIT2T-CHM13v2.0
Dbx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39749,281,247 - 49,286,583 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl749,281,247 - 49,286,597 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38749,631,499 - 49,636,835 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl749,631,499 - 49,636,849 (-)Ensemblmm10GRCm38
MGSCv37756,886,869 - 56,892,205 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36749,499,520 - 49,504,856 (-)NCBIMGSCv36mm8
Celera745,081,373 - 45,086,715 (-)NCBICelera
Cytogenetic Map7B4NCBI
cM Map731.44NCBI
Dbx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554761,018,715 - 1,022,545 (-)Ensembl
ChiLan1.0NW_0049554761,018,715 - 1,022,648 (-)NCBIChiLan1.0ChiLan1.0
DBX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2922,457,339 - 22,461,675 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11122,417,188 - 22,421,530 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01120,180,704 - 20,185,164 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11120,093,083 - 20,097,227 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1120,092,540 - 20,097,727 (-)EnsemblpanPan2panpan1.1
DBX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12142,207,205 - 42,214,954 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2142,208,346 - 42,212,415 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2141,685,661 - 41,689,593 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02143,330,076 - 43,334,024 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2143,328,937 - 43,334,024 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12142,332,505 - 42,336,439 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02142,508,028 - 42,511,957 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02142,888,831 - 42,892,779 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Dbx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494742,782,467 - 42,788,187 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366541,139,500 - 1,143,477 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366541,139,500 - 1,143,477 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DBX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl239,229,356 - 39,234,969 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1239,229,392 - 39,234,304 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2242,118,417 - 42,123,019 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DBX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1144,848,976 - 44,853,790 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl144,848,996 - 44,853,122 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666038142,183,250 - 142,188,142 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Dbx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476611,440,470 - 11,444,150 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462476611,431,699 - 11,444,150 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Dbx1
45 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:129
Count of miRNA genes:112
Interacting mature miRNAs:116
Transcripts:ENSRNOT00000019739
Prediction methods:Microtar, 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
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1102780511182384005Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)192963855109494029Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1101228864146228864Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183019780128019780Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)193903998191260518Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)184107164115183752Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)191302413136302413Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)1102359314153680016Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)199645382182701046Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)199645382221502378Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1103779152223964440Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)198879955208479939Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of, or within a discrete space in an open field apparatus (CMO:0001514)192683681137683681Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)192683681137683681Rat
737977Bp160Blood pressure QTL 1600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)197582336142582336Rat
2293142Bp314Blood pressure QTL 314arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1101594089146594089Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1100345976145345976Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)196717367160111531Rat


Expression

RNA-SEQ Expression

appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
5 2 44 7 7 2 2 1 15 7 43 3 25 5

Sequence


Ensembl Acc Id: ENSRNOT00000019739   ⟹   ENSRNOP00000019739
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1108,484,863 - 108,490,381 (-)Ensembl
mRatBN7.2 Ensembl199,349,608 - 99,354,038 (-)Ensembl
Rnor_6.0 Ensembl1104,969,218 - 104,973,648 (-)Ensembl
RefSeq Acc Id: NM_001009644   ⟹   NP_001009644
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81108,484,846 - 108,490,381 (-)NCBI
mRatBN7.2199,348,638 - 99,354,173 (-)NCBI
Rnor_6.01104,969,218 - 104,973,648 (-)NCBI
Rnor_5.01106,021,689 - 106,026,119 (-)NCBI
RGSC_v3.4199,437,189 - 99,441,619 (-)RGD
Celera193,549,691 - 93,554,121 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001009644 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAD83364 (Get FASTA)   NCBI Sequence Viewer  
  EDM07224 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019739
  ENSRNOP00000019739.1
GenBank Protein Q5NSW5 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001009644   ⟸   NM_001009644
- UniProtKB: Q5NSW5 (UniProtKB/Swiss-Prot),   A6JBG0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000019739   ⟸   ENSRNOT00000019739
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5NSW5-F1-model_v2 AlphaFold Q5NSW5 1-335 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308896 AgrOrtholog
BioCyc Gene G2FUF-59564 BioCyc
Ensembl Genes ENSRNOG00000014706 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000019739 ENTREZGENE
  ENSRNOT00000019739.3 UniProtKB/Swiss-Prot
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot
InterPro H2.0_Homeobox_NeuralPatt UniProtKB/Swiss-Prot
  Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Homeobox_metazoa UniProtKB/Swiss-Prot
  HTH_motif UniProtKB/Swiss-Prot
KEGG Report rno:292934 UniProtKB/Swiss-Prot
NCBI Gene 292934 ENTREZGENE
PANTHER DBX UniProtKB/Swiss-Prot
  HOMEOBOX PROTEIN DBX1 UniProtKB/Swiss-Prot
Pfam Homeodomain UniProtKB/Swiss-Prot
PhenoGen Dbx1 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot
  HTHREPRESSR UniProtKB/Swiss-Prot
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000014706 RatGTEx
SMART HOX UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot
UniProt A6JBG0 ENTREZGENE, UniProtKB/TrEMBL
  DBX1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Dbx1  developing brain homeobox 1  Dbx1_predicted  developing brain homeobox 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Dbx1_predicted  developing brain homeobox 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED