Dbx2 (developing brain homeobox 2) - Rat Genome Database

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Gene: Dbx2 (developing brain homeobox 2) Rattus norvegicus
Analyze
Symbol: Dbx2
Name: developing brain homeobox 2
RGD ID: 1359605
Description: Predicted to enable DNA binding activity and DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Orthologous to human DBX2 (developing brain homeobox 2); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil; atrazine.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: homeobox protein DBX2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87128,651,603 - 128,681,886 (-)NCBIGRCr8
mRatBN7.27126,772,389 - 126,802,625 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7126,772,227 - 126,802,564 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.07136,966,879 - 136,997,104 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7136,967,200 - 136,997,050 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07136,606,113 - 136,636,311 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47134,212,949 - 134,243,282 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17134,289,385 - 134,297,367 (-)NCBI
Celera7123,282,070 - 123,312,294 (-)NCBICelera
Cytogenetic Map7q35NCBI
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
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18801203  


Genomics

Comparative Map Data
Dbx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87128,651,603 - 128,681,886 (-)NCBIGRCr8
mRatBN7.27126,772,389 - 126,802,625 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7126,772,227 - 126,802,564 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.07136,966,879 - 136,997,104 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7136,967,200 - 136,997,050 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07136,606,113 - 136,636,311 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47134,212,949 - 134,243,282 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17134,289,385 - 134,297,367 (-)NCBI
Celera7123,282,070 - 123,312,294 (-)NCBICelera
Cytogenetic Map7q35NCBI
DBX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381245,014,672 - 45,051,099 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1245,014,672 - 45,051,099 (-)EnsemblGRCh38hg38GRCh38
GRCh371245,408,455 - 45,444,882 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361243,694,806 - 43,731,149 (-)NCBINCBI36Build 36hg18NCBI36
Celera1244,211,912 - 44,248,577 (-)NCBICelera
Cytogenetic Map12q12NCBI
HuRef1242,436,496 - 42,473,246 (-)NCBIHuRef
CHM1_11245,373,560 - 45,409,894 (-)NCBICHM1_1
T2T-CHM13v2.01244,973,282 - 45,009,708 (-)NCBIT2T-CHM13v2.0
Dbx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391595,521,444 - 95,552,838 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1595,521,444 - 95,553,841 (-)EnsemblGRCm39 Ensembl
GRCm381595,623,563 - 95,654,771 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1595,623,563 - 95,655,960 (-)EnsemblGRCm38mm10GRCm38
MGSCv371595,453,994 - 95,485,202 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361595,453,994 - 95,485,202 (-)NCBIMGSCv36mm8
Celera1597,769,717 - 97,800,856 (-)NCBICelera
Cytogenetic Map15E3NCBI
cM Map1550.47NCBI
Dbx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555004,213,183 - 4,231,844 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555004,212,848 - 4,238,727 (-)NCBIChiLan1.0ChiLan1.0
DBX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21049,126,883 - 49,167,284 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11249,123,668 - 49,164,042 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01243,688,140 - 43,728,531 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11244,556,961 - 44,593,152 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1244,556,531 - 44,593,152 (+)Ensemblpanpan1.1panPan2
DBX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1279,232,489 - 9,255,666 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl279,119,535 - 9,251,354 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2737,057,992 - 37,095,951 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0279,407,774 - 9,444,849 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl279,407,808 - 9,443,351 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1279,214,034 - 9,251,972 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0279,253,744 - 9,290,746 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02737,296,100 - 37,334,062 (-)NCBIUU_Cfam_GSD_1.0
Dbx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494569,788,219 - 69,823,531 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365123,345,549 - 3,376,577 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365123,345,334 - 3,376,721 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DBX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl575,945,871 - 75,980,496 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1575,945,866 - 75,983,466 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2578,874,750 - 78,875,486 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DBX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11141,190,840 - 41,230,057 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037205,228,432 - 205,268,945 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Dbx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248167,285,920 - 7,318,461 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248167,285,905 - 7,323,265 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Dbx2
108 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:276
Count of miRNA genes:172
Interacting mature miRNAs:195
Transcripts:ENSRNOT00000009143
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)7116677189127103496Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
D7Got240  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27126,774,776 - 126,774,903 (+)MAPPERmRatBN7.2
Rnor_6.07136,969,267 - 136,969,393NCBIRnor6.0
Rnor_5.07136,608,501 - 136,608,627UniSTSRnor5.0
RGSC_v3.47134,215,499 - 134,215,625UniSTSRGSC3.4
Celera7123,284,458 - 123,284,582UniSTS
Cytogenetic Map7q35UniSTS
BE096836  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27126,772,448 - 126,772,600 (+)MAPPERmRatBN7.2
Rnor_6.07136,966,939 - 136,967,090NCBIRnor6.0
Rnor_5.07136,606,173 - 136,606,324UniSTSRnor5.0
RGSC_v3.47134,213,171 - 134,213,322UniSTSRGSC3.4
Celera7123,282,130 - 123,282,281UniSTS
RH 3.4 Map71045.9UniSTS
Cytogenetic Map7q35UniSTS


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 musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 3
Low 63 4
Below cutoff 1 2 6 10 21 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009143   ⟹   ENSRNOP00000009143
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7126,772,227 - 126,802,564 (-)Ensembl
Rnor_6.0 Ensembl7136,967,200 - 136,997,050 (-)Ensembl
RefSeq Acc Id: XM_001053826   ⟹   XP_001053826
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87128,651,603 - 128,681,882 (-)NCBI
mRatBN7.27126,772,389 - 126,802,624 (-)NCBI
Rnor_6.07136,966,879 - 136,997,104 (-)NCBI
Rnor_5.07136,606,113 - 136,636,311 (-)NCBI
RGSC_v3.47134,212,949 - 134,243,282 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242286   ⟹   XP_006242348
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87128,651,603 - 128,681,886 (-)NCBI
mRatBN7.27126,772,389 - 126,802,625 (-)NCBI
Rnor_6.07136,966,879 - 136,997,104 (-)NCBI
Rnor_5.07136,606,113 - 136,636,311 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_001053826 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242348 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAD90597 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009143
  ENSRNOP00000009143.4
Reference Protein Sequences
RefSeq Acc Id: XP_001053826   ⟸   XM_001053826
- Peptide Label: isoform X1
- UniProtKB: F1LRM4 (UniProtKB/TrEMBL),   A6KC08 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242348   ⟸   XM_006242286
- Peptide Label: isoform X2
- UniProtKB: A6KC08 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009143   ⟸   ENSRNOT00000009143
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LRM4-F1-model_v2 AlphaFold F1LRM4 1-377 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:1359605 AgrOrtholog
BioCyc Gene G2FUF-32282 BioCyc
Ensembl Genes ENSRNOG00000006885 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009143.6 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_eu UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  HTH_lambrepressr UniProtKB/TrEMBL
KEGG Report rno:541457 UniProtKB/TrEMBL
NCBI Gene 541457 ENTREZGENE
PANTHER DBX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN DBX2 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Dbx2 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
  HTHREPRESSR UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006885 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6KC08 ENTREZGENE, UniProtKB/TrEMBL
  F1LRM4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-29 Dbx2  developing brain homeobox 2      Symbol and Name status set to provisional 70820 PROVISIONAL