Hdx (highly divergent homeobox) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Hdx (highly divergent homeobox) Rattus norvegicus
Analyze
Symbol: Hdx
Name: highly divergent homeobox
RGD ID: 1563666
Description: Predicted to enable DNA binding activity. Predicted to be located in nucleus. Orthologous to human HDX (highly divergent homeobox); INTERACTS WITH acrylamide; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC317617; LOC317617; RGD1563666; similar to chromosome X open reading frame 43; uncharacterized protein LOC317617
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
GRCr8X80,739,615 - 80,881,621 (-)NCBIGRCr8
mRatBN7.2X76,552,539 - 76,697,177 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX76,560,665 - 76,869,972 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX78,193,137 - 78,341,125 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X81,629,376 - 81,777,327 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X79,216,177 - 79,364,406 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X82,847,895 - 83,151,516 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX82,875,339 - 83,151,511 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X82,816,318 - 82,932,304 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X100,060,952 - 100,295,738 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX77,866,575 - 78,173,639 (-)NCBICelera
Cytogenetic MapXq31NCBI
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)

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

Genomics

Comparative Map Data
Hdx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X80,739,615 - 80,881,621 (-)NCBIGRCr8
mRatBN7.2X76,552,539 - 76,697,177 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX76,560,665 - 76,869,972 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX78,193,137 - 78,341,125 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X81,629,376 - 81,777,327 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X79,216,177 - 79,364,406 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X82,847,895 - 83,151,516 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX82,875,339 - 83,151,511 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X82,816,318 - 82,932,304 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X100,060,952 - 100,295,738 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX77,866,575 - 78,173,639 (-)NCBICelera
Cytogenetic MapXq31NCBI
HDX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X84,317,878 - 84,502,453 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX84,317,874 - 84,502,479 (-)EnsemblGRCh38hg38GRCh38
GRCh37X83,572,886 - 83,757,461 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X83,462,861 - 83,644,114 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X83,382,350 - 83,563,603NCBI
CeleraX83,811,669 - 83,996,281 (-)NCBICelera
Cytogenetic MapXq21.1NCBI
HuRefX77,147,094 - 77,330,346 (-)NCBIHuRef
CHM1_1X83,466,713 - 83,651,411 (-)NCBICHM1_1
T2T-CHM13v2.0X82,754,225 - 82,938,810 (-)NCBIT2T-CHM13v2.0
Hdx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X110,484,901 - 110,606,908 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX110,479,628 - 110,606,776 (-)EnsemblGRCm39 Ensembl
GRCm38X111,575,204 - 111,697,079 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX111,569,931 - 111,697,079 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X108,688,813 - 108,810,688 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X107,692,148 - 107,814,023 (-)NCBIMGSCv36mm8
CeleraX98,254,278 - 98,376,866 (-)NCBICelera
Cytogenetic MapXE1NCBI
cM MapX48.29NCBI
Hdx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555293,468,132 - 3,642,886 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555293,468,132 - 3,642,886 (-)NCBIChiLan1.0ChiLan1.0
HDX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X83,798,558 - 83,981,805 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X83,801,844 - 83,985,413 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X73,390,936 - 73,574,197 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X83,502,644 - 83,685,615 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX83,502,644 - 83,658,576 (-)Ensemblpanpan1.1panPan2
HDX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X65,160,863 - 65,429,384 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX65,160,786 - 65,429,531 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX55,905,327 - 56,186,179 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X66,477,060 - 66,670,338 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X64,126,733 - 64,407,539 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X65,758,566 - 66,040,616 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X65,332,584 - 65,613,388 (-)NCBIUU_Cfam_GSD_1.0
Hdx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X58,729,425 - 58,837,980 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365475,049,844 - 5,158,360 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365475,051,555 - 5,158,383 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX67,560,890 - 67,713,797 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X67,556,764 - 67,713,744 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X77,350,365 - 77,425,572 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HDX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X73,219,279 - 73,400,420 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX73,219,292 - 73,399,961 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660677,475,115 - 7,655,590 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hdx
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248523,826,829 - 4,063,989 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248523,826,878 - 4,063,466 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hdx
477 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:138
Count of miRNA genes:121
Interacting mature miRNAs:127
Transcripts:ENSRNOT00000057378
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat

Markers in Region
D5Mit8  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X82,981,120 - 82,981,241NCBIRnor6.0
Rnor_5.0X82,950,219 - 82,950,340UniSTSRnor5.0
RGSC_v3.4X100,103,660 - 100,103,789UniSTSRGSC3.4
RGSC_v3.1X100,177,092 - 100,177,222RGD
CeleraX77,996,730 - 77,996,859UniSTS
RH 3.4 MapX736.2UniSTS
Cytogenetic MapXq31UniSTS


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 2
Low 36 19 6 13 6 4 4 74 28 36 11 4
Below cutoff 2 6 17 14 5 14 4 5 5 3 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000057378   ⟹   ENSRNOP00000054189
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX76,560,665 - 76,869,972 (-)Ensembl
Rnor_6.0 EnsemblX82,875,476 - 83,151,511 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077587   ⟹   ENSRNOP00000075430
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX76,560,665 - 76,656,831 (-)Ensembl
Rnor_6.0 EnsemblX82,875,339 - 82,986,051 (-)Ensembl
RefSeq Acc Id: NM_001395571   ⟹   NP_001382500
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,739,615 - 80,881,512 (-)NCBI
mRatBN7.2X76,555,217 - 76,697,122 (-)NCBI
RefSeq Acc Id: NM_001395572   ⟹   NP_001382501
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,739,615 - 80,881,512 (-)NCBI
mRatBN7.2X76,555,217 - 76,697,122 (-)NCBI
RefSeq Acc Id: XM_039099856   ⟹   XP_038955784
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,782,469 - 80,881,618 (-)NCBI
mRatBN7.2X76,598,098 - 76,697,177 (-)NCBI
RefSeq Acc Id: XR_005498000
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,739,615 - 80,881,621 (-)NCBI
mRatBN7.2X76,555,217 - 76,697,177 (-)NCBI
RefSeq Acc Id: XR_005498003
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X80,751,739 - 80,881,614 (-)NCBI
mRatBN7.2X76,567,330 - 76,697,177 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001382500 (Get FASTA)   NCBI Sequence Viewer  
  NP_001382501 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955784 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07090 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000054189
  ENSRNOP00000054189.5
  ENSRNOP00000075430.2
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000054189   ⟸   ENSRNOT00000057378
RefSeq Acc Id: ENSRNOP00000075430   ⟸   ENSRNOT00000077587
RefSeq Acc Id: XP_038955784   ⟸   XM_039099856
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001382501   ⟸   NM_001395572
- Peptide Label: isoform 2
- UniProtKB: D4A457 (UniProtKB/TrEMBL),   A0A0G2KAK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001382500   ⟸   NM_001395571
- Peptide Label: isoform 1
- UniProtKB: A0A0G2KAK4 (UniProtKB/TrEMBL)
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A457-F1-model_v2 AlphaFold D4A457 1-660 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:1563666 AgrOrtholog
BioCyc Gene G2FUF-1841 BioCyc
Ensembl Genes ENSRNOG00000037799 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057378 ENTREZGENE
  ENSRNOT00000057378.5 UniProtKB/TrEMBL
  ENSRNOT00000077587.2 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
NCBI Gene 317617 ENTREZGENE
PANTHER HIGHLY DIVERGENT HOMEOBOX UniProtKB/TrEMBL
  POU DOMAIN UniProtKB/TrEMBL
PhenoGen Hdx PhenoGen
PROSITE HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000037799 RatGTEx
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A0G2KAK4 ENTREZGENE, UniProtKB/TrEMBL
  D4A457 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-28 Hdx  highly divergent homeobox  RGD1563666  similar to chromosome X open reading frame 43  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 RGD1563666  similar to chromosome X open reading frame 43  LOC100359635  highly divergent homeobox  Data merged from RGD:2325093 1643240 APPROVED
2010-05-20 LOC100359635  highly divergent homeobox      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1563666  similar to chromosome X open reading frame 43   RGD1563666_predicted  similar to chromosome X open reading frame 43 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563666_predicted  similar to chromosome X open reading frame 43 (predicted)  LOC317617  similar to chromosome X open reading frame 43  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317617  similar to chromosome X open reading frame 43      Symbol and Name status set to provisional 70820 PROVISIONAL