Hesx1 (HESX homeobox 1) - Rat Genome Database

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Gene: Hesx1 (HESX homeobox 1) Rattus norvegicus
Analyze
Symbol: Hesx1
Name: HESX homeobox 1
RGD ID: 1563858
Description: Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein homodimerization activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II and pituitary gland development. Predicted to act upstream of or within with a negative effect on canonical Wnt signaling pathway. Predicted to act upstream of or within several processes, including ERK1 and ERK2 cascade; cell surface receptor signaling pathway; and otic vesicle formation. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in septooptic dysplasia. Orthologous to human HESX1 (HESX homeobox 1); INTERACTS WITH bisphenol A; 17beta-estradiol (ortholog); 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: homeo box gene expressed in ES cells; homeobox expressed in ES cells 1; LOC498575; RGD1563858; similar to anterior-restricted homeobox protein
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
GRCr8162,198,589 - 2,200,694 (+)NCBIGRCr8
mRatBN7.2162,191,852 - 2,193,957 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl162,191,852 - 2,193,957 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx162,198,290 - 2,200,403 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0163,343,968 - 3,346,081 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0162,204,885 - 2,206,997 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0162,616,538 - 2,636,708 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl162,634,603 - 2,636,708 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0162,607,470 - 2,609,575 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4162,255,128 - 2,257,233 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera162,158,634 - 2,160,728 (+)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Mutations in the homeobox gene HESX1/Hesx1 associated with septo-optic dysplasia in human and mouse. Dattani MT, etal., Nat Genet. 1998 Jun;19(2):125-33.
2. 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.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:10882526   PMID:11291863   PMID:11748154   PMID:16678101   PMID:17445765   PMID:17931718   PMID:26781211  


Genomics

Comparative Map Data
Hesx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8162,198,589 - 2,200,694 (+)NCBIGRCr8
mRatBN7.2162,191,852 - 2,193,957 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl162,191,852 - 2,193,957 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx162,198,290 - 2,200,403 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0163,343,968 - 3,346,081 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0162,204,885 - 2,206,997 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0162,616,538 - 2,636,708 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl162,634,603 - 2,636,708 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0162,607,470 - 2,609,575 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4162,255,128 - 2,257,233 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera162,158,634 - 2,160,728 (+)NCBICelera
Cytogenetic Map16p16NCBI
HESX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38357,197,838 - 57,227,615 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl357,197,838 - 57,227,606 (-)EnsemblGRCh38hg38GRCh38
GRCh37357,231,866 - 57,261,643 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36357,207,265 - 57,209,320 (-)NCBINCBI36Build 36hg18NCBI36
Build 34357,207,264 - 57,209,320NCBI
Celera357,197,508 - 57,199,842 (-)NCBICelera
Cytogenetic Map3p14.3NCBI
HuRef357,280,999 - 57,283,330 (-)NCBIHuRef
CHM1_1357,182,092 - 57,184,428 (-)NCBICHM1_1
T2T-CHM13v2.0357,238,106 - 57,267,938 (-)NCBIT2T-CHM13v2.0
Hesx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391426,716,322 - 26,724,286 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1426,716,373 - 26,724,286 (+)EnsemblGRCm39 Ensembl
GRCm381426,994,419 - 27,002,329 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1426,994,416 - 27,002,329 (+)EnsemblGRCm38mm10GRCm38
MGSCv371427,813,548 - 27,815,512 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361425,827,246 - 25,829,210 (+)NCBIMGSCv36mm8
Celera1423,240,571 - 23,242,535 (+)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1416.09NCBI
Hesx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554306,955,575 - 6,956,991 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554306,955,575 - 6,956,991 (-)NCBIChiLan1.0ChiLan1.0
HESX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2257,177,672 - 57,196,280 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1357,182,366 - 57,201,048 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0357,131,419 - 57,161,205 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1358,341,955 - 58,370,338 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl358,341,965 - 58,370,347 (-)Ensemblpanpan1.1panPan2
HESX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12033,193,813 - 33,197,226 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2033,195,123 - 33,196,601 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2033,121,173 - 33,124,583 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02033,466,082 - 33,469,492 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2033,467,392 - 33,468,870 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12032,914,836 - 32,918,246 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02033,273,435 - 33,276,845 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02033,445,045 - 33,448,455 (+)NCBIUU_Cfam_GSD_1.0
Hesx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118174,407,622 - 174,433,673 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364737,545,839 - 7,548,013 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364737,545,982 - 7,572,222 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HESX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1339,046,465 - 39,088,875 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11339,046,961 - 39,088,926 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HESX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12218,517,067 - 18,546,882 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041148,324,605 - 148,352,750 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hesx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462482274,373 - 101,828 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462482274,344 - 102,484 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hesx1
4 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:146
Count of miRNA genes:100
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000019113
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
2325838Bp347Blood pressure QTL 3470.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1613080679Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)163802452995463Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
12903278Am16Aortic mass QTL 160.019aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)168323802995225Rat
12903279Cm115Cardiac mass QTL 1150.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)168323802995225Rat
12903281Cm116Cardiac mass QTL 1160.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)168323802995225Rat
12903952Cm117Cardiac mass QTL 1170.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)168323802995225Rat
12903954Bw186Body weight QTL 1860.011body mass (VT:0001259)body weight (CMO:0000012)168323802995225Rat
2301404Bp321Blood pressure QTL 3210.05arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)168323802995225Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)168323804227609Rat

Markers in Region
Hesx1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2162,192,225 - 2,193,143 (+)MAPPERmRatBN7.2
Rnor_6.0162,634,977 - 2,635,894NCBIRnor6.0
Rnor_5.0162,607,844 - 2,608,761UniSTSRnor5.0
RGSC_v3.4162,255,502 - 2,256,419UniSTSRGSC3.4
Celera162,159,008 - 2,159,914UniSTS
Cytogenetic Map16p16UniSTS
Hesx1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2162,193,130 - 2,193,726 (+)MAPPERmRatBN7.2
Rnor_6.0162,635,882 - 2,636,477NCBIRnor6.0
Rnor_5.0162,608,749 - 2,609,344UniSTSRnor5.0
RGSC_v3.4162,256,407 - 2,257,002UniSTSRGSC3.4
Celera162,159,902 - 2,160,497UniSTS
Cytogenetic Map16p16UniSTS


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 nervous system reproductive system
High
Medium
Low 10 10 10 2 8
Below cutoff 1 8 7 6 1 6 13 20

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019113   ⟹   ENSRNOP00000019113
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl162,191,852 - 2,193,957 (+)Ensembl
Rnor_6.0 Ensembl162,634,603 - 2,636,708 (+)Ensembl
RefSeq Acc Id: NM_001109106   ⟹   NP_001102576
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8162,198,589 - 2,200,694 (+)NCBI
mRatBN7.2162,191,852 - 2,193,957 (+)NCBI
Rnor_6.0162,634,603 - 2,636,708 (+)NCBI
Rnor_5.0162,607,470 - 2,609,575 (+)NCBI
RGSC_v3.4162,255,128 - 2,257,233 (+)RGD
Celera162,158,634 - 2,160,728 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102576 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75066 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019113
  ENSRNOP00000019113.2
Reference Protein Sequences
RefSeq Acc Id: NP_001102576   ⟸   NM_001109106
- UniProtKB: D4AEG9 (UniProtKB/TrEMBL),   A6KMK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019113   ⟸   ENSRNOT00000019113
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AEG9-F1-model_v2 AlphaFold D4AEG9 1-185 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:1563858 AgrOrtholog
BioCyc Gene G2FUF-12245 BioCyc
Ensembl Genes ENSRNOG00000014133 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019113 ENTREZGENE
  ENSRNOT00000019113.4 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Hesx1 UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:498575 UniProtKB/TrEMBL
NCBI Gene 498575 ENTREZGENE
PANTHER HOMEOBOX EXPRESSED IN ES CELLS 1 UniProtKB/TrEMBL
  PTHR46966 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Hesx1 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014133 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6KMK2 ENTREZGENE, UniProtKB/TrEMBL
  D4AEG9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-30 Hesx1  HESX homeobox 1  Hesx1  homeo box gene expressed in ES cells   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Hesx1  homeo box gene expressed in ES cells   Hesx1_predicted  homeo box gene expressed in ES cells (predicted)  'predicted' is removed 2292626 APPROVED
2007-03-21 Hesx1_predicted  homeo box gene expressed in ES cells (predicted)  RGD1563858_predicted  similar to anterior-restricted homeobox protein (predicted)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563858_predicted  similar to anterior-restricted homeobox protein (predicted)  LOC498575  similar to anterior-restricted homeobox protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498575  similar to anterior-restricted homeobox protein      Symbol and Name status set to provisional 70820 PROVISIONAL