Hoxa1 (homeobox A1) - Rat Genome Database

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Gene: Hoxa1 (homeobox A1) Mus musculus
Analyze
Symbol: Hoxa1
Name: homeobox A1
RGD ID: 732851
MGI Page MGI
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Acts upstream of or within several processes, including cellular response to ethanol; cellular response to retinoic acid; and nervous system development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including brain; embryo ectoderm; embryo mesenchyme; genitourinary system; and gut. Used to study Athabaskan brainstem dysgenesis syndrome. Human ortholog(s) of this gene implicated in Athabaskan brainstem dysgenesis syndrome and autistic disorder. Orthologous to human HOXA1 (homeobox A1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: early retinoic acid 1; ER; ERA1; homeo box A1; homeobox protein Hox-1.6; homeobox protein Hox-A1; homeoboxless protein ERA-1-399; homeotic protein ERA-1-993; Hox-1.; Hox-1.6
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39652,132,573 - 52,135,299 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl652,132,570 - 52,135,297 (-)EnsemblGRCm39 Ensembl
GRCm38652,155,367 - 52,160,007 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl652,155,590 - 52,158,317 (-)EnsemblGRCm38mm10GRCm38
MGSCv37652,105,366 - 52,108,316 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36652,084,950 - 52,087,900 (-)NCBIMGSCv36mm8
Celera652,677,008 - 52,679,958 (-)NCBICelera
Cytogenetic Map6B3NCBI
cM Map625.4NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-anisomycin  (EXP)
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
4,4'-sulfonyldiphenol  (EXP)
4-nonylphenol  (EXP)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
6-bromoindirubin-3'-oxime  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
alendronic acid  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP)
ammonium chloride  (ISO)
aristolochic acid A  (ISO)
arotinoid acid  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
bucladesine  (ISO)
butylated hydroxyanisole  (EXP)
cadmium dichloride  (ISO)
camptothecin  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (EXP)
CHIR 99021  (ISO)
chloroprene  (EXP)
chlorpyrifos  (EXP)
citral  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cortisol  (ISO)
cyclophosphamide  (ISO)
D-gluconic acid  (ISO)
decabromodiphenyl ether  (ISO)
deoxycholic acid  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (EXP,ISO)
dimethylarsinic acid  (ISO)
dioxygen  (EXP)
dipentyl phthalate  (EXP)
disulfiram  (EXP)
dorsomorphin  (ISO)
endosulfan  (ISO)
entinostat  (ISO)
ethanol  (EXP)
flusilazole  (EXP,ISO)
folic acid  (EXP)
formaldehyde  (ISO)
genistein  (EXP)
geranial  (EXP)
hexaconazole  (EXP)
hydrogen peroxide  (ISO)
kenpaullone  (EXP)
L-ascorbic acid 2-phosphate  (ISO)
lipopolysaccharide  (ISO)
LY294002  (EXP)
medroxyprogesterone acetate  (ISO)
methoxyacetic acid  (EXP)
methylisothiazolinone  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
N-nitrosodiethylamine  (ISO)
nickel sulfate  (ISO)
niclosamide  (EXP)
nitrofen  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pirinixic acid  (EXP)
raloxifene  (ISO)
resveratrol  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP)
testosterone  (EXP)
titanium dioxide  (EXP)
triadimefon  (EXP)
triclosan  (ISO)
triptonide  (EXP)
valproic acid  (EXP,ISO)
WIN 18446  (EXP)
XAV939  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleoplasm  (TAS)
nucleus  (IBA)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal aortic arch morphology  (IAGP)
abnormal basioccipital bone morphology  (IAGP)
abnormal blinking  (IAGP)
abnormal cardiac outflow tract development  (IAGP)
abnormal cardiovascular system morphology  (IAGP)
abnormal cochlea morphology  (IAGP)
abnormal cochlear sensory epithelium morphology  (IAGP)
abnormal cranial ganglia morphology  (IAGP)
abnormal cranial nerve morphology  (IAGP)
abnormal cranial neural crest cell migration  (IAGP)
abnormal cranium morphology  (IAGP)
abnormal crista ampullaris morphology  (IAGP)
abnormal digastric posterior belly morphology  (IAGP)
abnormal exoccipital bone morphology  (IAGP)
abnormal external carotid artery morphology  (IAGP)
abnormal facial nerve morphology  (IAGP)
abnormal geniculate ganglion morphology  (IAGP)
abnormal gland morphology  (IAGP)
abnormal glossopharyngeal nerve morphology  (IAGP)
abnormal head morphology  (IAGP)
abnormal hindbrain morphology  (IAGP)
abnormal inner ear morphology  (IAGP)
abnormal inner ear vestibule morphology  (IAGP)
abnormal internal carotid artery morphology  (IAGP)
abnormal interparietal bone morphology  (IAGP)
abnormal membranous labyrinth morphology  (IAGP)
abnormal middle ear morphology  (IAGP)
abnormal middle ear ossicle morphology  (IAGP)
abnormal neural crest cell delamination  (IAGP)
abnormal neural crest cell migration  (IAGP)
abnormal neuron differentiation  (IAGP)
abnormal otic capsule morphology  (IAGP)
abnormal otic vesicle development  (IAGP)
abnormal otic vesicle morphology  (IAGP)
abnormal outer ear morphology  (IAGP)
abnormal pharyngeal pouch morphology  (IAGP)
abnormal pons morphology  (IAGP)
abnormal reflex  (IAGP)
abnormal rhombomere boundary morphology  (IAGP)
abnormal rhombomere morphology  (IAGP)
abnormal semicircular canal morphology  (IAGP)
abnormal stylohyoid muscle morphology  (IAGP)
abnormal suckling behavior  (IAGP)
abnormal superior vagus ganglion morphology  (IAGP)
abnormal third pharyngeal pouch morphology  (IAGP)
abnormal trigeminal ganglion morphology  (IAGP)
abnormal tympanic ring morphology  (IAGP)
abnormal utricular macula morphology  (IAGP)
abnormal vagus nerve morphology  (IAGP)
abnormal vestibular saccular macula morphology  (IAGP)
abnormal vestibulocochlear ganglion morphology  (IAGP)
absent cochlea  (IAGP)
absent cochlear ganglion  (IAGP)
absent cochlear nerve  (IAGP)
absent common crus  (IAGP)
absent endolymphatic duct  (IAGP)
absent endolymphatic sac  (IAGP)
absent facial muscle  (IAGP)
absent facial nerve  (IAGP)
absent facial nuclei  (IAGP)
absent levator labii superioris muscle  (IAGP)
absent middle ear ossicles  (IAGP)
absent orbicularis oculi muscle  (IAGP)
absent outer ear  (IAGP)
absent parathyroid glands  (IAGP)
absent posterior semicircular canal  (IAGP)
absent rhombomere 4  (IAGP)
absent rhombomere 5  (IAGP)
absent scala media  (IAGP)
absent second pharyngeal arch  (IAGP)
absent second pharyngeal pouch  (IAGP)
absent semicircular canals  (IAGP)
absent stapes  (IAGP)
absent superior olivary complex  (IAGP)
absent superior semicircular canal  (IAGP)
absent utricle  (IAGP)
absent vestibular nerve  (IAGP)
absent vestibular saccule  (IAGP)
absent vestibulocochlear nerve  (IAGP)
absent zygomaticus muscle  (IAGP)
anoxia  (IAGP)
athymia  (IAGP)
bicuspid aortic valve  (IAGP)
cleft secondary palate  (IAGP)
cyanosis  (IAGP)
decreased rhombomere 4 size  (IAGP)
decreased rhombomere 5 size  (IAGP)
delayed neural tube closure  (IAGP)
facial paralysis  (IAGP)
fusion of glossopharyngeal and vagus nerve  (IAGP)
heart right ventricle hypertrophy  (IAGP)
increased hindbrain apoptosis  (IAGP)
increased rhombomere 3 size  (IAGP)
interrupted aortic arch, type b  (IAGP)
muscle spasm  (IAGP)
neonatal lethality, complete penetrance  (IAGP)
neonatal lethality, incomplete penetrance  (IAGP)
no abnormal phenotype detected  (IAGP)
overriding aortic valve  (IAGP)
paralysis  (IAGP)
parathyroid hypoplasia  (IAGP)
perinatal lethality, complete penetrance  (IAGP)
perinatal lethality, incomplete penetrance  (IAGP)
postnatal lethality, complete penetrance  (IAGP)
postnatal lethality, incomplete penetrance  (IAGP)
pulmonary hypoplasia  (IAGP)
respiratory failure  (IAGP)
retroesophageal right subclavian artery  (IAGP)
rhombomere fusion  (IAGP)
right aortic arch  (IAGP)
small ears  (IAGP)
small facial motor nucleus  (IAGP)
small geniculate ganglion  (IAGP)
small incus  (IAGP)
small malleus  (IAGP)
small middle ear ossicles  (IAGP)
small otic vesicle  (IAGP)
small second pharyngeal arch  (IAGP)
small superior glossopharyngeal ganglion  (IAGP)
small superior vagus ganglion  (IAGP)
small thymus  (IAGP)
small vestibular ganglion  (IAGP)
thymus hypoplasia  (IAGP)
ventricular septal defect  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Hox-1.6: a mouse homeo-box-containing gene member of the Hox-1 complex. Baron A, etal., EMBO J 1987 Oct;6(10):2977-86.
2. The clinical spectrum of homozygous HOXA1 mutations. Bosley TM, etal., Am J Med Genet A. 2008 May 15;146A(10):1235-40. doi: 10.1002/ajmg.a.32262.
3. Association between the HOXA1 A218G polymorphism and increased head circumference in patients with autism. Conciatori M, etal., Biol Psychiatry 2004 Feb 15;55(4):413-9.
4. No association between allelic variants of HOXA1/HOXB1 and autism. Gallagher L, etal., Am J Med Genet B Neuropsychiatr Genet. 2004 Jan 1;124B(1):64-7.
5. Changes in Hox1.6, c-jun, and Oct-3 gene expressions are associated with teratocarcinoma F9 cell differentiation in three different ways of induction. Iwai SA, etal., Exp Cell Res 1993 Mar;205(1):39-43.
6. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
7. MGDs mouse GO annotations MGD data from the GO Consortium
8. MGD IEA MGD IEA
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. Mouse MP Annotation Import Pipeline RGD automated import pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1346922   PMID:1348361   PMID:1358459   PMID:1360810   PMID:1611214   PMID:1673098   PMID:1680563   PMID:1682814   PMID:1688181   PMID:1693558   PMID:2511439   PMID:2569969  
PMID:2878432   PMID:2906112   PMID:3019676   PMID:7622051   PMID:7680626   PMID:7743939   PMID:7903600   PMID:7903632   PMID:7915637   PMID:7917011   PMID:7954431   PMID:7956823  
PMID:8096385   PMID:8102800   PMID:8105479   PMID:8287791   PMID:8833244   PMID:8950991   PMID:8999919   PMID:9053316   PMID:9126293   PMID:9291463   PMID:9383299   PMID:9415485  
PMID:9438427   PMID:9463349   PMID:9463359   PMID:9545490   PMID:9789037   PMID:9806922   PMID:9843211   PMID:10192400   PMID:10328847   PMID:10349636   PMID:10354604   PMID:10440864  
PMID:10529419   PMID:10529420   PMID:10662633   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11278854   PMID:11466434   PMID:11511348   PMID:11528388   PMID:11532923   PMID:11840501  
PMID:12412013   PMID:12466851   PMID:12477932   PMID:12482855   PMID:12563036   PMID:12702665   PMID:12805229   PMID:14522873   PMID:14681479   PMID:15042701   PMID:15367676   PMID:15465489  
PMID:15618518   PMID:15680324   PMID:15722554   PMID:15741322   PMID:15765518   PMID:16141072   PMID:16141073   PMID:16602821   PMID:16881056   PMID:16890163   PMID:16971476   PMID:16981007  
PMID:17652354   PMID:17986461   PMID:18287057   PMID:18287559   PMID:18417536   PMID:18512762   PMID:18787068   PMID:18973680   PMID:19091803   PMID:19115252   PMID:19204410   PMID:19922872  
PMID:20059953   PMID:20171203   PMID:20211142   PMID:20417598   PMID:20932939   PMID:21267068   PMID:21385575   PMID:21497760   PMID:21674689   PMID:21784065   PMID:21873635   PMID:21930923  
PMID:21940751   PMID:21957483   PMID:21982646   PMID:22219351   PMID:22701719   PMID:22711520   PMID:22988430   PMID:23088713   PMID:23723417   PMID:24005908   PMID:24075995   PMID:24244684  
PMID:24357327   PMID:24496616   PMID:24803591   PMID:24952961   PMID:25099890   PMID:25190705   PMID:25263278   PMID:25691658   PMID:26284287   PMID:26367869   PMID:26447130   PMID:26820751  
PMID:27956219   PMID:28041967   PMID:28188179   PMID:28189678   PMID:28380068   PMID:28609438   PMID:28784834   PMID:28982536   PMID:29471045   PMID:30169530   PMID:30561639   PMID:30992047  
PMID:31147716   PMID:31341279   PMID:32013856   PMID:32350257   PMID:32479258   PMID:33257809   PMID:33298461   PMID:33497014   PMID:33505317   PMID:36028102   PMID:36941270   PMID:37277355  
PMID:37397253   PMID:38421703  


Genomics

Comparative Map Data
Hoxa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39652,132,573 - 52,135,299 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl652,132,570 - 52,135,297 (-)EnsemblGRCm39 Ensembl
GRCm38652,155,367 - 52,160,007 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl652,155,590 - 52,158,317 (-)EnsemblGRCm38mm10GRCm38
MGSCv37652,105,366 - 52,108,316 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36652,084,950 - 52,087,900 (-)NCBIMGSCv36mm8
Celera652,677,008 - 52,679,958 (-)NCBICelera
Cytogenetic Map6B3NCBI
cM Map625.4NCBI
HOXA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38727,092,993 - 27,096,000 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl727,092,993 - 27,096,000 (-)EnsemblGRCh38hg38GRCh38
GRCh37727,132,612 - 27,135,619 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36727,099,137 - 27,102,150 (-)NCBINCBI36Build 36hg18NCBI36
Build 34726,905,855 - 26,908,834NCBI
Celera727,121,549 - 27,124,562 (-)NCBICelera
Cytogenetic Map7p15.2NCBI
HuRef727,013,203 - 27,016,216 (-)NCBIHuRef
CHM1_1727,132,309 - 27,135,322 (-)NCBICHM1_1
T2T-CHM13v2.0727,228,895 - 27,231,899 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2727,183,765 - 27,186,778 (-)NCBI
Hoxa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8482,586,505 - 82,589,209 (-)NCBIGRCr8
mRatBN7.2481,255,814 - 81,258,587 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl481,255,883 - 81,258,504 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx486,478,552 - 86,480,352 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0482,253,945 - 82,255,745 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0480,681,027 - 80,682,833 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0482,124,358 - 82,127,182 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl482,125,406 - 82,127,066 (-)EnsemblRnor6.0rn6Rnor6.0
Celera476,147,124 - 76,149,948 (-)NCBICelera
Cytogenetic Map4q24NCBI
Hoxa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541028,787,817 - 28,790,962 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541028,788,245 - 28,790,971 (-)NCBIChiLan1.0ChiLan1.0
HOXA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2631,922,434 - 31,925,259 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1780,246,850 - 80,249,860 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0727,737,432 - 27,740,442 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1727,336,737 - 27,339,747 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl727,335,710 - 27,339,747 (-)Ensemblpanpan1.1panPan2
HOXA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11440,267,033 - 40,272,212 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1440,267,528 - 40,269,681 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1439,698,088 - 39,703,711 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01440,205,795 - 40,211,418 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1440,206,290 - 40,208,443 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11440,319,907 - 40,325,530 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01440,004,976 - 40,010,599 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01440,363,561 - 40,369,177 (-)NCBIUU_Cfam_GSD_1.0
Hoxa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511884,509,768 - 84,512,994 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364783,721,662 - 3,724,433 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364783,721,662 - 3,724,471 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1845,477,461 - 45,480,152 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11845,477,561 - 45,480,306 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21850,110,695 - 50,113,440 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12131,272,410 - 31,275,503 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2131,272,889 - 31,275,551 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604273,458,340 - 73,461,050 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxa1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247393,508,838 - 3,511,864 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247393,509,020 - 3,511,890 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hoxa1
93 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1313
Count of miRNA genes:483
Interacting mature miRNAs:622
Transcripts:ENSMUST00000000964, ENSMUST00000120363
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25440480Moaq2_mmodifier of alien QTL 2 (mouse)63050001117476961Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139076998Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487403016Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396633110Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396633110Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396633110Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396633110Mouse
26884441Sklq3_mskull length QTL 3, 5 week (mouse)6760000080576983Mouse
27226726Tibmd7_mtibia midshaft diameter 7, 16 week (mouse)61769999953476985Mouse
1357442Dbts1_mdiabetes 1 (mouse)Not determined61823414773364675Mouse
12904940Edlmmq5_mextensor digitorum longus muscle mass QTL 5 (mouse)61961634653616346Mouse
12904943Tammq4_mtibialis anterior muscle mass QTL 4 (mouse)61961634653616346Mouse
12904952Gmmq4_mgastrocnemius muscle mass QTL 4 (mouse)61961634653616346Mouse
10412213Sxbq2_mSGC/Knj cross B6 QTL 2 (mouse)Not determined61991268571299759Mouse
10412107Desp4_mdespair 4 (mouse)Not determined62004983054049830Mouse
14700690Ccs6_mcolon cancer susceptibility 6 (mouse)62377693457776934Mouse
13208564Bmiq7_mbody mass index QTL 7 (mouse)62499999979976983Mouse
4141988Obrq3_mobesity resistance QTL 3 (mouse)Not determined2829099362291115Mouse
4141454Obrq4_mobesity resistance QTL 4 (mouse)Not determined3170349965703611Mouse
12880425V25Dq5_mvitamin D inactive form serum level QTL 5 (mouse)63267698066676980Mouse
4141782Mrdq5_mmodifier of retinal degeneration QTL 5 (mouse)Not determined3282758578215957Mouse
1300959Lxw2_mlupus BXSB x NZW 2 (mouse)Not determined63387226167872400Mouse
11252142Mom12_mModifier of Min 12 (mouse)63387226167872400Mouse
1300767Aliq4_macute lung injury QTL 4 (mouse)Not determined63627333270273435Mouse
1357539Bsbob3_mBSB obesity 3 (mouse)Not determined63644845670448576Mouse
4141094Hrtr1_mheart rate 1 (mouse)Not determined3674146370741463Mouse
14746995Manh60_mmandible shape 60 (mouse)63720266271202662Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63864656092584431Mouse
1301326Trbv4c2_mT cell receptor beta variable 4 (mouse)Not determined64086823071356155Mouse
12880424V25Dq4_mvitamin D inactive form serum level QTL 4 (mouse)64157698575576985Mouse
11040600Lmr4c_mleishmaniasis resistance 4c (mouse)64209335876093500Mouse
11040601Lmr4a_mleishmaniasis resistance 4a (mouse)64209335876093500Mouse
11533915Mts4_mmammary tumor susceptibility 4 (mouse)64209335876093500Mouse
1301266Lmr4_mleishmaniasis resistance 4 (mouse)Not determined64209335876093500Mouse
12910785Pwgrq16_mpost-weaning growth rate QTL 16 (mouse)64380374777788506Mouse
12910798Pwgrq5_mpre-weaning growth rate QTL 5 (mouse)64380374777788506Mouse
12910802Pwbwq12_mpost-weaning body weight QTL 12 (mouse)64380374777788506Mouse
12910807Pwbwq11_mpost-weaning body weight QTL 11 (mouse)64380374777788506Mouse
12910809Pwbwq10_mpost-weaning body weight QTL 10 (mouse)64380374777788506Mouse
12910820Ogrq3_moverall growth rate QTL 3 (mouse)64380374777788506Mouse
10043885Cia6c_mcollagen induced arthritis QTL 6c (mouse)Not determined64444280571096451Mouse
1300618Pgia19_mproteoglycan induced arthritis 19 (mouse)Not determined64529099387403016Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645290993128811995Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46912919136400690Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648696934125336963Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648696934148351498Mouse
4140983Srilp_msleep response to influenza, light phase (mouse)Not determined4870349075424693Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648703490125333748Mouse
1301254Skts11_mskin tumor susceptibility 11 (mouse)Not determined65115613485156284Mouse
14696807Rbcn2_mrod bipolar cell number 2 (mouse)65118698056186985Mouse

Markers in Region
Hoxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
MGSCv37652,107,893 - 52,108,114UniSTSGRCm37
MGSCv37652,105,457 - 52,105,770UniSTSGRCm37
Celera652,677,099 - 52,677,412UniSTS
Celera652,679,535 - 52,679,756UniSTS
Cytogenetic Map6B3UniSTS
cM Map626.28UniSTS
cM Map626.28UniSTS
RH94642  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38652,156,591 - 52,156,689UniSTSGRCm38
MGSCv37652,106,590 - 52,106,688UniSTSGRCm37
Celera652,678,232 - 52,678,330UniSTS
Cytogenetic Map6B3UniSTS
cM Map626.28UniSTS
M22115  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38652,156,400 - 52,156,552UniSTSGRCm38
MGSCv37652,106,399 - 52,106,551UniSTSGRCm37
Celera652,678,041 - 52,678,193UniSTS
Cytogenetic Map6B3UniSTS
cM Map626.28UniSTS
Whitehead_YAC6 UniSTS
REN100302  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38652,156,739 - 52,157,010UniSTSGRCm38
MGSCv37652,106,738 - 52,107,009UniSTSGRCm37
Celera652,678,380 - 52,678,651UniSTS
Cytogenetic Map6B3UniSTS
cM Map626.28UniSTS
Hoxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38652,155,458 - 52,155,771UniSTSGRCm38
MGSCv37652,105,457 - 52,105,770UniSTSGRCm37
Celera652,677,099 - 52,677,412UniSTS
Cytogenetic Map6B3UniSTS
Hoxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38652,157,894 - 52,158,115UniSTSGRCm38
MGSCv37652,107,893 - 52,108,114UniSTSGRCm37
Celera652,679,535 - 52,679,756UniSTS
Cytogenetic Map6B3UniSTS
cM Map626.28UniSTS
M22115  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38652,156,039 - 52,156,118UniSTSGRCm38
MGSCv37652,106,038 - 52,106,117UniSTSGRCm37
Celera652,677,680 - 52,677,759UniSTS
Cytogenetic Map6B3UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000000964   ⟹   ENSMUSP00000000964
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl652,132,570 - 52,135,297 (-)Ensembl
GRCm38.p6 Ensembl652,155,590 - 52,158,317 (-)Ensembl
RefSeq Acc Id: ENSMUST00000120363   ⟹   ENSMUSP00000113724
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl652,132,575 - 52,135,297 (-)Ensembl
GRCm38.p6 Ensembl652,155,595 - 52,158,317 (-)Ensembl
RefSeq Acc Id: NM_001311118   ⟹   NP_001298047
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39652,132,573 - 52,135,299 (-)NCBI
GRCm38652,155,367 - 52,158,317 (-)NCBI
Sequence:
RefSeq Acc Id: NM_010449   ⟹   NP_034579
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39652,132,573 - 52,135,299 (-)NCBI
GRCm38652,155,367 - 52,158,317 (-)NCBI
MGSCv37652,105,366 - 52,108,316 (-)RGD
Celera652,677,008 - 52,679,958 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_034579   ⟸   NM_010449
- Peptide Label: isoform 1
- UniProtKB: B9EHK7 (UniProtKB/TrEMBL),   Q8BNI8 (UniProtKB/TrEMBL),   B9EHK8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001298047   ⟸   NM_001311118
- Peptide Label: isoform 2
- UniProtKB: D3Z4E1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000000964   ⟸   ENSMUST00000000964
RefSeq Acc Id: ENSMUSP00000113724   ⟸   ENSMUST00000120363
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P09022-F1-model_v2 AlphaFold P09022 1-331 view protein structure

Promoters
RGD ID:6839564
Promoter ID:MM_KWN:45998
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6
Transcripts:LINCRNA_851,   NM_010449,   OTTMUST00000065043,   UC009BXX.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36652,108,281 - 52,109,182 (+)MPROMDB
RGD ID:6889716
Promoter ID:EPDNEW_M8309
Type:single initiation site
Name:Hoxa1_1
Description:Mus musculus homeobox A1 , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38652,158,229 - 52,158,289EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:96170 AgrOrtholog
Ensembl Genes ENSMUSG00000029844 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000000964 ENTREZGENE
  ENSMUST00000000964.6 UniProtKB/TrEMBL
  ENSMUST00000120363 ENTREZGENE
  ENSMUST00000120363.2 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HXA1/B1/D1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:15394 UniProtKB/TrEMBL
MGD MGI:96170 ENTREZGENE
NCBI Gene 15394 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-A1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR45946 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hoxa1 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B9EHK7 ENTREZGENE, UniProtKB/TrEMBL
  B9EHK8 ENTREZGENE, UniProtKB/TrEMBL
  D3Z4E1 ENTREZGENE, UniProtKB/TrEMBL
  HXA1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q8BNI8 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary P15463 UniProtKB/Swiss-Prot