Hoxa9 (homeobox A9) - Rat Genome Database

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Gene: Hoxa9 (homeobox A9) Rattus norvegicus
Analyze
Symbol: Hoxa9
Name: homeobox A9
RGD ID: 1310001
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 enzyme binding activity. Involved in prostate gland development and response to testosterone. Predicted to be located in nucleoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human HOXA9 (homeobox A9); INTERACTS WITH 17alpha-ethynylestradiol; 6-propyl-2-thiouracil; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeo box A9; homeobox A9-like; homeobox protein Hox-A9; homeobox protein Hox-A9-like; Hoxa9l; LOC100909740; LOC100911710; LOC103689925; LOC297099; RGD1310001; similar to Hoxa-9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8482,653,847 - 82,659,958 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl482,653,825 - 82,662,093 (-)EnsemblGRCr8
mRatBN7.2481,323,235 - 81,329,344 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl481,323,382 - 81,326,358 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx486,545,019 - 86,548,222 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0482,320,408 - 82,323,613 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0480,747,545 - 80,750,729 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0482,191,804 - 82,199,025 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl482,192,963 - 82,194,927 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl482,192,963 - 82,194,927 (-)NCBIrn6Rnor6.0
Rnor_5.04146,858,635 - 146,861,993 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4480,524,246 - 80,526,491NCBIRGSC_v3.4RGSC_v3.4rn4
Celera476,213,941 - 76,221,355 (-)NCBICelera
RGSC_v3.1480,802,831 - 80,804,796NCBI
Cytogenetic Map4q24NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)
transcription regulator complex  (ISO)

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Posterior Hox gene expression and differential androgen regulation in the developing and adult rat prostate lobes. Huang L, etal., Endocrinology. 2007 Mar;148(3):1235-45. Epub 2006 Nov 30.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8625797   PMID:9013929   PMID:9343407   PMID:9892669   PMID:10082572   PMID:11438208   PMID:15161102   PMID:17327400   PMID:17626057   PMID:17761289   PMID:22269951   PMID:23760953  
PMID:32233950   PMID:34461109  


Genomics

Comparative Map Data
Hoxa9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8482,653,847 - 82,659,958 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl482,653,825 - 82,662,093 (-)EnsemblGRCr8
mRatBN7.2481,323,235 - 81,329,344 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl481,323,382 - 81,326,358 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx486,545,019 - 86,548,222 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0482,320,408 - 82,323,613 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0480,747,545 - 80,750,729 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0482,191,804 - 82,199,025 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl482,192,963 - 82,194,927 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl482,192,963 - 82,194,927 (-)NCBIrn6Rnor6.0
Rnor_5.04146,858,635 - 146,861,993 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4480,524,246 - 80,526,491NCBIRGSC_v3.4RGSC_v3.4rn4
Celera476,213,941 - 76,221,355 (-)NCBICelera
RGSC_v3.1480,802,831 - 80,804,796NCBI
Cytogenetic Map4q24NCBI
HOXA9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38727,162,438 - 27,165,537 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl727,162,438 - 27,175,180 (-)Ensemblhg38GRCh38
GRCh37727,202,057 - 27,205,156 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36727,168,582 - 27,171,674 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34726,975,297 - 26,978,389NCBI
Celera727,190,996 - 27,194,088 (-)NCBICelera
Cytogenetic Map7p15.2NCBI
HuRef727,082,468 - 27,085,560 (-)NCBIHuRef
CHM1_1727,201,773 - 27,204,865 (-)NCBICHM1_1
T2T-CHM13v2.0727,298,433 - 27,301,532 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2727,253,232 - 27,256,324 (-)NCBI
Hoxa9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39652,200,077 - 52,203,169 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl652,200,080 - 52,208,069 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38652,223,097 - 52,227,370 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl652,223,100 - 52,231,089 (-)Ensemblmm10GRCm38
MGSCv37652,174,053 - 52,177,369 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36652,153,637 - 52,156,953 (-)NCBIMGSCv36mm8
Celera652,745,693 - 52,749,009 (-)NCBICelera
Cytogenetic Map6B3NCBI
cM Map625.4NCBI
Hoxa9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541028,856,661 - 28,861,803 (-)Ensembl
ChiLan1.0NW_00495541028,856,661 - 28,861,803 (-)NCBIChiLan1.0ChiLan1.0
HOXA9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2631,991,641 - 31,998,248 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1780,316,365 - 80,319,466 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0727,806,942 - 27,810,304 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1727,406,624 - 27,409,984 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl727,405,931 - 27,409,984 (-)EnsemblpanPan2panpan1.1
HOXA9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11440,336,829 - 40,340,533 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1440,337,999 - 40,339,923 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1439,767,687 - 39,772,557 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01440,275,489 - 40,280,356 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1440,275,952 - 40,278,578 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11440,389,486 - 40,394,356 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01440,074,555 - 40,079,418 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01440,433,160 - 40,438,030 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Hoxa9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511884,578,230 - 84,583,058 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364783,789,961 - 3,793,845 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364783,789,961 - 3,793,116 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXA9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1845,408,375 - 45,411,509 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11845,404,594 - 45,411,512 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21850,039,919 - 50,044,537 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXA9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12131,199,573 - 31,206,455 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2131,203,422 - 31,206,433 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604273,527,386 - 73,530,633 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxa9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247393,439,217 - 3,443,449 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247393,440,328 - 3,443,362 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Hoxa9
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1688,833,595 - 88,839,549 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Hoxa9
88 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:227
Count of miRNA genes:130
Interacting mature miRNAs:144
Transcripts:ENSRNOT00000071668, ENSRNOT00000071729, ENSRNOT00000072302
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
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)439431983123203361Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)459753119104753119Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44140057786400577Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44442502489425024Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)427730518170099664Rat
1357342Bw40Body weight QTL 400.001body mass (VT:0001259)body weight (CMO:0000012)474233320119233320Rat
631556Bp135Blood pressure QTL 1350.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)480212111119233320Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)458817672103817672Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)426234499134199155Rat
70167Bw22Body weight QTL 223.1body mass (VT:0001259)body weight (CMO:0000012)474233320119233320Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)471647492116647492Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)427862204126119996Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44140060386400603Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)475939858140508796Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)465060960127749483Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)445429897149763204Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)451085655113588029Rat
2317586Eae25Experimental allergic encephalomyelitis QTL 259.300000190734863nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)48021363484338055Rat
61364Iddm2Insulin dependent diabetes mellitus QTL 2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)480216705104243248Rat
2317588Eae27Experimental allergic encephalomyelitis QTL 27nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)469036742114036742Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)440490442117737312Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)457613339151163960Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)457613242102613242Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)457613242102613242Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)464084079109084079Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)457613242102613242Rat
2306547Iddm38Insulin dependent diabetes mellitus QTL 38blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)468353567113353567Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)460916264184426481Rat
2306545Iddm39Insulin dependent diabetes mellitus QTL 39blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)478687630123687630Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41170660492690519Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)464084079109084079Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)474169813134199155Rat
2312569Pur19Proteinuria QTL 193.40.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)459836842104836842Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)475939858140508796Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)445429897149763204Rat
634344Hcar7Hepatocarcinoma resistance QTL 77.8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)46104105794638356Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45889999148002343Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264174095838Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)445429709157555683Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)463245026129846354Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)464209744109209744Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)460916264184426481Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)44140057786400577Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)457664252127749483Rat
2306899Bp338Blood pressure QTL 3380.071arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)482336765127336765Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45807987592690793Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)465495851159259805Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)464084079109084079Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)463224393108224393Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46390045888813920Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)433538597116185060Rat

Markers in Region
Hoxa7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,315,812 - 81,316,035 (+)MAPPERmRatBN7.2
Rnor_6.0482,270,177 - 82,270,399NCBIRnor6.0
Rnor_6.0482,184,382 - 82,184,604NCBIRnor6.0
Rnor_5.04146,851,213 - 146,851,435UniSTSRnor5.0
Rnor_5.04146,937,008 - 146,937,230UniSTSRnor5.0
RGSC_v3.4480,515,705 - 80,515,927UniSTSRGSC3.4
Celera476,206,525 - 76,206,747UniSTS
Cytogenetic Map4q24UniSTS
RH135228  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,315,812 - 81,315,998 (+)MAPPERmRatBN7.2
Rnor_6.0482,270,177 - 82,270,362NCBIRnor6.0
Rnor_6.0482,184,382 - 82,184,567NCBIRnor6.0
Rnor_5.04146,937,008 - 146,937,193UniSTSRnor5.0
Rnor_5.04146,851,213 - 146,851,398UniSTSRnor5.0
RGSC_v3.4480,515,705 - 80,515,890UniSTSRGSC3.4
Celera476,206,525 - 76,206,710UniSTS
RH 3.4 Map4514.4UniSTS
Cytogenetic Map4q24UniSTS
stSG609369  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,324,397 - 81,325,653 (+)MAPPERmRatBN7.2
Rnor_6.0482,278,762 - 82,280,017NCBIRnor6.0
Rnor_6.0482,192,967 - 82,194,222NCBIRnor6.0
Rnor_5.04146,859,798 - 146,861,053UniSTSRnor5.0
Rnor_5.04146,945,593 - 146,946,848UniSTSRnor5.0
RGSC_v3.4480,524,290 - 80,525,545UniSTSRGSC3.4
Celera476,215,104 - 76,216,355UniSTS
Cytogenetic Map4q24UniSTS
Hoxa9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,323,863 - 81,324,428 (+)MAPPERmRatBN7.2
Rnor_6.0482,278,228 - 82,278,792NCBIRnor6.0
Rnor_6.0482,192,433 - 82,192,997NCBIRnor6.0
Rnor_5.04146,859,264 - 146,859,828UniSTSRnor5.0
Rnor_5.04146,945,059 - 146,945,623UniSTSRnor5.0
RGSC_v3.4480,523,756 - 80,524,320UniSTSRGSC3.4
Celera476,214,570 - 76,215,134UniSTS
Cytogenetic Map4q24UniSTS
REN100580  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,317,426 - 81,317,651 (+)MAPPERmRatBN7.2
Rnor_6.0482,271,791 - 82,272,015NCBIRnor6.0
Rnor_6.0482,185,996 - 82,186,220NCBIRnor6.0
Rnor_5.04146,852,827 - 146,853,051UniSTSRnor5.0
Rnor_5.04146,938,622 - 146,938,846UniSTSRnor5.0
RGSC_v3.4480,517,319 - 80,517,543UniSTSRGSC3.4
Celera476,208,139 - 76,208,363UniSTS
Cytogenetic Map4q24UniSTS
REN100619  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,325,953 - 81,326,200 (+)MAPPERmRatBN7.2
Rnor_6.0482,280,318 - 82,280,564NCBIRnor6.0
Rnor_6.0482,194,523 - 82,194,769NCBIRnor6.0
Rnor_5.04146,861,354 - 146,861,600UniSTSRnor5.0
Rnor_5.04146,947,149 - 146,947,395UniSTSRnor5.0
RGSC_v3.4480,525,846 - 80,526,092UniSTSRGSC3.4
Celera476,216,656 - 76,216,902UniSTS
Cytogenetic Map4q24UniSTS
REN100620  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,326,180 - 81,326,436 (+)MAPPERmRatBN7.2
Rnor_6.0482,280,545 - 82,280,800NCBIRnor6.0
Rnor_6.0482,194,750 - 82,195,005NCBIRnor6.0
Rnor_5.04146,861,581 - 146,861,836UniSTSRnor5.0
Rnor_5.04146,947,376 - 146,947,631UniSTSRnor5.0
RGSC_v3.4480,526,073 - 80,526,328UniSTSRGSC3.4
Celera476,216,883 - 76,217,138UniSTS
Cytogenetic Map4q24UniSTS
Hoxa7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,317,167 - 81,317,466 (+)MAPPERmRatBN7.2
Rnor_6.0482,271,532 - 82,271,830NCBIRnor6.0
Rnor_6.0482,185,737 - 82,186,035NCBIRnor6.0
Rnor_5.04146,852,568 - 146,852,866UniSTSRnor5.0
Rnor_5.04146,938,363 - 146,938,661UniSTSRnor5.0
RGSC_v3.4480,517,060 - 80,517,358UniSTSRGSC3.4
Celera476,207,880 - 76,208,178UniSTS
Cytogenetic Map4q24UniSTS
Hoxa9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,324,429 - 81,325,829 (+)MAPPERmRatBN7.2
Rnor_6.0482,278,794 - 82,280,193NCBIRnor6.0
Rnor_6.0482,192,999 - 82,194,398NCBIRnor6.0
Rnor_5.04146,859,830 - 146,861,229UniSTSRnor5.0
Rnor_5.04146,945,625 - 146,947,024UniSTSRnor5.0
RGSC_v3.4480,524,322 - 80,525,721UniSTSRGSC3.4
Celera476,215,136 - 76,216,531UniSTS
Cytogenetic Map4q24UniSTS
Hoxa7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,317,430 - 81,317,507 (+)MAPPERmRatBN7.2
Rnor_6.0482,186,000 - 82,186,076NCBIRnor6.0
Rnor_6.0482,271,795 - 82,271,871NCBIRnor6.0
Rnor_5.04146,938,626 - 146,938,702UniSTSRnor5.0
Rnor_5.04146,852,831 - 146,852,907UniSTSRnor5.0
Celera476,208,143 - 76,208,219UniSTS
Cytogenetic Map4q24UniSTS
Hoxa9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2481,326,155 - 81,326,222 (+)MAPPERmRatBN7.2
Rnor_6.0482,194,725 - 82,194,791NCBIRnor6.0
Rnor_6.0482,280,520 - 82,280,586NCBIRnor6.0
Rnor_5.04146,947,351 - 146,947,417UniSTSRnor5.0
Rnor_5.04146,861,556 - 146,861,622UniSTSRnor5.0
Celera476,216,858 - 76,216,924UniSTS
Cytogenetic Map4q24UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
19 1 14 58 54 48 30 32 30 12 195 80 11 33 66 75 18 2 2

Sequence


Ensembl Acc Id: ENSRNOT00000109222   ⟹   ENSRNOP00000089182
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl482,653,825 - 82,662,093 (-)Ensembl
mRatBN7.2 Ensembl481,323,382 - 81,326,358 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000136975   ⟹   ENSRNOP00000099113
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl482,653,847 - 82,659,014 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000169660   ⟹   ENSRNOP00000099654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl482,656,396 - 82,657,171 (-)Ensembl
RefSeq Acc Id: NM_001401868   ⟹   NP_001388797
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8482,653,847 - 82,657,048 (-)NCBI
mRatBN7.2481,323,235 - 81,326,434 (-)NCBI
RefSeq Acc Id: XM_039108678   ⟹   XP_038964606
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8482,653,847 - 82,659,958 (-)NCBI
mRatBN7.2481,323,235 - 81,329,344 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001388797 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964606 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL88155 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000089182.2
  ENSRNOP00000099113.1
  ENSRNOP00000099654.1
RefSeq Acc Id: XP_038964606   ⟸   XM_039108678
- Peptide Label: isoform X1
- UniProtKB: A6K0R3 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000089182   ⟸   ENSRNOT00000109222
RefSeq Acc Id: NP_001388797   ⟸   NM_001401868
- UniProtKB: D3ZSU5 (UniProtKB/TrEMBL),   A6K0R2 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000099654   ⟸   ENSRNOT00000169660
Ensembl Acc Id: ENSRNOP00000099113   ⟸   ENSRNOT00000136975
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZSU5-F1-model_v2 AlphaFold D3ZSU5 1-271 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:1310001 AgrOrtholog
BioCyc Gene G2FUF-44816 BioCyc
Ensembl Genes ENSRNOG00000047484 Ensembl
  ENSRNOG00000064322 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000109222.2 UniProtKB/TrEMBL
  ENSRNOT00000136975.1 UniProtKB/TrEMBL
  ENSRNOT00000169660.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Abd-B_homeobox_TF UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_Hox9 UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Hox9_activation_N UniProtKB/TrEMBL
NCBI Gene 297099 ENTREZGENE
PANTHER AGAP004664-PA UniProtKB/TrEMBL
  HOMEOBOX PROTEIN HOX-A9 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
  Hox9_act UniProtKB/TrEMBL
PhenoGen Hoxa9 PhenoGen
PIRSF Homeobox_Hox9 UniProtKB/TrEMBL
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047484 RatGTEx
  ENSRNOG00000064322 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0ABK0L624_RAT UniProtKB/TrEMBL
  A6K0R2 ENTREZGENE, UniProtKB/TrEMBL
  A6K0R3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZSU5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Hoxa9  homeobox A9  Hoxa9  homeobox A9  Data merged from RGD:149736449 737654 PROVISIONAL
2021-08-09 Hoxa9  homeobox A9      Symbol and Name status set to provisional 45752 PROVISIONAL
2021-03-09 Hoxa9  homeobox A9  LOC103689925  homeobox protein Hox-A9  Data merged from RGD:9112350 737654 PROVISIONAL
2015-07-29 Hoxa9  homeobox A9  LOC100911710  homeobox protein Hox-A9-like  Data merged from RGD:6491245 737654 PROVISIONAL
2015-07-29 Hoxa9  homeobox A9  LOC100909740  homeobox protein Hox-A9-like  Data merged from RGD:6501997 737654 PROVISIONAL
2014-08-25 LOC103689925  homeobox protein Hox-A9      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-17 Hoxa9  homeobox A9  Hoxa9l  homeobox A9-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911710  homeobox protein Hox-A9-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-05 LOC100909740  homeobox protein Hox-A9-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-05-14 Hoxa9l  homeobox A9-like  Hoxa9_predicted  homeo box A9 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Hoxa9_predicted  homeo box A9 (predicted)  RGD1310001_predicted  similar to Hoxa-9 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1310001_predicted  similar to Hoxa-9 (predicted)  LOC297099_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC297099_predicted  similar to Hoxa-9 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL