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Gene: Hoxa6 (homeobox A6) Rattus norvegicus

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Symbol:

Hoxa6

Name:

homeobox A6

RGD ID:

1590236

Description:

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within embryonic skeletal system development. Predicted to be active in nucleus. Orthologous to human HOXA6 (homeobox A6); INTERACTS WITH bisphenol A; boric acid; gentamycin.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

homeobox protein Hox-A6; homeobox protein Hox-A6-like; LOC100909604; LOC685732; similar to Homeobox protein Hox-A6 (Hox-1.2) (M5-4)

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	HOXA6 (homeobox A6)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, OrthoDB, OrthoMCL, Treefam
Mus musculus (house mouse):	Hoxa6 (homeobox A6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hoxa6 (homeobox A6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXA6 (homeobox A6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXA7 (homeobox A7)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxa6 (homeobox A6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXA6 (homeobox A6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HOXA6 (homeobox A6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxa6 (homeobox A6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Hoxa6 (homeobox A6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	HOXA6 (homeobox A6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Hoxa6 (homeobox A6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxb6b (homeobox B6b)	Alliance	DIOPT (Ensembl Compara\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Antp	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	egl-5	Alliance	DIOPT (Ensembl Compara\|InParanoid\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	lin-39	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoInspector)
Drosophila melanogaster (fruit fly):	abd-A	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Drosophila melanogaster (fruit fly):	abd-A	Alliance	DIOPT (Ensembl Compara\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	ftz	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	hoxa6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	hoxa6	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	82,637,024 - 82,639,463 (-)	NCBI	GRCr8	GRCr8		GRCr8
mRatBN7.2	4	81,304,918 - 81,313,184 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	81,306,407 - 81,308,850 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	86,528,202 - 86,530,634 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	82,303,592 - 82,306,020 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	80,730,736 - 80,733,161 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	82,173,478 - 82,183,597 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	82,173,293 - 82,263,302 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	146,840,309 - 146,848,992 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	80,506,290 - 80,508,743 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	76,197,110 - 76,199,563 (-)	NCBI		Celera
Cytogenetic Map	4	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2,3,7,8-tetrachlorodibenzodioxine (ISO)

all-trans-retinoic acid (ISO)

amosite asbestos (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

boric acid (EXP)

cadmium atom (ISO)

crocidolite asbestos (ISO)

dieldrin (ISO)

gentamycin (EXP)

iron dichloride (ISO)

letrozole (ISO)

mono(2-ethylhexyl) phthalate (ISO)

Monobutylphthalate (EXP)

nitrogen dioxide (ISO)

paracetamol (EXP)

sodium arsenite (ISO)

titanium dioxide (ISO)

trichloroethene (EXP)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (ISO)

embryonic skeletal system development (ISO)

Cellular Component

nuclear speck (ISO)

nucleoplasm (ISO)

Molecular Function

sequence-specific double-stranded DNA binding (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.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:7918106	PMID:8033212	PMID:17626057	PMID:32428246

Genomics

Comparative Map Data

Hoxa6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	82,637,024 - 82,639,463 (-)	NCBI	GRCr8	GRCr8		GRCr8
mRatBN7.2	4	81,304,918 - 81,313,184 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	81,306,407 - 81,308,850 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	86,528,202 - 86,530,634 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	82,303,592 - 82,306,020 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	80,730,736 - 80,733,161 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	82,173,478 - 82,183,597 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	82,173,293 - 82,263,302 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	146,840,309 - 146,848,992 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	80,506,290 - 80,508,743 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	76,197,110 - 76,199,563 (-)	NCBI		Celera
Cytogenetic Map	4	q24	NCBI

HOXA6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	27,145,396 - 27,147,774 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	27,145,396 - 27,150,603 (-)	Ensembl			hg38	GRCh38
GRCh37	7	27,185,015 - 27,187,393 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	27,151,641 - 27,153,893 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	7	26,958,355 - 26,960,608	NCBI
Celera	7	27,174,050 - 27,176,302 (-)	NCBI		Celera
Cytogenetic Map	7	p15.2	NCBI
HuRef	7	27,065,590 - 27,067,779 (-)	NCBI		HuRef
CHM1_1	7	27,184,908 - 27,187,099 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	7	27,281,372 - 27,283,742 (-)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	27,236,351 - 27,238,542 (-)	NCBI

Hoxa6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	52,181,838 - 52,185,652 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	52,183,268 - 52,185,702 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	6	52,204,858 - 52,208,672 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	52,206,288 - 52,208,722 (-)	Ensembl			mm10	GRCm38
MGSCv37	6	52,156,364 - 52,158,623 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	6	52,135,948 - 52,138,207 (-)	NCBI		MGSCv36	mm8
Celera	6	52,728,017 - 52,730,275 (-)	NCBI		Celera
Cytogenetic Map	6	B3	NCBI
cM Map	6	25.4	NCBI

Hoxa6
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955410	28,839,924 - 28,844,328 (-)	Ensembl
ChiLan1.0	NW_004955410	28,839,924 - 28,844,328 (-)	NCBI	ChiLan1.0	ChiLan1.0

HOXA6
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	6	31,972,764 - 31,978,440 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	7	80,299,527 - 80,301,622 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	7	27,790,031 - 27,792,348 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	7	27,389,679 - 27,391,997 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	27,389,679 - 27,391,997 (-)	Ensembl			panPan2	panpan1.1

HOXA7
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	14	40,327,918 - 40,334,073 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	14	40,329,127 - 40,330,842 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	39,758,776 - 39,765,091 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	14	40,266,574 - 40,272,893 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	14	40,267,783 - 40,269,502 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	14	40,380,588 - 40,386,885 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	14	40,065,649 - 40,071,956 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	14	40,424,253 - 40,430,564 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Hoxa6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405118	84,561,483 - 84,563,903 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936478	3,772,773 - 3,775,707 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936478	3,773,131 - 3,775,461 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXA6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	18	45,423,530 - 45,429,947 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	18	50,059,189 - 50,063,501 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXA6
(Chlorocebus sabaeus - green monkey)

No map positions available.

Hoxa6
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624739	3,455,606 - 3,460,102 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624739	3,455,513 - 3,460,130 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Hoxa6
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	6	88,849,153 - 88,857,458 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Hoxa6
31 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	113
Count of miRNA genes:	73
Interacting mature miRNAs:	78
Transcripts:	ENSRNOT00000008542, ENSRNOT00000074452
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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	39431983	123203361	Rat
1549843	Bw53	Body weight QTL 53		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	59753119	104753119	Rat
61445	Strs3	Sensitivity to stroke QTL 3	3		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	4	41400577	86400577	Rat
6893678	Bw108	Body weight QTL 108	2.6	0.006	body mass (VT:0001259)	body weight (CMO:0000012)	4	44425024	89425024	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	27730518	170099664	Rat
1357342	Bw40	Body weight QTL 40		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	4	74233320	119233320	Rat
631556	Bp135	Blood pressure QTL 135		0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	80212111	119233320	Rat
1358363	Sradr3	Stress Responsive Adrenal Weight QTL 3	6.19		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	58817672	103817672	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	26234499	134199155	Rat
70167	Bw22	Body weight QTL 22	3.1		body mass (VT:0001259)	body weight (CMO:0000012)	4	74233320	119233320	Rat
1549839	Bw52	Body weight QTL 52		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	71647492	116647492	Rat
6909128	Pancm4	Pancreatic morphology QTL 4	11.35		pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	4	27862204	126119996	Rat
8694439	Bw168	Body weight QTL 168	9.57	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	4	41400603	86400603	Rat
61476	Aia3	Adjuvant induced arthritis QTL 3	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	75939858	140508796	Rat
1641919	Alc22	Alcohol consumption QTL 22		0.0005	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	65060960	127749483	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	45429897	149763204	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	51085655	113588029	Rat
2317586	Eae25	Experimental allergic encephalomyelitis QTL 25	9.300000190734863		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis duration (CMO:0001424)	4	80213634	84338055	Rat
61364	Iddm2	Insulin dependent diabetes mellitus QTL 2			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	80216705	104243248	Rat
2317588	Eae27	Experimental allergic encephalomyelitis QTL 27			nervous system integrity trait (VT:0010566)	percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)	4	69036742	114036742	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	40490442	117737312	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	57613339	151163960	Rat
4889969	Bss96	Bone structure and strength QTL 96	4.9		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	4	57613242	102613242	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	12212457	182430611	Rat
4889972	Bss97	Bone structure and strength QTL 97	5.6		tibia size trait (VT:0100001)	tibia total bone volume (CMO:0001724)	4	57613242	102613242	Rat
6478684	Anxrr30	Anxiety related response QTL 30		0.00087	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	64084079	109084079	Rat
5685009	Bmd86	Bone mineral density QTL 86	3.7		tibia mineral mass (VT:1000283)	bone mineral density (CMO:0001226)	4	57613242	102613242	Rat
2306547	Iddm38	Insulin dependent diabetes mellitus QTL 38			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	68353567	113353567	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	60916264	184426481	Rat
2306545	Iddm39	Insulin dependent diabetes mellitus QTL 39			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	78687630	123687630	Rat
631261	Tcas3	Tongue tumor susceptibility QTL 3	6.88		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	4	11706604	92690519	Rat
6478772	Anxrr49	Anxiety related response QTL 49		0.15488	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	64084079	109084079	Rat
631646	Stl4	Serum triglyceride level QTL 4	6.5	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	4	74169813	134199155	Rat
2312569	Pur19	Proteinuria QTL 19	3.4	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	4	59836842	104836842	Rat
61406	Scwia1	Streptococcal cell wall induced arthritis QTL 1	2.3		joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	4	75939858	140508796	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	45429897	149763204	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	4	61041057	94638356	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5889999	148002343	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	60916264	174095838	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	45429709	157555683	Rat
631651	Bp124	Blood pressure QTL 124	3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	64209744	109209744	Rat
61418	Pia5	Pristane induced arthritis QTL 5	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	63245026	129846354	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	60916264	184426481	Rat
1558651	Swd3	Spike wave discharge measurement QTL 3	4.62	0.000024	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	4	41400577	86400577	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	57664252	127749483	Rat
2306899	Bp338	Blood pressure QTL 338		0.071	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	82336765	127336765	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	65495851	159259805	Rat
631546	Bp86	Blood pressure QTL 86	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	58079875	92690793	Rat
6478743	Anxrr40	Anxiety related response QTL 40		0.83076	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	64084079	109084079	Rat
61434	Cia3	Collagen induced arthritis QTL 3	4.8		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	63224393	108224393	Rat
7394826	Bw126	Body weight QTL 126		0.002	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	63900458	88813920	Rat
12798520	Anxrr55	Anxiety related response QTL 55	4.45	0.01	locomotor behavior trait (VT:0001392)	number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)	4	33538597	116185060	Rat

Markers in Region

UniSTS:467537

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,308,406 - 81,308,741 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,262,772 - 82,263,106	NCBI	Rnor6.0
Rnor_6.0	4	82,176,977 - 82,177,311	NCBI	Rnor6.0
Rnor_5.0	4	146,843,808 - 146,844,142	UniSTS	Rnor5.0
Rnor_5.0	4	146,929,603 - 146,929,937	UniSTS	Rnor5.0
RGSC_v3.4	4	80,508,300 - 80,508,634	UniSTS	RGSC3.4
Celera	4	76,199,120 - 76,199,454	UniSTS
Cytogenetic Map	4	q24	UniSTS

REN100533

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,306,670 - 81,306,931 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,261,026 - 82,261,286	NCBI	Rnor6.0
Rnor_6.0	4	82,175,231 - 82,175,491	NCBI	Rnor6.0
Rnor_5.0	4	146,842,062 - 146,842,322	UniSTS	Rnor5.0
Rnor_5.0	4	146,927,857 - 146,928,117	UniSTS	Rnor5.0
RGSC_v3.4	4	80,506,554 - 80,506,814	UniSTS	RGSC3.4
Celera	4	76,197,374 - 76,197,634	UniSTS
Cytogenetic Map	4	q24	UniSTS

Hoxa6

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,308,677 - 81,308,745 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,177,248 - 82,177,315	NCBI	Rnor6.0
Rnor_6.0	4	82,263,043 - 82,263,110	NCBI	Rnor6.0
Rnor_5.0	4	146,929,874 - 146,929,941	UniSTS	Rnor5.0
Rnor_5.0	4	146,844,079 - 146,844,146	UniSTS	Rnor5.0
Celera	4	76,199,391 - 76,199,458	UniSTS
Cytogenetic Map	4	q24	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	hemolymphoid system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system
9	5	9	25	10	14	14	122	39	10	18	70	62	14

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001191087	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017592893	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC122669	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474011	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000008542 ⟹ ENSRNOP00000008542

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	4	82,260,838 - 82,263,117 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000074452 ⟹ ENSRNOP00000064985

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	81,306,407 - 81,308,850 (-)	Ensembl
Rnor_6.0 Ensembl	4	82,174,967 - 82,177,420 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000082933 ⟹ ENSRNOP00000075013

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	4	82,173,293 - 82,263,302 (-)	Ensembl

RefSeq Acc Id:

NM_001191087 ⟹ NP_001178016

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	82,637,024 - 82,639,463 (-)	NCBI
mRatBN7.2	4	81,306,407 - 81,308,850 (-)	NCBI
Rnor_6.0	4	82,174,967 - 82,177,420 (-)	NCBI
Rnor_5.0	4	146,840,309 - 146,848,992 (-)	NCBI
Celera	4	76,197,110 - 76,199,563 (-)	NCBI

Sequence:

show sequence

TTCGGCCATCCAGAAACAAACCAGTTCGATGACTACTAATAGTTATAGCCAGATGTACTAATAC
ACAACAAATCACAGTCCTGCAGAGGGGCGCGCAAATGAGTTCCTATTTTGTGAATCCCACTTTC
CCTGGGAGCCTGCCCAGCGGCCAGGACTCCTTCTTGGGCCAGCTGCCCCTCTACCCGGCCGGCT
ATGACGCGCTGAGGCCCTTCCCGGCCTCTTATGGGGCGTCGAGTCTTCCGGACAAGACATACAC
CTCACCTTGTTTCTACCAACAGTCCAACTCGGTCCTGGCCTGCAACCGGGCATCCTACGAGTAC
GGGGCCTCATGTTTCTATTCTGATAAGGACCTCAGTGGCGCCTCACCCTCGGGCAATAGCAAGC
AGAGGGGCCCCGGGGACTACCTGCACTTTTCTCCCGAGCAGCAGTACAAACCTGACAGCAGCAG
CGTGCAGGGCAAAGCCCTCCATGAGGAAGGCACCGACCGGAAGTACACAAGCCCTGTTTACCCC
TGGATGCAGCGGATGAATTCCTGTGCGGGTGCTGTGTATGGGAGTCACGGGCGCAGAGGCCGCC
AGACCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAATTCCACTTCAACCGCTACCTGAC
TCGGCGGCGCCGCATCGAGATCGCCAACGCGCTCTGCCTCACCGAGCGCCAGATCAAGATCTGG
TTCCAGAATCGGCGCATGAAGTGGAAAAAGGAAAATAAACTCATCAATTCCACGCAGGCCAGCG
GGGAAGACTCTGAGGCCAAGGCGGGCGAGTAGACTCCAGGCAGGGACCAGGCCATCGTTGTAAC
CTCTATTGGCTTTGCCCCCTGGTGCCCTTGCCTGCTCCCCAAGT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001178016	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL88163	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001178016 ⟸ NM_001191087

- UniProtKB:

G3V6T4 (UniProtKB/TrEMBL), A6K0Q8 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSSYFVNPTFPGSLPSGQDSFLGQLPLYPAGYDALRPFPASYGASSLPDKTYTSPCFYQQSNSV
LACNRASYEYGASCFYSDKDLSGASPSGNSKQRGPGDYLHFSPEQQYKPDSSSVQGKALHEEGT
DRKYTSPVYPWMQRMNSCAGAVYGSHGRRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIANAL
CLTERQIKIWFQNRRMKWKKENKLINSTQASGEDSEAKAGE

hide sequence

Ensembl Acc Id:

ENSRNOP00000075013 ⟸ ENSRNOT00000082933

Ensembl Acc Id:

ENSRNOP00000064985 ⟸ ENSRNOT00000074452

Ensembl Acc Id:

ENSRNOP00000008542 ⟸ ENSRNOT00000008542

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-G3V6T4-F1-model_v2	AlphaFold	G3V6T4	1-233	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1590236	AgrOrtholog
BioCyc Gene	G2FUF-44818	BioCyc
Ensembl Genes	ENSRNOG00000048917	Ensembl
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Antp_homeobox	UniProtKB/TrEMBL
	Homeobox	UniProtKB/TrEMBL
	Homeobox_antennapedia	UniProtKB/TrEMBL
	Homeobox_Antennapedia_CS	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_eu	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
KEGG Report	rno:685732	UniProtKB/TrEMBL
NCBI Gene	685732	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN HOX	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN HOX-A6	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
PhenoGen	Hoxa6	PhenoGen
PRINTS	ANTENNAPEDIA	UniProtKB/TrEMBL
	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	ANTENNAPEDIA	UniProtKB/TrEMBL
	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000048917	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A6K0Q8	ENTREZGENE, UniProtKB/TrEMBL
	G3V6T4	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	Hoxa6	homeobox A6	LOC100909604	homeobox protein Hox-A6-like	Data merged from RGD:6502601	737654	PROVISIONAL
2012-07-05	LOC100909604	homeobox protein Hox-A6-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-03-05	Hoxa6	homeobox A6	LOC685732	similar to Homeobox protein Hox-A6 (Hox-1.2) (M5-4)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-01-09	LOC685732	similar to Homeobox protein Hox-A6 (Hox-1.2) (M5-4)	LOC681956	similar to Homeobox protein Hox-A6 (Hox-1.2) (M5-4)	Data merged from RGD:1589323	1643240	APPROVED
2006-11-20	LOC685732	similar to Homeobox protein Hox-A6 (Hox-1.2) (M5-4)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-19	LOC681956	similar to Homeobox protein Hox-A6 (Hox-1.2) (M5-4)			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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