Hoxa13 (homeo box A13) - Rat Genome Database

Name: Hoxa13
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Hoxa13 (homeo box A13) Rattus norvegicus

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Symbol:

Hoxa13

Name:

homeo box A13

RGD ID:

1562483

Description:

Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in embryonic hindgut morphogenesis; prostate gland development; and response to testosterone. Predicted to be located in chromosome; intermediate filament cytoskeleton; and nucleoplasm. Biomarker of hypospadias. Human ortholog(s) of this gene implicated in Guttmacher syndrome and hand-foot-genital syndrome. Orthologous to human HOXA13 (homeobox A13); INTERACTS WITH 3,7-dihydropurine-6-thione; bisphenol A; dibutyl phthalate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

homeobox A13; homeobox protein Hox-A13; homeobox protein Hox-A13-like; LOC100910298; LOC103692142; LOC500129; RGD1562483; similar to transcription factor HOXA13

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):	HOXA13 (homeobox A13)	HGNC	Ensembl, HomoloGene, Inparanoid
Mus musculus (house mouse):	Hoxa13 (homeobox A13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hoxa13 (homeobox A13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXA13 (homeobox A13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXA13 (homeobox A13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxa13 (homeobox A13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXA13 (homeobox A13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HOXA13 (homeobox A13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxa13 (homeobox A13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	HOXA13 (homeobox A13)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Hoxa13 (homeobox A13)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxa13a (homeobox A13a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	hoxa13b (homeobox A13b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	hoxa13	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	82,689,566 - 82,691,701 (-)	NCBI		GRCr8
mRatBN7.2	4	81,358,956 - 81,361,091 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	81,358,956 - 81,361,091 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	86,580,795 - 86,582,928 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	82,356,180 - 82,358,313 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	80,783,284 - 80,785,419 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	82,313,383 - 82,315,550 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	82,228,017 - 82,229,397 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	146,980,144 - 146,982,279 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	80,558,841 - 80,561,053	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	4	76,249,534 - 76,251,232 (-)	NCBI		Celera
Cytogenetic Map	4	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Anorectal Malformations (IEP)

Congenital Hand Deformities (ISO)

Female Urogenital Diseases (ISO)

genetic disease (ISO)

Guttmacher syndrome (ISO)

hand-foot-genital syndrome (ISO,ISS)

hepatocellular carcinoma (ISO)

hypospadias (IEP)

pleomorphic xanthoastrocytoma (ISO)

Urogenital Abnormalities (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

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

3,7-dihydropurine-6-thione (EXP)

4-hydroperoxycyclophosphamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

amosite asbestos (ISO)

aristolochic acid A (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

chlorpyrifos (ISO)

copper atom (ISO)

copper(0) (ISO)

crocidolite asbestos (ISO)

diazinon (ISO)

dibutyl phthalate (EXP)

epoxiconazole (ISO)

Ethylenethiourea (EXP)

fonofos (ISO)

fulvestrant (ISO)

genistein (ISO)

hydrogen peroxide (ISO)

mercaptopurine (EXP)

mono(2-ethylhexyl) phthalate (ISO)

parathion (ISO)

purine-6-thiol (EXP)

resveratrol (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sotorasib (ISO)

terbufos (ISO)

testosterone (EXP)

thapsigargin (ISO)

titanium dioxide (ISO)

trametinib (ISO)

tunicamycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anatomical structure morphogenesis (ISO)

animal organ morphogenesis (ISO)

artery morphogenesis (ISO)

branching involved in prostate gland morphogenesis (ISO)

embryonic forelimb morphogenesis (ISO)

embryonic hindgut morphogenesis (IMP)

endothelial cell fate specification (ISO)

endothelial cell morphogenesis (ISO)

inner ear development (ISO)

male genitalia development (ISO)

mesenchymal cell apoptotic process (ISO)

mitotic nuclear division (ISO)

positive regulation of mesenchymal cell apoptotic process (ISO)

positive regulation of mitotic nuclear division (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

prostate gland development (IEP)

regulation of BMP signaling pathway (ISO)

response to testosterone (IEP)

tissue homeostasis (ISO)

transcription by RNA polymerase II (ISO)

vasculogenesis (ISO)

ventricular septum development (ISO)

Cellular Component

chromosome (IEA,ISO)

intermediate filament cytoskeleton (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (ISO)

Molecular Function

cis-regulatory region sequence-specific DNA binding (ISO)

DNA binding (ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO)

DNA-binding transcription factor activity (ISO)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (ISO)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

transcription cis-regulatory region 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.	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.
3.	Sonic hedgehog, BMP4, and Hox genes in the development of anorectal malformations in Ethylenethiourea-exposed fetal rats.	Mandhan P, etal., J Pediatr Surg. 2006 Dec;41(12):2041-5.
4.	Mutation of HOXA13 in hand-foot-genital syndrome.	Mortlock DP and Innis JW, Nat Genet. 1997 Feb;15(2):179-80.
5.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
6.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
8.	Comprehensive gene review and curation	RGD comprehensive gene curation
9.	Maternal exposure to di-n-butyl phthalate (DBP) induces combined anorectal and urogenital malformations in male rat offspring.	Zhu YP, etal., Reprod Toxicol. 2016 Jun;61:169-76. doi: 10.1016/j.reprotox.2016.04.007. Epub 2016 Apr 11.

Additional References at PubMed

PMID:10210434	PMID:12783783	PMID:15342482	PMID:15617687	PMID:15733672	PMID:16314414	PMID:18483557	PMID:19168674	PMID:21829694	PMID:23332764	PMID:27706137

Genomics

Comparative Map Data

Hoxa13
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	82,689,566 - 82,691,701 (-)	NCBI		GRCr8
mRatBN7.2	4	81,358,956 - 81,361,091 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	81,358,956 - 81,361,091 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	86,580,795 - 86,582,928 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	82,356,180 - 82,358,313 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	80,783,284 - 80,785,419 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	82,313,383 - 82,315,550 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	82,228,017 - 82,229,397 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	146,980,144 - 146,982,279 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	80,558,841 - 80,561,053	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	4	76,249,534 - 76,251,232 (-)	NCBI		Celera
Cytogenetic Map	4	q24	NCBI

HOXA13
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	27,194,364 - 27,200,091 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	27,193,503 - 27,200,091 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	7	27,233,983 - 27,239,710 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	27,203,024 - 27,206,250 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	7	27,009,738 - 27,012,936	NCBI
Celera	7	27,225,437 - 27,228,662 (-)	NCBI		Celera
Cytogenetic Map	7	p15.2	NCBI
HuRef	7	27,117,064 - 27,119,882 (-)	NCBI		HuRef
CHM1_1	7	27,236,223 - 27,239,448 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	7	27,330,371 - 27,336,079 (-)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	27,287,684 - 27,290,909 (-)	NCBI

Hoxa13
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	52,235,833 - 52,237,865 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	52,234,674 - 52,237,788 (-)	Ensembl		GRCm39 Ensembl
GRCm38	6	52,258,853 - 52,260,880 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	52,257,694 - 52,260,880 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	52,208,852 - 52,210,874 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	52,188,436 - 52,190,458 (-)	NCBI		MGSCv36	mm8
Celera	6	52,780,486 - 52,782,142 (-)	NCBI		Celera
Cytogenetic Map	6	B3	NCBI
cM Map	6	25.41	NCBI

Hoxa13
(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	28,890,171 - 28,893,515 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955410	28,887,952 - 28,893,515 (-)	NCBI	ChiLan1.0	ChiLan1.0

HOXA13
(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	32,026,168 - 32,029,267 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	7	80,346,803 - 80,353,992 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	7	27,838,656 - 27,844,562 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	7	27,441,171 - 27,443,793 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

HOXA13
(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	40,371,234 - 40,375,261 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	14	40,373,059 - 40,375,980 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	39,801,720 - 39,806,138 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	14	40,309,583 - 40,314,003 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	14	40,311,665 - 40,314,704 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	14	40,423,492 - 40,427,909 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	14	40,108,556 - 40,112,977 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	14	40,467,202 - 40,471,624 (-)	NCBI		UU_Cfam_GSD_1.0

Hoxa13
(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	84,612,984 - 84,615,546 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936478	3,824,715 - 3,827,277 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936478	3,824,715 - 3,827,277 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXA13
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	18	45,373,440 - 45,376,325 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	18	45,373,340 - 45,379,046 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	18	50,007,054 - 50,008,334 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXA13
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	21	31,168,239 - 31,175,960 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	21	31,168,793 - 31,173,056 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666042	73,559,316 - 73,565,124 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hoxa13
(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	3,406,436 - 3,410,851 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624739	3,405,860 - 3,410,426 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Hoxa13
2 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	78
Count of miRNA genes:	69
Interacting mature miRNAs:	70
Transcripts:	ENSRNOT00000010441
Prediction methods:	Microtar, Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

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	38465774	146803430	Rat
1549843	Bw53	Body weight QTL 53		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	61697658	103194791	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	40433388	85433388	Rat
6893678	Bw108	Body weight QTL 108	2.6	0.006	body mass (VT:0001259)	body weight (CMO:0000012)	4	43457976	88457976	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	26775591	168368347	Rat
1357342	Bw40	Body weight QTL 40		0.001	body mass (VT:0001259)	body weight (CMO:0000012)	4	76647384	117676292	Rat
631556	Bp135	Blood pressure QTL 135		0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	78881294	117676292	Rat
1358363	Sradr3	Stress Responsive Adrenal Weight QTL 3	6.19		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	57486946	102486946	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	70362013	132642728	Rat
70167	Bw22	Body weight QTL 22	3.1		body mass (VT:0001259)	body weight (CMO:0000012)	4	76647384	117676292	Rat
1549839	Bw52	Body weight QTL 52		0.0001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	61697658	115089733	Rat
724522	Bp146	Blood pressure QTL 146	2.2	0.0021	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	73630210	118630210	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	40433414	85433414	Rat
1641919	Alc22	Alcohol consumption QTL 22		0.0005	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	81192555	126192555	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	44463908	148090542	Rat
2300179	Bmd50	Bone mineral density QTL 50	5.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	4	60928534	105928534	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	50119848	146803430	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	4	62933508	114921294	Rat
2317586	Eae25	Experimental allergic encephalomyelitis QTL 25	9.300000190734863		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis duration (CMO:0001424)	4	78882817	83007655	Rat
61364	Iddm2	Insulin dependent diabetes mellitus QTL 2			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	78885890	102684881	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	39524264	116179656	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	56647873	149491524	Rat
1578657	Bss12	Bone structure and strength QTL 12	8.9		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	4	60220938	105220938	Rat
1578658	Bss13	Bone structure and strength QTL 13	8		femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	4	60220938	105220938	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	11320076	180699135	Rat
6478684	Anxrr30	Anxiety related response QTL 30		0.00087	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
2302051	Pia28	Pristane induced arthritis QTL 28	5.3	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)	4	73630210	118630210	Rat
8552782	Vie1	Viral induced encephalitis QTL 1	26.4		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	34430484	82490359	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	59948935	154902892	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	10814170	91360527	Rat
2312567	Glom19	Glomerulus QTL 19	1.9	0.006	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	4	45456990	146803430	Rat
738015	Pia9	Pristane induced arthritis QTL 9	4.5	0.048	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	80694870	125694870	Rat
6478772	Anxrr49	Anxiety related response QTL 49		0.15488	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
631646	Stl4	Serum triglyceride level QTL 4	6.5	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	4	73169846	132642728	Rat
2312569	Pur19	Proteinuria QTL 19	3.4	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	4	65882107	96130297	Rat
8655961	Kidm43	Kidney mass QTL 43	18		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	36303261	103194984	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	44463908	148090542	Rat
634344	Hcar7	Hepatocarcinoma resistance QTL 7	7.8		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	4	70808386	115808386	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5214602	146446691	Rat
8552801	Bw143	Body weight QTL 143	7.3		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	4	34430484	82490359	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	59948935	154902892	Rat
8552807	Vie4	Viral induced encephalitis QTL 4	7.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	62933508	82490359	Rat
631662	Hcar2	Hepatocarcinoma resistance QTL 2	3.1	0.0003	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	78878504	123878504	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	44463720	155883716	Rat
61418	Pia5	Pristane induced arthritis QTL 5	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	62277855	128289560	Rat
631651	Bp124	Blood pressure QTL 124	3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	62879517	107879517	Rat
8552809	Vie5	Viral induced encephalitis QTL 5	25.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	34430484	82490359	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	59948935	154902892	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	58432133	92991462	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	56698790	126192555	Rat
2306899	Bp338	Blood pressure QTL 338		0.071	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	81006124	120102625	Rat
631546	Bp86	Blood pressure QTL 86	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	57114432	91360801	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	64528739	157573521	Rat
6478743	Anxrr40	Anxiety related response QTL 40		0.83076	defecation behavior trait (VT:0010462)	defecation rate (CMO:0000998)	4	62753847	107753847	Rat
7394826	Bw126	Body weight QTL 126		0.002	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	62933269	87483707	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	32583980	114627242	Rat

Markers in Region

Hoxa13

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,359,291 - 81,359,494 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,313,649 - 82,313,851	NCBI	Rnor6.0
Rnor_6.0	4	82,228,125 - 82,228,327	NCBI	Rnor6.0
Rnor_5.0	4	146,894,956 - 146,895,158	UniSTS	Rnor5.0
Rnor_5.0	4	146,980,480 - 146,980,682	UniSTS	Rnor5.0
RGSC_v3.4	4	80,559,177 - 80,559,379	UniSTS	RGSC3.4
Celera	4	76,249,870 - 76,250,072	UniSTS
Cytogenetic Map	4	q24	UniSTS

REN99807

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,182,588 - 81,182,820 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,051,259 - 82,051,490	NCBI	Rnor6.0
Rnor_6.0	4	82,230,363 - 82,230,594	NCBI	Rnor6.0
Rnor_5.0	4	146,897,194 - 146,897,425	UniSTS	Rnor5.0
Rnor_5.0	4	146,718,090 - 146,718,321	UniSTS	Rnor5.0
RGSC_v3.4	4	80,382,483 - 80,382,714	UniSTS	RGSC3.4
Celera	4	76,074,173 - 76,074,404	UniSTS

REN100771

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	81,360,339 - 81,360,566 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	82,229,173 - 82,229,399	NCBI	Rnor6.0
Rnor_5.0	4	146,981,528 - 146,981,754	UniSTS	Rnor5.0
Rnor_5.0	4	146,896,004 - 146,896,230	UniSTS	Rnor5.0
RGSC_v3.4	4	80,560,225 - 80,560,451	UniSTS	RGSC3.4
Celera	4	76,250,918 - 76,251,144	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	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
12	6	6	21	24	20	8	6	8	6	63	29	9	8	32	12

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001271355	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_002726375	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003749759	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003749760	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_575481	(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:

ENSRNOT00000089432 ⟹ ENSRNOP00000073843

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	81,358,956 - 81,361,091 (-)	Ensembl
Rnor_6.0 Ensembl	4	82,228,017 - 82,229,397 (-)	Ensembl

RefSeq Acc Id:

NM_001271355 ⟹ NP_001258284

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	82,689,566 - 82,691,701 (-)	NCBI
mRatBN7.2	4	81,358,956 - 81,361,091 (-)	NCBI
Rnor_5.0	4	146,980,144 - 146,982,279 (-)	NCBI
Celera	4	76,249,534 - 76,251,232 (-)	NCBI

Sequence:

show sequence

GTCTTCTCCATGCGGCTCGGGCTATGACAGCCTCCGTGCTCCTCCACCCCCGCTGGATCGAGCC
CACCGTCATGTTTCTCTACGACAACGGCGGCGGCCTGGTGGCCGACGAGCTCAACAAGAACATG
GAAGGGGCGGCGGCGGCGGCAGCGGCGGCGGCAGCGGCAGCGGCGGCGGGAGCTGGGGGCGGGG
GCTTCCCCCACCCGGCTGCGGCGGCCGCGGGGGGCAACTTCTCGGTGGCCGCAGCGGCTGCCGC
CGCCGCCGCCGCCGCGGCCAACCAGTGCCGCAACCTGATGGCGCATCCCGCACCACTGGCGCCG
GGCGCCGCGGCCGCGTACAGCAGCGCCCCGGGGGAGGCGCCCCCGACCGCCGCCGCCGCCGCCG
CTGCCGCTGCTGCCGCCGCCGCCGCCGCGGCTGCCGCGTCGTCGTCGGGAGGGCCCGGACCGGC
GGGGCCCGCGGGTGCCGAGGCCGCCAAGCAGTGTAGTCCCTGCTCGGCGGCGGCACAAAGCTCG
TCGGGTCCCGCGGCGCTGCCCTATGGCTACTTCGGCAGCGGCTACTACCCGTGCGCCCGCATGG
GCCCGCACCCCAACGCCATCAAGTCCTGCGCGCAGCCTGCCTCGGCTGCGGCCGCCTTCGCCGA
CAAGTACATGGACACCGCCGGCCCCGCGGCCGAGGAGTTCAGCTCCCGCGCCAAGGAGTTTGCC
TTCTACCACCAGGGCTACGCAGCCGGGCCTTACCACCACCACCAGCCCGTGCCCGGCTATCTGG
ATATGCCAGTGGTTCCGGGGCTCGGGGGTCCTGGCGAGTCGCGCCACGAGCCTCTGGGGCTTCC
TATGGAAAGCTATCAGCCCTGGGCTCTGCCCAACGGCTGGAACGGCCAAATGTACTGCCCCAAA
GAGCAGACGCAGCCTCCCCACCTCTGGAAGTCCACTCTGCCCGACGTCGTCTCCCATCCTTCAG
ACGCCAGCTCCTATAGGAGGGGGAGAAAGAAGCGGGTGCCTTACACTAAGGTGCAGTTGAAAGA
ACTCGAACGGGAATACGCTACGAACAAATTCATTACCAAGGACAAACGGAGGAGGATATCAGCC
ACAACGAACCTCTCTGAGAGGCAGGTCACAATCTGGTTCCAGAACAGGAGGGTCAAAGAGAAAA
AAGTCATCAATAAACTCAAGACCACGAGTTAATGGATTAAAATGCGGAGTAGAGGGCAGCTTGA
AGAAACGCGTAAGGACTTGTTTCTTTGCCCAGATCATAAGAATGCGTAATAATAACTGAAGAAT
GGGATAGAGAGACACTGACGTTTTGCTCTCCTAAGGGGACTCCTCTTCAATGGAATCTACAATT
AAAAAAAAAAAACTTAAGAAATGGTAAAGATTGCCAGTTCTCCCGACAAACCCACCAGACCGTT
AAGT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001258284	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL88149	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000073843.2

RefSeq Acc Id:

NP_001258284 ⟸ NM_001271355

- UniProtKB:

A0A0G2K6K0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MTASVLLHPRWIEPTVMFLYDNGGGLVADELNKNMEGAAAAAAAAAAAAAAGAGGGGFPHPAAA
AAGGNFSVAAAAAAAAAAAANQCRNLMAHPAPLAPGAAAAYSSAPGEAPPTAAAAAAAAAAAAA
AAAAASSSGGPGPAGPAGAEAAKQCSPCSAAAQSSSGPAALPYGYFGSGYYPCARMGPHPNAIK
SCAQPASAAAAFADKYMDTAGPAAEEFSSRAKEFAFYHQGYAAGPYHHHQPVPGYLDMPVVPGL
GGPGESRHEPLGLPMESYQPWALPNGWNGQMYCPKEQTQPPHLWKSTLPDVVSHPSDASSYRRG
RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLKT
TS

hide sequence

Ensembl Acc Id:

ENSRNOP00000073843 ⟸ ENSRNOT00000089432

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-A0A0G2K5C1-F1-model_v2	AlphaFold	A0A0G2K5C1	1-386	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:1562483	AgrOrtholog
BioCyc Gene	G2FUF-44808	BioCyc
Ensembl Genes	ENSRNOG00000057061	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000089432.2	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	AP_axis_regulatory_Homeobox	UniProtKB/TrEMBL
	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	HoxA13_N	UniProtKB/TrEMBL
KEGG Report	rno:500129	UniProtKB/TrEMBL
NCBI Gene	500129	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN HOX-A13	UniProtKB/TrEMBL
	SEGMENTATION PROTEIN FUSHI TARAZU-LIKE PROTEIN	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
	HoxA13_N	UniProtKB/TrEMBL
PhenoGen	Hoxa13	PhenoGen
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000057061	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A0A0G2K6K0	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	Hoxa13	homeo box A13	LOC103692142	homeobox protein Hox-A13	Data merged from RGD:9360896	737654	PROVISIONAL
2015-07-21	Hoxa13	homeo box A13	LOC100910298	homeobox protein Hox-A13-like	Data merged from RGD:6499266	737654	APPROVED
2014-08-25	LOC103692142	homeobox protein Hox-A13			Symbol and Name status set to provisional	70820	PROVISIONAL
2012-07-05	LOC100910298	homeobox protein Hox-A13-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-04-30	Hoxa13	homeo box A13	Hoxa13_predicted	homeo box A13 (predicted)	'predicted' is removed	2292626	APPROVED
2007-02-06	Hoxa13_predicted	homeo box A13 (predicted)	RGD1562483_predicted	similar to transcription factor HOXA13 (predicted)	Symbol and Name updated to reflect Human and Mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1562483_predicted	similar to transcription factor HOXA13 (predicted)	LOC500129	similar to transcription factor HOXA13	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC500129	similar to transcription factor HOXA13			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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