Nkx3-2 (NK3 homeobox 2) - Rat Genome Database

Name: Nkx3-2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Nkx3-2 (NK3 homeobox 2) Mus musculus

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Symbol:

Nkx3-2

Name:

NK3 homeobox 2

RGD ID:

1621641

MGI Page

MGI

Description:

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of chondrocyte differentiation and negative regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including intestinal epithelial cell development; middle ear morphogenesis; and skeletal system development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and limb. Orthologous to human NKX3-2 (NK3 homeobox 2).

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

bagpipe homeobox gene 1 homolog; bagpipe homeobox protein homolog 1; Bap; Bapx1; homeobox protein NK-3 homolog B; homeobox protein Nkx-3.2; homeodomain protein Nkx-3.2; Nkx-3.; Nkx-3.2; NKX3.2

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):	NKX3-2 (NK3 homeobox 2)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Rattus norvegicus (Norway rat):	Nkx3-2 (NK3 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Nkx3-2 (NK3 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NKX3-2 (NK3 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NKX3-2 (NK3 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nkx3-2 (NK3 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NKX3-2 (NK3 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NKX3-2 (NK3 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nkx3-2 (NK3 homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NKX3-2 (NK3 homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Rattus norvegicus (Norway rat):	Nkx3-2 (NK3 homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	nkx3.2 (NK3 homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid\|ZFIN)
Drosophila melanogaster (fruit fly):	bap	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	nkx3-2	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCm39 - Mouse Genome Assembly GRCm39

Position:

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	41,918,826 - 41,921,563 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	41,918,826 - 41,921,844 (-)	Ensembl		GRCm39 Ensembl
GRCm38	5	41,761,483 - 41,764,220 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	41,761,483 - 41,764,501 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	42,152,722 - 42,155,459 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	42,049,696 - 42,052,468 (-)	NCBI		MGSCv36	mm8
Celera	5	39,220,946 - 39,223,683 (-)	NCBI		Celera
Cytogenetic Map	5	B3	NCBI
cM Map	5	22.58	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

connective tissue disease (ISO)

genetic disease (ISO)

Spondylo-Megaepiphyseal-Metaphyseal Dysplasia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

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

acrylamide (EXP)

aflatoxin B1 (ISO)

aristolochic acid A (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (EXP)

copper(II) sulfate (ISO)

diarsenic trioxide (ISO)

lipopolysaccharide (EXP)

N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (ISO)

pirinixic acid (ISO)

potassium dichromate (EXP)

silicon dioxide (ISO)

sunitinib (ISO)

Theaflavin 3,3'-digallate (ISO)

triclosan (ISO)

valproic acid (ISO)

zinc sulfate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

animal organ development (IMP)

animal organ formation (IMP)

cell differentiation (IBA)

determination of left/right symmetry (IMP)

digestive system development (IMP)

embryonic skeletal system development (IMP)

intestinal epithelial cell development (IGI)

middle ear morphogenesis (IMP)

negative regulation of apoptotic process (IMP)

negative regulation of chondrocyte differentiation (IMP)

negative regulation of transcription by RNA polymerase II (IDA)

pancreas development (IMP)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IBA)

skeletal system development (IMP)

skeletal system morphogenesis (IMP)

spleen development (IMP)

Cellular Component

nucleoplasm (TAS)

nucleus (IBA)

Molecular Function

DNA binding (IEA)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

DNA-binding transcription repressor activity, RNA polymerase II-specific (IDA)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,IDA)

sequence-specific double-stranded DNA binding (ISO)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

abnormal axial skeleton morphology (IAGP)

abnormal basicranium morphology (IAGP)

abnormal basioccipital bone morphology (IAGP)

abnormal basisphenoid bone morphology (IAGP)

abnormal bone ossification (IAGP)

abnormal cartilage development (IAGP)

abnormal cartilage morphology (IAGP)

abnormal cervical atlas morphology (IAGP)

abnormal cervical axis morphology (IAGP)

abnormal cervical vertebrae morphology (IAGP)

abnormal craniofacial bone morphology (IAGP)

abnormal cranium morphology (IAGP)

abnormal digestive organ placement (IAGP)

abnormal digestive system development (IAGP)

abnormal digestive system morphology (IAGP)

abnormal enteric neuron morphology (IAGP)

abnormal enterocyte proliferation (IAGP)

abnormal exoccipital bone morphology (IAGP)

abnormal forestomach-glandular stomach junction morphology (IAGP)

abnormal gastric parietal cell morphology (IAGP)

abnormal hyoid bone body morphology (IAGP)

abnormal intervertebral disk morphology (IAGP)

abnormal intestinal enteroendocrine cell morphology (IAGP)

abnormal intestinal goblet cell morphology (IAGP)

abnormal intestinal smooth muscle morphology (IAGP)

abnormal intestine development (IAGP)

abnormal intestine physiology (IAGP)

abnormal left-right axis patterning (IAGP)

abnormal lumbar vertebrae morphology (IAGP)

abnormal malleus morphology (IAGP)

abnormal middle ear morphology (IAGP)

abnormal middle ear ossicle morphology (IAGP)

abnormal neurocranium morphology (IAGP)

abnormal notochord morphology (IAGP)

abnormal odontoid process morphology (IAGP)

abnormal pancreas development (IAGP)

abnormal rib morphology (IAGP)

abnormal sclerotome morphology (IAGP)

abnormal skeleton morphology (IAGP)

abnormal stomach epithelium morphology (IAGP)

abnormal stomach glandular epithelium morphology (IAGP)

abnormal stomach morphology (IAGP)

abnormal stomach pyloric region morphology (IAGP)

abnormal stomach smooth muscle circular layer morphology (IAGP)

abnormal supraoccipital bone morphology (IAGP)

abnormal thoracic cavity morphology (IAGP)

abnormal thoracic vertebrae morphology (IAGP)

abnormal tympanic ring morphology (IAGP)

abnormal vertebrae development (IAGP)

abnormal vertebrae morphology (IAGP)

abnormal vertebral arch development (IAGP)

abnormal vertebral arch morphology (IAGP)

abnormal vertebral body development (IAGP)

abnormal vertebral body morphology (IAGP)

abnormal vertebral column morphology (IAGP)

absent arcus anterior (IAGP)

absent basioccipital bone (IAGP)

absent basisphenoid bone (IAGP)

absent gonial bone (IAGP)

absent intervertebral disk (IAGP)

absent spleen (IAGP)

absent supraoccipital bone (IAGP)

absent ventral tubercle of atlas (IAGP)

absent vertebral body (IAGP)

axial skeleton hypoplasia (IAGP)

barrel chest (IAGP)

basioccipital bone hypoplasia (IAGP)

basisphenoid bone hypoplasia (IAGP)

decreased body height (IAGP)

decreased body length (IAGP)

decreased cell proliferation (IAGP)

gonial bone hypoplasia (IAGP)

kinked tail (IAGP)

lethality throughout fetal growth and development, complete penetrance (IAGP)

neonatal lethality, complete penetrance (IAGP)

no abnormal phenotype detected (IAGP)

perinatal lethality, complete penetrance (IAGP)

persistence of notochord tissue (IAGP)

respiratory distress (IAGP)

short tail (IAGP)

short vertebral column (IAGP)

small basioccipital bone (IAGP)

small basisphenoid bone (IAGP)

small caudal vertebrae (IAGP)

small exoccipital bone (IAGP)

small forestomach (IAGP)

small stomach (IAGP)

small vertebrae (IAGP)

thick tail (IAGP)

vertebral body hypoplasia (IAGP)

vertebral compression (IAGP)

References

References - curated

#	Reference Title	Reference Citation
1.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
2.	Mouse MP Annotation Import Pipeline	RGD automated import pipeline
3.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:9256352	PMID:9271676	PMID:9271679	PMID:9344671	PMID:9621431	PMID:10449756	PMID:10469600	PMID:10572046	PMID:10843805	PMID:10886375	PMID:10926756	PMID:10944221
PMID:11440720	PMID:11517919	PMID:11523821	PMID:12163410	PMID:12204261	PMID:12441295	PMID:12477932	PMID:12490554	PMID:12646629	PMID:12746429	PMID:14504237	PMID:14681479
PMID:14973294	PMID:15024065	PMID:15329346	PMID:15618518	PMID:15703179	PMID:15829524	PMID:15944191	PMID:15951842	PMID:16221728	PMID:16251273	PMID:16421188	PMID:16602821
PMID:16678811	PMID:16791844	PMID:16912273	PMID:17078065	PMID:17310243	PMID:17477400	PMID:17586487	PMID:17855428	PMID:18287559	PMID:18452913	PMID:19208343	PMID:19217813
PMID:19306868	PMID:19325248	PMID:19520072	PMID:19762422	PMID:20430747	PMID:21267068	PMID:21303853	PMID:21307095	PMID:21606193	PMID:21677750	PMID:21750033	PMID:21873635
PMID:21909240	PMID:21913311	PMID:22093831	PMID:22216134	PMID:22507129	PMID:22511961	PMID:22768305	PMID:22902530	PMID:23473983	PMID:23645682	PMID:24948604	PMID:24952961
PMID:25902370	PMID:26057579	PMID:27253464	PMID:27381226	PMID:27892540	PMID:27986952	PMID:28479297	PMID:28943241	PMID:29031732	PMID:29246974	PMID:29700203	PMID:30630826
PMID:30771302	PMID:31167144	PMID:31169497	PMID:31604927	PMID:31953387	PMID:32155439	PMID:32857951	PMID:33057429	PMID:34330063	PMID:34499867	PMID:35858546	PMID:36941669
PMID:36967785

Genomics

Comparative Map Data

Nkx3-2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	41,918,826 - 41,921,563 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	41,918,826 - 41,921,844 (-)	Ensembl		GRCm39 Ensembl
GRCm38	5	41,761,483 - 41,764,220 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	41,761,483 - 41,764,501 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	42,152,722 - 42,155,459 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	42,049,696 - 42,052,468 (-)	NCBI		MGSCv36	mm8
Celera	5	39,220,946 - 39,223,683 (-)	NCBI		Celera
Cytogenetic Map	5	B3	NCBI
cM Map	5	22.58	NCBI

NKX3-2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	13,540,830 - 13,547,744 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	13,540,830 - 13,544,508 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	13,542,454 - 13,546,132 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	13,151,552 - 13,155,212 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	4	13,218,722 - 13,222,307	NCBI
Celera	4	14,008,663 - 14,012,323 (-)	NCBI		Celera
Cytogenetic Map	4	p15.33	NCBI
HuRef	4	12,880,106 - 12,883,766 (-)	NCBI		HuRef
CHM1_1	4	13,541,051 - 13,544,711 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	4	13,520,522 - 13,527,516 (-)	NCBI		T2T-CHM13v2.0

Nkx3-2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	73,396,198 - 73,398,585 (+)	NCBI		GRCr8
mRatBN7.2	14	69,183,795 - 69,186,182 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	69,183,820 - 69,186,061 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	73,637,752 - 73,640,139 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	74,874,057 - 74,876,444 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	71,332,485 - 71,334,872 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	73,813,531 - 73,818,489 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	73,813,528 - 73,815,757 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	73,825,360 - 73,828,802 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	14	68,115,963 - 68,118,823 (+)	NCBI		Celera
Cytogenetic Map	14	q21	NCBI

Nkx3-2
(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_004955480	10,213,761 - 10,216,860 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955480	10,212,929 - 10,215,814 (+)	NCBI	ChiLan1.0	ChiLan1.0

NKX3-2
(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	3	13,794,967 - 13,801,569 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	13,996,015 - 13,999,693 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	7,958,218 - 7,961,844 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	13,258,949 - 13,262,458 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	13,258,949 - 13,262,458 (-)	Ensembl	panpan1.1		panPan2

NKX3-2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	3	66,543,046 - 66,546,779 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	3	66,543,046 - 66,545,580 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	3	69,066,358 - 69,070,091 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	3	67,147,048 - 67,150,794 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	3	67,147,020 - 67,149,587 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	3	66,524,627 - 66,528,359 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	3	66,717,740 - 66,721,472 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	3	67,087,659 - 67,091,382 (+)	NCBI		UU_Cfam_GSD_1.0

Nkx3-2
(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_024405285	60,297,353 - 60,300,979 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936477	13,999,045 - 14,001,659 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936477	13,999,045 - 14,001,659 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NKX3-2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	9,179,232 - 9,182,892 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	8	9,179,061 - 9,183,340 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	8,716,507 - 8,720,758 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NKX3-2
(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	27	36,641,837 - 36,647,917 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	27	36,641,932 - 36,644,353 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666047	83,389,830 - 83,393,630 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Nkx3-2
(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_004624755	18,070,740 - 18,072,883 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624755	18,070,706 - 18,073,847 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Nkx3-2
99 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	136
Count of miRNA genes:	129
Interacting mature miRNAs:	134
Transcripts:	ENSMUST00000060820
Prediction methods:	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 (GRCm39)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
36049766	Ars22_m	antibody response to SARS-CoV 22, day 29, IgG3 (mouse)					5	36957344	45457342	Mouse
4140990	Lgq6_m	late growth QTL 6 (mouse)			Not determined			32133234	100777931	Mouse
36049767	Ars23_m	antibody response to SARS-CoV 23, day 29, Total IgG (mouse)					5	36957344	45457342	Mouse
10043995	Hbnr9_m	Heligmosomoides bakeri nematode resistance 9 (mouse)			Not determined		5	33488667	67488876	Mouse
1301776	Skts3_m	skin tumor susceptibility 3 (mouse)			Not determined		5	21667295	55667403	Mouse
1300951	Gbvq1_m	gallstone bladder volume QTL 1 (mouse)			Not determined		5	38111681	72111798	Mouse
1301845	Lxw4_m	lupus BXSB x NZW 4 (mouse)			Not determined		5	35694462	69694594	Mouse
1301524	Lmb2_m	lupus in MRL and B6 F2 cross (mouse)			Not determined		5	37581488	112465722	Mouse
1301403	Alcp9_m	alcohol preference locus 9 (mouse)			Not determined		5	31024275	65024480	Mouse
36049774	Ars16_m	antibody response to SARS-CoV 16, day 7, Total IgG (mouse)					5	36957344	45457342	Mouse
36049775	Ars17_m	antibody response to SARS-CoV 17, day 15, IgG2a+IgG2c (mouse)					5	36957344	45457342	Mouse
36049772	Ars20_m	antibody response to SARS-CoV 20, day 15, Total IgG (mouse)					5	36957344	45457342	Mouse
36049773	Ars21_m	antibody response to SARS-CoV 21, day 29, IgG2a+IgG2c (mouse)					5	36957344	45457342	Mouse
36049770	Ars14_m	antibody response to SARS-CoV 14, day 7, IgG3 (mouse)					5	36957344	45457342	Mouse
36049771	Ars15_m	antibody response to SARS-CoV 15, day 7, IgM (mouse)					5	36957344	45457342	Mouse
1300701	Cd8ts1_m	CD8 T cell subset 1 (mouse)			Not determined		5	27215348	61215451	Mouse
11353827	Hplq1_m	hot plate latency 1 (mouse)					5	31570458	65570458	Mouse
36049768	Ars24_m	antibody response to SARS-CoV 24, 4 days post-rechallenge, IgG3 (mouse)					5	36957344	45457342	Mouse
36049769	Ars13_m	antibody response to SARS-CoV 13, day 7, IgG2a+IgG2c (mouse)					5	36957344	45457342	Mouse
36049776	Ars18_m	antibody response to SARS-CoV 18, day 15, IgG3 (mouse)					5	36957344	45457342	Mouse
36049777	Ars19_m	antibody response to SARS-CoV 19, day 15, IgM (mouse)					5	36957344	45457342	Mouse
4141219	W10q16_m	weight 10 weeks QTL 16 (mouse)			Not determined			32133234	100777931	Mouse
1301555	Alcp10_m	alcohol preference locus 10 (mouse)			Not determined		5	31024275	65024480	Mouse
1301170	Lith13_m	lithogenic gene 13 (mouse)			Not determined		5	36494486	70494598	Mouse
1301685	Estq2_m	estradiol regulated response QTL 2 (mouse)			Not determined		5	15634084	49634190	Mouse
11537367	Hmtb11_m	hemostasis and thrombosis 11 (mouse)					5	22100823	64806579	Mouse
4141207	Imrfq1_m	immune response to Factor IX QTL 1 (mouse)			Not determined		5	8124117	42124239	Mouse
11537368	Hmtb10_m	hemostasis and thrombosis 10 (mouse)					5	22100823	54500318	Mouse
1300926	Hpi2_m	hepatic PMN infiltration 2 (mouse)			Not determined		5	37581488	64806579	Mouse
1301693	Sle6_m	systemic lupus erythematosus susceptibility 6 (mouse)			Not determined		5	8890693	87841837	Mouse
4141647	Hrvhf1_m	heart rate variability, high frequency 1 (mouse)			Not determined			36433423	70433423	Mouse
11049561	Lmr24e_m	leishmaniasis resistance 24e (mouse)					5	35694462	69694594	Mouse
13464252	Ahl10_m	age related hearing loss, early onset 10 (mouse)					5	35854568	69854714	Mouse
1301223	Hdlq7_m	HDL QTL 7 (mouse)			Not determined		5	35854568	69854714	Mouse
13464245	Ahl12_m	age related hearing loss, early onset 12 (mouse)					5	38111681	72111798	Mouse
11341716	Rvfs3_m	Rift Valley fever susceptibility 3 (mouse)					5	26441234	138455402	Mouse
14696730	Kidlq1_m	kidney weight, left QTL 1 (mouse)					5	13563152	47563152	Mouse
13464246	Ahl11_m	age related hearing loss, early onset 11 (mouse)					5	37643777	71643896	Mouse
1300719	Iba5_m	induction of brown adipocytes 5 (mouse)			Not determined		5	20686993	54687134	Mouse
11049558	Lmr24b_m	leishmaniasis resistance 24b (mouse)					5	35694462	69694594	Mouse
35673310	Ari4_m	antibody response to influenza 4, day 15-45, IgG2b (mouse)					5	36957344	45457342	Mouse
11049559	Lmr24c_m	leishmaniasis resistance 24c (mouse)					5	35694462	69694594	Mouse

Markers in Region

Bapx1

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
GRCm38	5	41,763,994 - 41,764,198	UniSTS	GRCm38
MGSCv37	5	42,155,233 - 42,155,437	UniSTS	GRCm37
Celera	5	39,223,457 - 39,223,661	UniSTS
Cytogenetic Map	5	B3	UniSTS
cM Map	5	23.0	UniSTS

PMC22272P1

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
GRCm38	5	41,763,442 - 41,763,720	UniSTS	GRCm38
MGSCv37	5	42,154,681 - 42,154,959	UniSTS	GRCm37
Celera	5	39,222,905 - 39,223,183	UniSTS
Cytogenetic Map	5	B3	UniSTS
cM Map	5	23.0	UniSTS

Nkx3-2

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	5	B3	UniSTS
cM Map	5	23.0	UniSTS

Bapx1

Mouse Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	5	B3	UniSTS
cM Map	5	23.0	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.

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_007524	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC102858	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC021014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC145872	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC145874	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH466524	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U87957	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U88716	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSMUST00000060820 ⟹ ENSMUSP00000051990

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39 Ensembl	5	41,918,826 - 41,921,844 (-)	Ensembl
GRCm38.p6 Ensembl	5	41,761,483 - 41,764,501 (-)	Ensembl

RefSeq Acc Id:

NM_007524 ⟹ NP_031550

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Mouse Assembly	Chr	Position (strand)	Source
GRCm39	5	41,918,826 - 41,921,563 (-)	NCBI
GRCm38	5	41,761,483 - 41,764,220 (-)	ENTREZGENE
MGSCv37	5	42,152,722 - 42,155,459 (-)	RGD
Celera	5	39,220,946 - 39,223,683 (-)	RGD
cM Map	5		ENTREZGENE

Sequence:

show sequence

GAAGAGATAATCGGCCGGGCTGTAGGAGAAGAGCATCTGGCGCTGGATTCCAGGGGAGGGGGTC
CTGGCGAGGTGGGCCTGTGAGGTGGGGTGAGGGTCGGCGCGGATCCTGGAACTGAGGGGGGCGG
GGGCTGCTGTGCTGCGCAGGAGTGGGTTGCGGGGGCCTGGCGCGCCCCTCTCACTCGCGCTGAG
GTCGCCCAGAGCTCCGTGTCAGGCTCGAAGCTGTCCCCGCGCCCCAGTTGCCCTCCTGGCTGCC
GGCTCCGATCTGCGGCGCAGATGGCTGTGCGCGGCAGCGGCACCTTGACGCCCTTCTCCATCCA
GGCGATCCTCAACAAGAAAGAGGAGCGCGGCGGGTTGGCTACGCCGGAGGGGCGCCCGGCACCA
GGGGGCACAGAGGTGGCGGTGACCGCGGCGCCCGCCGTCTGCTGCTGGCGGATCTTCGGGGAGA
CCGAGGCCGGTGCGCTGGGGGGCGCCGAGGACTCTCTTCTGGCATCTCCCGCCCGAACCAGAAC
AGCCGTGGGGCAGAGCGCAGAGAGTCCGGGAGGTTGGGACTCAGACTCAGCCCTGAGCGAAGAG
AACGAGGGCAGGAGGCGCTGCGCCGATGTCCCGGGAGCCAGTGGAACCGGCCGCGCCAGGGTGA
CCCTGGGCCTGGACCAGCCAGGCTGCGAGCTGCACGCCGCCAAGGACCTGGAGGAGGAAGCCCC
GGTCCGCAGCGACAGCGAGATGTCAGCCAGCGTTTCAGGCGACCACAGCCCGAGAGGCGAGGAT
GACAGCGTTAGCCCTGGAGGTGCACGCGTGCCTGGGTTGCGCGGCGCCGCGGGCAGCGGGGCTA
GCGGCGGGCAGGCGGGCGGCGTGGAGGAGGAGGAAGAGCCCGCAGCCCCTAAACCGCGAAAGAA
GCGCTCCCGGGCCGCCTTCTCGCACGCCCAGGTCTTCGAGCTGGAGCGCCGCTTTAACCATCAG
CGCTACCTGTCCGGGCCGGAGCGCGCAGACCTGGCAGCTTCGCTGAAGCTCACAGAGACGCAAG
TGAAGATCTGGTTTCAGAACCGTCGCTACAAGACCAAACGCCGGCAGATGGCCGCCGACCTGCT
CGCCTCTGCACCCGCCGCCAAGAAAGTGGCCGTAAAGGTGCTGGTGCGTGACGACCAAAGACAG
TATTTGCCCGGAGAGGTGCTGAGGCCACCTTCCCTTCTGCCACTGCAGCCCTCCTACTACTACC
CTTACTACTGTCTCCCGGGCTGGGCGCTGTCCACGTGCGCGGCCGCTGCTGGTACCCAGTGAAG
CCCTTGGGACGAGGCAAAGAAGGATTCCTGCGTCCCCCGTATGCACCGCCACGGACAGGTGTAC
TCTGTGCAGGCGAGTTCTGCTCAACTGGGGATGAGGCAGGTGGGGAATGAAATCCTGCTGGGAC
TTGACACACCTATCCAGGGTGACAGGGCC

hide sequence

Protein Sequences


Protein RefSeqs	NP_031550	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB47764	(Get FASTA)	NCBI Sequence Viewer
	AAB48514	(Get FASTA)	NCBI Sequence Viewer
	AAI45873	(Get FASTA)	NCBI Sequence Viewer
	AAI45875	(Get FASTA)	NCBI Sequence Viewer
	EDL37578	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSMUSP00000051990
	ENSMUSP00000051990.7
GenBank Protein	P97503	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_031550 ⟸ NM_007524

- UniProtKB:

A6H6G9 (UniProtKB/Swiss-Prot), P97503 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAVRGSGTLTPFSIQAILNKKEERGGLATPEGRPAPGGTEVAVTAAPAVCCWRIFGETEAGALG
GAEDSLLASPARTRTAVGQSAESPGGWDSDSALSEENEGRRRCADVPGASGTGRARVTLGLDQP
GCELHAAKDLEEEAPVRSDSEMSASVSGDHSPRGEDDSVSPGGARVPGLRGAAGSGASGGQAGG
VEEEEEPAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQN
RRYKTKRRQMAADLLASAPAAKKVAVKVLVRDDQRQYLPGEVLRPPSLLPLQPSYYYPYYCLPG
WALSTCAAAAGTQ

hide sequence

Ensembl Acc Id:

ENSMUSP00000051990 ⟸ ENSMUST00000060820

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P97503-F1-model_v2	AlphaFold	P97503	1-333	view protein structure

Promoters

RGD ID:

6837950

Promoter ID:

MM_KWN:42139

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

Kidney, MEF_B4

Transcripts:

UC008XHC.1

Position:

Mouse Assembly	Chr	Position (strand)	Source
MGSCv36	5	42,155,134 - 42,155,634 (-)	MPROMDB

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	MGI:108015	AgrOrtholog
Ensembl Genes	ENSMUSG00000049691	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSMUST00000060820	ENTREZGENE
	ENSMUST00000060820.8	UniProtKB/Swiss-Prot
Gene3D-CATH	Homeodomain-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_NK-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	mmu:12020	UniProtKB/Swiss-Prot
MGD	MGI:108015	ENTREZGENE
NCBI Gene	12020	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN NKX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX PROTEIN NKX-3.2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Nkx3-2	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	HOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A6H6G9	ENTREZGENE
	NKX32_MOUSE	UniProtKB/Swiss-Prot, ENTREZGENE
	P97938_MOUSE	UniProtKB/TrEMBL
UniProt Secondary	A6H6G9	UniProtKB/Swiss-Prot

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Mammalian Phenotype

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Imported Disease Annotations - ClinVar

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Mammalian Phenotype