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Gene: Atp6v1d (ATPase H+ transporting V1 subunit D) Rattus norvegicus

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Symbol:

Atp6v1d

Name:

ATPase H+ transporting V1 subunit D

RGD ID:

735119

Description:

Predicted to enable proton-transporting ATPase activity, rotational mechanism. Predicted to be involved in cilium assembly; protein localization to cilium; and synaptic vesicle lumen acidification. Is extrinsic component of synaptic vesicle membrane. Orthologous to human ATP6V1D (ATPase H+ transporting V1 subunit D); PARTICIPATES IN oxidative phosphorylation pathway; phagocytosis pathway; rheumatoid arthritis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 1-nitropropane; 2,4-diaminotoluene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D; ATPase, H+ transporting, lysosomal V1 subunit D; ATPase, H+ transporting, V1 subunit D; V-type proton ATPase subunit D

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):	ATP6V1D (ATPase H+ transporting V1 subunit D)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Atp6v1d (ATPase, H+ transporting, lysosomal V1 subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Atp6v1d (ATPase H+ transporting V1 subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	ATP6V1D (ATPase H+ transporting V1 subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	ATP6V1D (ATPase H+ transporting V1 subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101968194 (V-type proton ATPase subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	ATP6V1D (ATPase H+ transporting V1 subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	ATP6V1D (ATPase H+ transporting V1 subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Atp6v1d (ATPase H+ transporting V1 subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Atp6v1d (ATPase H+ transporting V1 subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	ATP6V1D (ATPase H+ transporting V1 subunit D)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	ATP6V1D (ATPase H+ transporting V1 subunit D)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Mus musculus (house mouse):	Atp6v1d (ATPase, H+ transporting, lysosomal V1 subunit D)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	atp6v1d (ATPase H+ transporting V1 subunit D)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	atp6v1d (ATPase H+ transporting V1 subunit D)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	VMA8	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Vha36-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Vha36-3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	vha-14	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Vha36-2	Alliance	DIOPT (Ensembl Compara\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	atp6v1d	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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	6	103,389,778 - 103,405,346 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	6	103,389,783 - 103,405,346 (-)	Ensembl				GRCr8
mRatBN7.2	6	97,656,725 - 97,672,295 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	97,656,576 - 97,672,303 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	6	98,086,262 - 98,101,815 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	98,385,424 - 98,400,977 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	97,772,371 - 97,787,931 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	102,032,271 - 102,047,754 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	102,032,276 - 102,047,758 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	6	111,407,085 - 111,421,779 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	101,479,417 - 101,494,826 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	96,044,738 - 96,060,175 (-)	NCBI		Celera
RGSC_v3.1	6	101,482,872 - 101,498,282 (-)	NCBI
Cytogenetic Map	6	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Chemical and Drug Induced Liver Injury (ISO)

Experimental Liver Cirrhosis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

1-nitropropane (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

2,4-diaminotoluene (EXP)

2,4-dinitrotoluene (EXP)

2,6-diaminotoluene (EXP)

2,6-dinitrotoluene (EXP)

2-acetamidofluorene (EXP)

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

2-nitro-p-phenylenediamine (EXP)

2-nitrofluorene (EXP)

2-nitropropane (EXP)

3H-1,2-dithiole-3-thione (EXP)

4,4'-diaminodiphenylmethane (EXP)

4,4'-sulfonyldiphenol (EXP,ISO)

4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one (EXP)

4-acetylaminofluorene (EXP)

4-nitro-1,2-phenylenediamine (EXP)

acrolein (ISO)

acrylamide (EXP)

aflatoxin B1 (EXP,ISO)

alpha-pinene (ISO)

anthracen-2-amine (EXP)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

beta-lapachone (ISO)

bisphenol A (EXP,ISO)

bisphenol F (EXP)

Brodifacoum (EXP)

cadmium dichloride (ISO)

caffeine (ISO)

captan (ISO)

chloropicrin (ISO)

clofibric acid (EXP)

cocaine (EXP)

copper(II) sulfate (ISO)

CU-O LINKAGE (ISO)

cyclosporin A (ISO)

deoxynivalenol (ISO)

dicrotophos (ISO)

diethylstilbestrol (EXP)

doxorubicin (EXP,ISO)

epoxiconazole (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

finasteride (EXP)

flutamide (EXP)

folic acid (ISO)

folpet (ISO)

furan (EXP)

gentamycin (EXP)

GSK-J4 (ISO)

Heliotrine (EXP)

hydrazine (EXP)

hydrogen peroxide (ISO)

isoniazide (ISO)

isotretinoin (ISO)

ivermectin (ISO)

ketoconazole (EXP)

methidathion (ISO)

methyl methanesulfonate (ISO)

N-nitrosodiethylamine (EXP)

N-nitrosodimethylamine (EXP)

N-nitrosomorpholine (EXP)

nefazodone (EXP)

okadaic acid (ISO)

osimertinib (EXP)

ozone (ISO)

paracetamol (EXP,ISO)

perfluorooctanoic acid (EXP)

picoxystrobin (ISO)

pirinixic acid (EXP)

piroxicam (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

rac-lactic acid (ISO)

resveratrol (ISO)

rotenone (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium dichromate (EXP,ISO)

Soman (EXP)

tamoxifen (ISO)

temozolomide (ISO)

thimerosal (ISO)

thioacetamide (EXP)

thiram (ISO)

titanium dioxide (ISO)

trichloroethene (EXP)

trichostatin A (ISO)

triphenyl phosphate (ISO)

tunicamycin (ISO)

urethane (ISO)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cilium assembly (IEA,ISO)

monoatomic ion transport (IEA)

protein localization to cilium (IEA,ISO)

proton transmembrane transport (IEA)

synaptic vesicle lumen acidification (IEA,ISO)

vacuolar acidification (IBA)

Cellular Component

centrosome (IEA,ISO)

cilium (IEA,ISO)

clathrin-coated vesicle membrane (IEA)

extrinsic component of synaptic vesicle membrane (EXP,IDA,IEP)

membrane (IEA,ISO)

plasma membrane (IEA,ISO)

proton-transporting V-type ATPase complex (IBA,IEA,ISO)

Molecular Function

protein binding (ISO)

proton transmembrane transporter activity (IEA,ISO)

proton-transporting ATPase activity, rotational mechanism (IBA,IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

oxidative phosphorylation pathway (IEA)

phagocytosis pathway (IEA)

rheumatoid arthritis pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Structure of V-ATPase from the mammalian brain.	Abbas YM, etal., Science. 2020 Mar 13;367(6483):1240-1246. doi: 10.1126/science.aaz2924.
2.	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.
3.	cDNA cloning, chromosomal localization and evolutionary analysis of mouse vacuolar ATPase subunit D, Atp6m.	Kennell JA, etal., Cytogenet Cell Genet 2001;92(3-4):337-41.
4.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
5.	GOA pipeline	RGD automated data pipeline
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
7.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:17897319	PMID:18752060	PMID:19056867	PMID:19199708	PMID:21844891	PMID:23376485	PMID:25931508

Genomics

Comparative Map Data

Atp6v1d
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	103,389,778 - 103,405,346 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	6	103,389,783 - 103,405,346 (-)	Ensembl				GRCr8
mRatBN7.2	6	97,656,725 - 97,672,295 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	97,656,576 - 97,672,303 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	6	98,086,262 - 98,101,815 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	98,385,424 - 98,400,977 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	97,772,371 - 97,787,931 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	102,032,271 - 102,047,754 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	102,032,276 - 102,047,758 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	6	111,407,085 - 111,421,779 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	101,479,417 - 101,494,826 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	96,044,738 - 96,060,175 (-)	NCBI		Celera
RGSC_v3.1	6	101,482,872 - 101,498,282 (-)	NCBI
Cytogenetic Map	6	q24	NCBI

ATP6V1D
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	67,337,872 - 67,359,804 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	67,294,371 - 67,360,265 (-)	Ensembl			hg38	GRCh38
GRCh37	14	67,804,589 - 67,826,521 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	66,874,342 - 66,896,344 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	14	66,874,342 - 66,896,344	NCBI
Celera	14	47,863,642 - 47,885,645 (-)	NCBI		Celera
Cytogenetic Map	14	q23.3	NCBI
HuRef	14	47,974,504 - 47,996,644 (-)	NCBI		HuRef
CHM1_1	14	67,743,271 - 67,765,404 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	14	61,544,996 - 61,566,929 (-)	NCBI		T2T-CHM13v2.0

Atp6v1d
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	78,889,756 - 78,908,810 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	78,887,499 - 78,908,412 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	12	78,842,982 - 78,862,008 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	78,840,725 - 78,861,638 (-)	Ensembl			mm10	GRCm38
MGSCv37	12	79,943,969 - 79,962,625 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	12	79,761,822 - 79,780,478 (-)	NCBI		MGSCv36	mm8
Celera	12	80,307,557 - 80,326,098 (-)	NCBI		Celera
Cytogenetic Map	12	C3	NCBI
cM Map	12	35.51	NCBI

Atp6v1d
(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_004955466	2,854,889 - 2,869,950 (+)	Ensembl
ChiLan1.0	NW_004955466	2,855,597 - 2,869,319 (+)	NCBI	ChiLan1.0	ChiLan1.0

ATP6V1D
(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	15	68,443,858 - 68,465,639 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	67,660,171 - 67,682,150 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	47,913,254 - 47,935,376 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	66,792,168 - 66,813,714 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2

ATP6V1D
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	41,332,581 - 41,354,058 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	41,333,021 - 41,354,320 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	41,024,328 - 41,045,781 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	41,559,923 - 41,581,418 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	41,559,926 - 41,581,376 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	41,178,800 - 41,200,277 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	41,252,376 - 41,273,861 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	41,611,332 - 41,632,798 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

LOC101968194
(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	89,779,360 - 89,854,240 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936478	8,991,091 - 9,065,865 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ATP6V1D
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	91,064,396 - 91,084,913 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	7	91,065,998 - 91,084,908 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	97,375,524 - 97,394,503 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ATP6V1D
(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	24	44,578,057 - 44,598,918 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	24	44,578,807 - 44,598,394 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666053	32,808,011 - 32,828,557 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Atp6v1d
(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_004624734	33,640,839 - 33,657,745 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624734	33,640,842 - 33,669,471 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Atp6v1d
(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	7	92,957,034 - 92,972,752 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Atp6v1d
55 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	58
Count of miRNA genes:	51
Interacting mature miRNAs:	57
Transcripts:	ENSRNOT00000012101
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2293088	Iddm28	Insulin dependent diabetes mellitus QTL 28	5.21		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	6	68767270	135411972	Rat
1331799	Bp211	Blood pressure QTL 211	3.66407		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	88019181	136741135	Rat
61329	Eae9	Experimental allergic encephalomyelitis QTL 9	3.7		body mass (VT:0001259)	change in body weight (CMO:0002045)	6	84490437	129490437	Rat
2313399	Anxrr28	Anxiety related response QTL 28			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	6	101593607	138161926	Rat
1331789	Rf37	Renal function QTL 37	3.224		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	86494122	112380234	Rat
1331725	Bp212	Blood pressure QTL 212	3.52475		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	99437079	125323237	Rat
1331722	Thshl1	Thyroid stimulating hormone level QTL 1	11.7	0.0001	blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	6	99708426	112483760	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	71278722	116278722	Rat
70176	Mcsm1	Mammary carcinoma susceptibility modifier QTL 1			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	64367996	109367996	Rat
10054138	Gmadr3	Adrenal mass QTL 3	3.68	0.00045	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	6	90871046	135871046	Rat
1581563	Uae33	Urinary albumin excretion QTL 33			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	93560258	136550638	Rat
1641917	Colcr5	Colorectal carcinoma resistance QTL 5	3.18	0.0009	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	6	98944780	143944780	Rat
61414	Pia3	Pristane induced arthritis QTL 3	4.5		joint integrity trait (VT:0010548)	post-insult time to onset of experimental arthritis (CMO:0001450)	6	100704576	136029228	Rat
724524	Uae2	Urinary albumin excretion QTL 2	2.7	0.0005	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	79198463	144254945	Rat
737827	Hcar11	Hepatocarcinoma resistance QTL 11	4.4		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	6	46050607	116278722	Rat
2303624	Vencon5	Ventilatory control QTL 5	4.45		respiration trait (VT:0001943)	minute ventilation (CMO:0000132)	6	93778632	138778632	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	20859430	113082285	Rat
2293837	Kiddil1	Kidney dilation QTL 1	3.7		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	86867923	110125012	Rat
2293842	Kiddil3	Kidney dilation QTL 3	4.3		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	86867923	110125012	Rat
10054123	Srcrt6	Stress Responsive Cort QTL 6	2.5	0.0043	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	90871046	135871046	Rat
724536	Uae7	Urinary albumin excretion QTL 7	3.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	93560258	136550638	Rat
1576302	Schws4	Schwannoma susceptibility QTL 4		0.0078	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	78204640	123204640	Rat
1581550	Pur8	Proteinuria QTL 8			urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	93560258	136550638	Rat
1300075	Glom7	Glomerulus QTL 7	5.6	0.0000002	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	6	76937178	121937178	Rat
12801471	Schws9	Schwannoma susceptibility QTL 9			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	101593607	146593607	Rat

Markers in Region

RH134082

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	97,662,888 - 97,663,095 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	102,038,435 - 102,038,641	NCBI	Rnor6.0
Rnor_5.0	6	111,413,249 - 111,413,455	UniSTS	Rnor5.0
RGSC_v3.4	6	101,485,581 - 101,485,787	UniSTS	RGSC3.4
Celera	6	96,050,902 - 96,051,108	UniSTS
RH 3.4 Map	6	690.1	UniSTS
Cytogenetic Map	6	q24	UniSTS

RH141312

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	97,656,830 - 97,657,033 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	102,032,377 - 102,032,579	NCBI	Rnor6.0
Rnor_5.0	6	111,407,191 - 111,407,393	UniSTS	Rnor5.0
RGSC_v3.4	6	101,479,523 - 101,479,725	UniSTS	RGSC3.4
Celera	6	96,044,844 - 96,045,046	UniSTS
RH 3.4 Map	6	691.7	UniSTS
Cytogenetic Map	6	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	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_199386	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC120917	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC063177	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213312	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214434	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ216046	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000012101 ⟹ ENSRNOP00000012101

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	6	103,389,783 - 103,405,346 (-)	Ensembl
mRatBN7.2 Ensembl	6	97,656,722 - 97,672,231 (-)	Ensembl
Rnor_6.0 Ensembl	6	102,032,276 - 102,047,758 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000093857 ⟹ ENSRNOP00000083754

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	97,658,665 - 97,672,303 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000103277 ⟹ ENSRNOP00000084384

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	6	103,390,772 - 103,405,346 (-)	Ensembl
mRatBN7.2 Ensembl	6	97,656,576 - 97,672,234 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000116517 ⟹ ENSRNOP00000092525

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	6	103,390,253 - 103,401,441 (-)	Ensembl
mRatBN7.2 Ensembl	6	97,657,200 - 97,668,388 (-)	Ensembl

RefSeq Acc Id:

NM_199386 ⟹ NP_955418

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	103,389,778 - 103,405,346 (-)	NCBI
mRatBN7.2	6	97,656,725 - 97,672,295 (-)	NCBI
Rnor_6.0	6	102,032,271 - 102,047,754 (-)	NCBI
Rnor_5.0	6	111,407,085 - 111,421,779 (-)	NCBI
RGSC_v3.4	6	101,479,417 - 101,494,826 (-)	RGD
Celera	6	96,044,738 - 96,060,175 (-)	RGD

Sequence:

show sequence

GGCTCTGTGGTAACAGTTCTGGAGGTGTTGCGGTCCCGATTGTCCCACTGGGGACCCGAGCCGA
GTCACCGTCAGAATGTCGGGCAAAGACCGGATTGAAATCTTCCCTTCGCGAATGGCACAGACCA
TCATGAAGGCTCGGTTAAAAGGAGCACAGACTGGTCGAAACCTCCTGAAGAAAAAGTCTGATGC
CTTAACTCTTCGATTTCGACAGATCCTGAAGAAGATAATAGAGACTAAGATGCTGATGGGTGAG
GTGATGAGAGAAGCTGCCTTCTCATTGGCTGAGGCCAAATTCACAGCAGGGGACTTCAGCACCA
CAGTTATACAAAATGTAAATAAAGCCCAGGTGAAGATCCGAGCAAAGAAAGACAATGTAGCAGG
TGTCACCTTACCAGTGTTTGAACATTACCACGAAGGAACTGACAGCTATGAACTAACCGGTTTA
GCCAGAGGTGGGGAGCAGCTGGCGAAACTTAAGCGGAATTATGCCAAAGCAGTGGAACTACTGG
TGGAACTGGCTTCCCTGCAGACTTCCTTTGTTACTCTGGATGAAGCCATTAAGATAACCAACAG
GCGTGTAAATGCTATTGAGCATGTCATCATTCCCCGGATTGAACGCACCCTTGCTTATATCATC
ACAGAACTGGATGAGAGAGAGCGAGAAGAATTCTATAGGTTAAAGAAAATCCAGGAGAAGAAAA
AGATTATCAAGGAGAAAAGCGAGAAGGACTTGGAGCGGCGGAGAGCAGCTGGAGAGGTGATGGA
GCCCGCCAACCTCCTGGCGGAAGAGAAGGACGAGGACCTGCTGTTCGAGTAGCTGCCCGCTGCT
CCCTTCAGGCTGAGCATCATTTAACTCAGTGTGCAGGTTCGGTATGTGCGGGTATTTATTTTGG
CAGAAGAGTTCATCTGGCTGTAAGATTTATCAGAATGCTGTGTGAGACCATTTTTCCTGCATCA
TAATTCAGCAACCTGAGATTTGTAAAACCCACCCAGCACTTACAGAATCTCCCCAGTGAAAGAG
TCATACCATCCTATTTACACTAGTTTGACTGATGTGTTTAAAACTTTAGGAAATACTTACTATA
AACATTCATGGTCTCAGGCAAATGCTGAGCAGCCTTCCTTCCTACCCACTTGTAAACCTTGGCA
CTGTTGTCTGAGGCTGTGCAGCCATTGTGTTACTGTGGACTCAACTCTATGCCTACTTTTCTTT
GCACGATGTGTCTGTGTGTAATGGAAGTGGTTCTGCCCATTTAAATATGACTTATGAACAGAGT
AAAATGATTTAAAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_955418	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH63177	(Get FASTA)	NCBI Sequence Viewer
	EDM03701	(Get FASTA)	NCBI Sequence Viewer
	EDM03702	(Get FASTA)	NCBI Sequence Viewer
	EDM03703	(Get FASTA)	NCBI Sequence Viewer
	EDM03704	(Get FASTA)	NCBI Sequence Viewer
	EDM03705	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000012101
	ENSRNOP00000012101.6
	ENSRNOP00000084384.2
	ENSRNOP00000092525.1

RefSeq Acc Id:

NP_955418 ⟸ NM_199386

- UniProtKB:

Q6P503 (UniProtKB/TrEMBL), A0A8I6A161 (UniProtKB/TrEMBL), F7EUL0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMRE
AAFSLAEAKFTAGDFSTTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGG
EQLAKLKRNYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELD
EREREEFYRLKKIQEKKKIIKEKSEKDLERRRAAGEVMEPANLLAEEKDEDLLFE

hide sequence

Ensembl Acc Id:

ENSRNOP00000012101 ⟸ ENSRNOT00000012101

Ensembl Acc Id:

ENSRNOP00000084384 ⟸ ENSRNOT00000103277

Ensembl Acc Id:

ENSRNOP00000083754 ⟸ ENSRNOT00000093857

Ensembl Acc Id:

ENSRNOP00000092525 ⟸ ENSRNOT00000116517

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q6P503-F1-model_v2	AlphaFold	Q6P503	1-247	view protein structure

Transcriptome

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

Promoters

RGD ID:

13694687

Promoter ID:

EPDNEW_R5212

Type:

initiation region

Name:

Atp6v1d_1

Description:

ATPase H+ transporting V1 subunit D

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	102,047,770 - 102,047,830	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:735119	AgrOrtholog
BioCyc Gene	G2FUF-36987	BioCyc
BioCyc Pathway	PWY-7980 [ATP biosynthesis]	BioCyc
BioCyc Pathway Image	PWY-7980	BioCyc
Ensembl Genes	ENSRNOG00000009080	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000012101	ENTREZGENE
	ENSRNOT00000012101.8	UniProtKB/TrEMBL
	ENSRNOT00000103277.2	UniProtKB/TrEMBL
	ENSRNOT00000116517.2	UniProtKB/TrEMBL
Gene3D-CATH	1.10.287.3240	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:6891415	IMAGE-MGC_LOAD
InterPro	ATPase_V1/A1-cplx_dsu	UniProtKB/TrEMBL
KEGG Report	rno:299159	UniProtKB/TrEMBL
MGC_CLONE	MGC:72940	IMAGE-MGC_LOAD
NCBI Gene	299159	ENTREZGENE
PANTHER	ATPase_V1/A1_D	UniProtKB/TrEMBL
Pfam	ATP-synt_D	UniProtKB/TrEMBL
PhenoGen	Atp6v1d	PhenoGen
RatGTEx	ENSRNOG00000009080	RatGTEx
UniProt	A0A8I6A161	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6AHT1_RAT	UniProtKB/TrEMBL
	A6HCE7_RAT	UniProtKB/TrEMBL
	A6HCE8_RAT	UniProtKB/TrEMBL
	A6HCE9_RAT	UniProtKB/TrEMBL
	A6HCF0_RAT	UniProtKB/TrEMBL
	F7EUL0	ENTREZGENE, UniProtKB/TrEMBL
	Q6P503	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-02-25	Atp6v1d	ATPase H+ transporting V1 subunit D	Atp6v1d	ATPase, H+ transporting, lysosomal V1 subunit D	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-03	Atp6v1d	ATPase, H+ transporting, lysosomal V1 subunit D	Atp6v1d	ATPase, H+ transporting, V1 subunit D	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-07-08	Atp6v1d	ATPase, H+ transporting, V1 subunit D		ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D	Name updated	1299863	APPROVED

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 - CTD

Imported Annotations - KEGG (archival)

BioCyc Pathways

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Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

BioCyc Pathways