Atp10d (ATPase phospholipid transporting 10D (putative)) - Rat Genome Database

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Gene: Atp10d (ATPase phospholipid transporting 10D (putative)) Rattus norvegicus
Analyze
Symbol: Atp10d
Name: ATPase phospholipid transporting 10D (putative)
RGD ID: 1588541
Description: Predicted to enable glycosylceramide flippase activity. Predicted to be involved in phospholipid translocation. Predicted to be located in endoplasmic reticulum and nucleoplasm. Predicted to be part of phospholipid-translocating ATPase complex. Predicted to be active in plasma membrane. Orthologous to human ATP10D (ATPase phospholipid transporting 10D (putative)); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: ATPase, class V, type 10D; LOC360932; probable phospholipid-transporting ATPase VD; similar to Probable phospholipid-transporting ATPase VD (ATPVD)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21435,911,728 - 36,012,549 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,912,141 - 36,012,564 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01438,475,956 - 38,575,937 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,477,330 - 38,575,785 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01438,286,791 - 38,385,764 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41438,340,037 - 38,433,736 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1435,144,020 - 35,242,784 (-)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. GOA pipeline RGD automated data 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:21914794  


Genomics

Comparative Map Data
Atp10d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21435,911,728 - 36,012,549 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,912,141 - 36,012,564 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01438,475,956 - 38,575,937 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,477,330 - 38,575,785 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01438,286,791 - 38,385,764 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41438,340,037 - 38,433,736 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1435,144,020 - 35,242,784 (-)NCBICelera
Cytogenetic Map14p11NCBI
ATP10D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38447,485,275 - 47,593,486 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl447,485,275 - 47,593,486 (+)EnsemblGRCh38hg38GRCh38
GRCh37447,487,292 - 47,595,503 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36447,182,167 - 47,290,260 (+)NCBINCBI36Build 36hg18NCBI36
Build 34447,328,337 - 47,436,431NCBI
Celera447,936,627 - 48,044,747 (+)NCBICelera
Cytogenetic Map4p12NCBI
HuRef446,806,888 - 46,915,057 (+)NCBIHuRef
CHM1_1447,486,421 - 47,594,454 (+)NCBICHM1_1
T2T-CHM13v2.0447,452,618 - 47,560,826 (+)NCBIT2T-CHM13v2.0
Atp10d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39572,360,672 - 72,456,114 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl572,360,672 - 72,456,118 (+)EnsemblGRCm39 Ensembl
GRCm38572,203,329 - 72,298,771 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl572,203,329 - 72,298,775 (+)EnsemblGRCm38mm10GRCm38
MGSCv37572,594,568 - 72,690,010 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36572,482,478 - 72,590,429 (+)NCBIMGSCv36mm8
Celera569,456,406 - 69,552,109 (+)NCBICelera
Cytogenetic Map5C3.2NCBI
Atp10d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955443968,495 - 1,072,800 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955443972,967 - 1,072,797 (-)NCBIChiLan1.0ChiLan1.0
ATP10D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1485,287,676 - 85,399,406 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl485,287,676 - 85,399,406 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0474,556,104 - 74,668,218 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ATP10D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11343,401,038 - 43,500,254 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1343,401,153 - 43,499,254 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1343,351,188 - 43,450,783 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01344,006,066 - 44,105,242 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1344,006,071 - 44,104,249 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11343,685,508 - 43,785,323 (+)NCBIUMICH_Zoey_3.1
UU_Cfam_GSD_1.01344,100,385 - 44,199,519 (+)NCBIUU_Cfam_GSD_1.0
Atp10d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528532,557,363 - 32,659,165 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493648213,639,077 - 13,740,985 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP10D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl837,407,711 - 37,530,373 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1837,407,677 - 37,531,707 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2839,330,073 - 39,415,359 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATP10D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1272,664,932 - 2,771,045 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl272,661,899 - 2,771,009 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604748,704,580 - 48,812,248 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Atp10d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476119,407,954 - 19,527,049 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476119,408,249 - 19,527,007 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Atp10d
684 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:44
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000003146
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat

Markers in Region
RH129002  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21435,911,848 - 35,912,035 (+)MAPPERmRatBN7.2
Rnor_6.01438,476,077 - 38,476,263NCBIRnor6.0
Rnor_5.01438,286,912 - 38,287,098UniSTSRnor5.0
RGSC_v3.41438,341,979 - 38,342,165UniSTSRGSC3.4
Celera1435,144,141 - 35,144,327UniSTS
Cytogenetic Map14p11UniSTS
RH135113  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21435,910,418 - 35,910,597 (+)MAPPERmRatBN7.2
Rnor_6.01438,474,647 - 38,474,825NCBIRnor6.0
Rnor_5.01438,285,482 - 38,285,660UniSTSRnor5.0
RGSC_v3.41438,340,549 - 38,340,727UniSTSRGSC3.4
Celera1435,142,711 - 35,142,889UniSTS
Cytogenetic Map14p11UniSTS
UniSTS:235197  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21435,911,781 - 35,912,033 (+)MAPPERmRatBN7.2
Rnor_6.01438,476,010 - 38,476,261NCBIRnor6.0
Rnor_5.01438,286,845 - 38,287,096UniSTSRnor5.0
RGSC_v3.41438,341,912 - 38,342,163UniSTSRGSC3.4
Celera1435,144,074 - 35,144,325UniSTS
Cytogenetic Map14p11UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 2 10 2 19 2 8 22 34 11
Low 1 41 47 39 39 8 11 66 13 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003146   ⟹   ENSRNOP00000003146
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1435,912,141 - 36,012,564 (-)Ensembl
Rnor_6.0 Ensembl1438,477,330 - 38,575,785 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099677   ⟹   ENSRNOP00000089956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1435,982,359 - 36,012,415 (-)Ensembl
RefSeq Acc Id: XM_039092718   ⟹   XP_038948646
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21435,911,728 - 36,012,549 (-)NCBI
RefSeq Acc Id: XM_039092719   ⟹   XP_038948647
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21435,911,728 - 36,012,549 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038948646 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948647 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89999 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000003146   ⟸   ENSRNOT00000003146
RefSeq Acc Id: XP_038948646   ⟸   XM_039092718
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948647   ⟸   XM_039092719
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000089956   ⟸   ENSRNOT00000099677
Protein Domains
PhoLip_ATPase_C   PhoLip_ATPase_N

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZN41-F1-model_v2 AlphaFold D3ZN41 1-1468 view protein structure

Transcriptome

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

Promoters
RGD ID:13699310
Promoter ID:EPDNEW_R9826
Type:initiation region
Name:Atp10d_1
Description:ATPase phospholipid transporting 10D
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01438,575,872 - 38,575,932EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588541 AgrOrtholog
BioCyc Gene G2FUF-15846 BioCyc
Ensembl Genes ENSRNOG00000002312 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003146 ENTREZGENE
  ENSRNOP00000003146.5 UniProtKB/TrEMBL
  ENSRNOP00000089956.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003146 ENTREZGENE
  ENSRNOT00000003146.5 UniProtKB/TrEMBL
  ENSRNOT00000099677.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.1110.10 UniProtKB/TrEMBL
  3.40.50.1000 UniProtKB/TrEMBL
InterPro ATP10D UniProtKB/TrEMBL
  ATPase_P-typ_ATPase-assoc-dom UniProtKB/TrEMBL
  ATPase_P-typ_cyto_domN UniProtKB/TrEMBL
  ATPase_P-typ_ion-transptr UniProtKB/TrEMBL
  ATPase_P-typ_P_site UniProtKB/TrEMBL
  ATPase_P-typ_Plipid-transl UniProtKB/TrEMBL
  ATPase_P-typ_TM_dom UniProtKB/TrEMBL
  HAD-like_dom UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/TrEMBL
  P-type_ATPase_N UniProtKB/TrEMBL
  P_typ_ATPase_c UniProtKB/TrEMBL
  P_typ_ATPase_HD_dom UniProtKB/TrEMBL
NCBI Gene 360932 ENTREZGENE
PANTHER PTHR24092:SF84 UniProtKB/TrEMBL
Pfam PhoLip_ATPase_C UniProtKB/TrEMBL
  PhoLip_ATPase_N UniProtKB/TrEMBL
PhenoGen Atp10d PhenoGen
PROSITE ATPASE_E1_E2 UniProtKB/TrEMBL
Superfamily-SCOP ATPase_cation_domN UniProtKB/TrEMBL
  HAD-like_dom UniProtKB/TrEMBL
  SSF81653 UniProtKB/TrEMBL
  SSF81665 UniProtKB/TrEMBL
TIGRFAMs ATPase-Plipid UniProtKB/TrEMBL
  ATPase_P-type UniProtKB/TrEMBL
UniProt A0A8I6ADJ0_RAT UniProtKB/TrEMBL
  D3ZN41_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Atp10d  ATPase phospholipid transporting 10D (putative)  Atp10d  ATPase, class V, type 10D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Atp10d  ATPase, class V, type 10D  LOC360932  similar to Probable phospholipid-transporting ATPase VD (ATPVD)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC360932  similar to Probable phospholipid-transporting ATPase VD (ATPVD)      Symbol and Name status set to provisional 70820 PROVISIONAL