Nipal1 (NIPA-like domain containing 1) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Nipal1 (NIPA-like domain containing 1) Rattus norvegicus
Analyze
Symbol: Nipal1
Name: NIPA-like domain containing 1
RGD ID: 1310092
Description: Predicted to enable magnesium ion transmembrane transporter activity. Predicted to be involved in magnesium ion transport. Predicted to be located in Golgi apparatus. Predicted to be active in membrane. Orthologous to human NIPAL1 (NIPA like domain containing 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC289594; magnesium transporter NIPA3; Npal1; RGD1310092; similar to NIPA2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81435,891,645 - 35,915,658 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1435,891,647 - 35,915,658 (-)EnsemblGRCr8
mRatBN7.21435,537,641 - 35,561,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,540,324 - 35,561,659 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1435,903,133 - 35,927,070 (-)NCBIUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01437,207,879 - 37,231,816 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01435,696,250 - 35,720,191 (-)NCBIUTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd1436,181,961 - 36,205,899 (-)NCBI
Lyon_Normotensive1436,294,927 - 36,318,864 (-)NCBI
Lyon_Hypertensive1436,292,172 - 36,316,109 (-)NCBI
F344_StmMcwi1436,314,243 - 36,338,180 (-)NCBI
Rnor_6.01438,104,027 - 38,128,038 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,104,047 - 38,128,024 (-)EnsemblRnor_6.0 Ensemblrn6Rnor6.0
Rnor_5.01437,914,565 - 37,938,564 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41437,965,997 - 37,990,014 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1434,793,332 - 34,814,626 (-)NCBICelera
RGSC_v3.11437,969,451 - 37,993,302 (-)NCBI
Cytogenetic Map14p11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
Golgi apparatus  (IEA,ISO)
Golgi membrane  (ISO)
membrane  (IBA,IEA)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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:18667602  


Genomics

Comparative Map Data
Nipal1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81435,891,645 - 35,915,658 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1435,891,647 - 35,915,658 (-)EnsemblGRCr8
mRatBN7.21435,537,641 - 35,561,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,540,324 - 35,561,659 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1435,903,133 - 35,927,070 (-)NCBIUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01437,207,879 - 37,231,816 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01435,696,250 - 35,720,191 (-)NCBIUTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd1436,181,961 - 36,205,899 (-)NCBI
Lyon_Normotensive1436,294,927 - 36,318,864 (-)NCBI
Lyon_Hypertensive1436,292,172 - 36,316,109 (-)NCBI
F344_StmMcwi1436,314,243 - 36,338,180 (-)NCBI
Rnor_6.01438,104,027 - 38,128,038 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,104,047 - 38,128,024 (-)EnsemblRnor_6.0 Ensemblrn6Rnor6.0
Rnor_5.01437,914,565 - 37,938,564 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41437,965,997 - 37,990,014 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1434,793,332 - 34,814,626 (-)NCBICelera
RGSC_v3.11437,969,451 - 37,993,302 (-)NCBI
Cytogenetic Map14p11NCBI
NIPAL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38448,016,772 - 48,040,173 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl447,914,142 - 48,052,430 (+)EnsemblGRCh38.p14 Ensemblhg38GRCh38
GRCh37448,018,789 - 48,042,190 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36447,713,548 - 47,733,841 (+)NCBIBuild 36Build 36hg18NCBI36
Celera448,467,642 - 48,487,933 (+)NCBICelera
Cytogenetic Map4p12NCBI
HuRef447,339,019 - 47,359,298 (+)NCBIHuRef
CHM1_1448,017,882 - 48,038,161 (+)NCBICHM1_1
T2T-CHM13v2.0447,983,845 - 48,007,239 (+)NCBIT2T-CHM13v2.0
Nipal1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39572,805,139 - 72,828,421 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl572,805,138 - 72,828,421 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38572,647,796 - 72,671,078 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl572,647,795 - 72,671,078 (+)EnsemblGRCm38.p6 Ensemblmm10GRCm38
MGSCv37573,039,035 - 73,062,317 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36572,926,931 - 72,950,213 (+)NCBIMGSCv36mm8
Celera569,896,584 - 69,919,867 (+)NCBICelera
Cytogenetic Map5C3.2NCBI
cM Map538.44NCBI
Nipal1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955443584,451 - 609,324 (-)EnsemblChiLan1.0 Ensembl
ChiLan1.0NW_004955443584,451 - 608,451 (-)NCBIChiLan1.0ChiLan1.0
NIPAL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2379,818,547 - 79,841,862 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1480,077,796 - 80,103,368 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0474,106,699 - 74,130,102 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1484,838,778 - 84,862,172 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl484,838,778 - 84,862,170 (-)EnsemblPanPan1.1 EnsemblpanPan2panpan1.1
NIPAL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11343,877,377 - 43,900,871 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1343,877,393 - 43,897,671 (+)EnsemblCanFam3.1 EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1343,829,924 - 43,853,246 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01344,477,241 - 44,500,597 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1344,477,205 - 44,499,733 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11344,154,655 - 44,177,990 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01343,686,663 - 43,709,959 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01344,569,803 - 44,593,134 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nipal1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mIctTri1.hap1936,839,985 - 36,863,805 (+)NCBImIctTri1.hap1
HiC_Itri_2NW_02440528532,130,309 - 32,150,720 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648214,147,667 - 14,169,074 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648214,147,716 - 14,168,758 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NIPAL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl837,936,847 - 37,962,908 (+)EnsemblSscrofa11.1 EnsemblsusScr11Sscrofa11.1
Sscrofa11.1837,936,812 - 37,963,492 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NIPAL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mChlSab1.0.hap1272,370,665 - 2,392,859 (-)NCBImChlSab1.0.hap1
Vero_WHO_p1.0NW_02366604748,224,804 - 48,246,768 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
ChlSab1.1272,211,034 - 2,231,648 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl272,211,562 - 2,231,617 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Nipal1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476118,923,352 - 18,949,288 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
HetGla_female_1.0 EnsemblNW_00462476118,923,369 - 18,949,324 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
Naked mole-rat maternal Ensembl1018,805,257 - 18,828,840 (-)Ensembl
Nipal1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11129,460,845 - 29,484,509 (+)NCBIRrattus_CSIRO_v1Rrattus_CSIRO_v1

Variants

.
Variants in Nipal1
225 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:35
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000034642
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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141787564536079022Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14939329839411170Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143123808072970315Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143067446985041098Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143112133339507682Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14862139853621398Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141891545442433608Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142252151767521517Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141889519263895192Rat
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)141790672654251504Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14862139853621398Rat

Markers in Region
RH142374  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21435,516,296 - 35,516,460 (+)MAPPERmRatBN7.2
Rnor_6.01438,082,671 - 38,082,834NCBIRnor6.0
Rnor_5.01437,892,966 - 37,893,129UniSTSRnor5.0
RGSC_v3.41437,919,924 - 37,920,087UniSTSRGSC3.4
RGSC_v3.41437,972,923 - 37,973,086UniSTSRGSC3.4
Celera1434,770,158 - 34,770,321UniSTS
Cytogenetic Map14p11UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
259 156 552 1330 2294 1006 1724 128 870 486 854 154 4925 2306 414 2205 38 1375 709 907 152 150

Sequence


Ensembl Acc Id: ENSRNOT00000034642   ⟹   ENSRNOP00000031068
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1435,540,324 - 35,561,640 (-)Ensembl
Rnor_6.0 Ensembl1438,106,712 - 38,128,024 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000090303   ⟹   ENSRNOP00000073165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1438,104,047 - 38,128,015 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000103689   ⟹   ENSRNOP00000081827
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1435,891,647 - 35,915,658 (-)Ensembl
mRatBN7.2 Ensembl1435,540,324 - 35,561,659 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000153791   ⟹   ENSRNOP00000111667
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1435,891,647 - 35,915,658 (-)Ensembl
RefSeq Acc Id: NM_001401452   ⟹   NP_001388381
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81435,891,647 - 35,915,658 (-)NCBI
mRatBN7.21435,537,641 - 35,561,656 (-)NCBI
Dahl_SR_JrHsd1436,181,961 - 36,205,899 (-)NCBI
Lyon_Normotensive1436,294,927 - 36,318,864 (-)NCBI
Lyon_Hypertensive1436,292,172 - 36,316,109 (-)NCBI
F344_StmMcwi1436,314,243 - 36,338,180 (-)NCBI
RefSeq Acc Id: XM_039091702   ⟹   XP_038947630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81435,891,645 - 35,897,293 (-)NCBI
mRatBN7.21435,537,641 - 35,543,288 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001388381 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947630 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89988 (Get FASTA)   NCBI Sequence Viewer  
  EDL89989 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000081827
  ENSRNOP00000081827.1
  ENSRNOP00000111667.1
Ensembl Acc Id: ENSRNOP00000073165   ⟸   ENSRNOT00000090303
Ensembl Acc Id: ENSRNOP00000031068   ⟸   ENSRNOT00000034642
RefSeq Acc Id: XP_038947630   ⟸   XM_039091702
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000081827   ⟸   ENSRNOT00000103689
RefSeq Acc Id: NP_001388381   ⟸   NM_001401452
- UniProtKB: A0A0G2K4T6 (UniProtKB/TrEMBL),   A0ABK0M8A9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000111667   ⟸   ENSRNOT00000153791

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K4T6-F1-model_v2 AlphaFold A0A0G2K4T6 1-416 view protein structure

Transcriptome

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

Promoters
RGD ID:13699301
Promoter ID:EPDNEW_R9824
Type:initiation region
Name:Nipal1_1
Description:NIPA-like domain containing 1
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_6.01438,128,000 - 38,128,060EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310092 AgrOrtholog
BioCyc Gene G2FUF-15852 BioCyc
Ensembl Genes ENSRNOG00000025882 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000103689 ENTREZGENE
  ENSRNOT00000103689.2 UniProtKB/TrEMBL
  ENSRNOT00000153791.1 UniProtKB/TrEMBL
InterPro DUF803 UniProtKB/TrEMBL
  EmrE-like UniProtKB/TrEMBL
KEGG Report rno:289594 UniProtKB/TrEMBL
NCBI Gene 289594 ENTREZGENE
PANTHER DUF803 UniProtKB/TrEMBL
  MAGNESIUM TRANSPORTER NIPA3 UniProtKB/TrEMBL
Pfam DUF803 UniProtKB/TrEMBL
PhenoGen Nipal1 PhenoGen
RatGTEx ENSRNOG00000025882 RatGTEx
Superfamily-SCOP Multidrug resistance efflux transporter EmrE UniProtKB/TrEMBL
UniProt A0A0G2K4T6 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0M8A9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Nipal1  NIPA-like domain containing 1  Npal1  NIPA-like domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Npal1  NIPA-like domain containing 1   Npal1_predicted  NIPA-like domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Npal1_predicted  NIPA-like domain containing 1 (predicted)  RGD1310092_predicted  similar to NIPA2 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1310092_predicted  similar to NIPA2 (predicted)  LOC289594_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC289594_predicted  similar to NIPA2 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL