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

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Gene: Nipal1 (NIPA-like domain containing 1) Rattus norvegicus
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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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81435,891,645 - 35,915,658 (-)NCBIGRCr8
mRatBN7.21435,537,641 - 35,561,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,540,324 - 35,561,659 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1435,903,133 - 35,927,070 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01437,207,879 - 37,231,816 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01435,696,250 - 35,720,191 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01438,104,027 - 38,128,038 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,104,047 - 38,128,024 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01437,914,565 - 37,938,564 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41437,965,997 - 37,990,014 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11437,969,451 - 37,993,302 (-)NCBI
Celera1434,793,332 - 34,814,626 (-)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. 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 (-)NCBIGRCr8
mRatBN7.21435,537,641 - 35,561,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,540,324 - 35,561,659 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1435,903,133 - 35,927,070 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01437,207,879 - 37,231,816 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01435,696,250 - 35,720,191 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01438,104,027 - 38,128,038 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1438,104,047 - 38,128,024 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01437,914,565 - 37,938,564 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41437,965,997 - 37,990,014 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11437,969,451 - 37,993,302 (-)NCBI
Celera1434,793,332 - 34,814,626 (-)NCBICelera
Cytogenetic Map14p11NCBI
NIPAL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38448,016,772 - 48,040,173 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl447,914,142 - 48,040,173 (+)EnsemblGRCh38hg38GRCh38
GRCh37448,018,789 - 48,042,190 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36447,713,548 - 47,733,841 (+)NCBINCBI36Build 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 Ensembl
GRCm38572,647,796 - 72,671,078 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl572,647,795 - 72,671,078 (+)EnsemblGRCm38mm10GRCm38
MGSCv37573,039,035 - 73,062,317 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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
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 (-)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1343,829,924 - 43,853,246 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01344,477,241 - 44,500,597 (+)NCBIROS_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_1.0
Nipal1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528532,130,309 - 32,150,720 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648214,147,667 - 14,169,074 (+)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1837,936,812 - 37,963,492 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NIPAL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1272,211,034 - 2,231,648 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl272,211,562 - 2,231,617 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604748,224,804 - 48,246,768 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nipal1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476118,923,369 - 18,949,324 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476118,923,352 - 18,949,288 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nipal1
156 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
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
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
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
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142216796767167967Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
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
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat

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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 10 47 99 91 90 59 25 59 6 215 94 79 45 60 31

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
mRatBN7.2 Ensembl1435,540,324 - 35,561,659 (-)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
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 ENSRNOP00000031068.4
  ENSRNOP00000081827.1
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),   A6JD67 (UniProtKB/TrEMBL)

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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034642.5 UniProtKB/TrEMBL
  ENSRNOT00000103689.1 UniProtKB/TrEMBL
InterPro DUF803 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
  A6JD66_RAT UniProtKB/TrEMBL
  A6JD67 ENTREZGENE, UniProtKB/TrEMBL
  D3Z8L4_RAT 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