Human Gene NIPA2 (uc001yuz.3)
  Description: Homo sapiens non imprinted in Prader-Willi/Angelman syndrome 2 (NIPA2), transcript variant 3, mRNA.
RefSeq Summary (NM_001008892): This gene encodes a possible magnesium transporter. This gene is located adjacent to the imprinted domain in the Prader-Willi syndrome deletion region of chromosome 15. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 7 and 21.[provided by RefSeq, May 2010].
Transcript (Including UTRs)
   Position: hg19 chr15:23,004,684-23,034,427 Size: 29,744 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr15:23,006,221-23,021,336 Size: 15,116 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:23,004,684-23,034,427)mRNA (may differ from genome)Protein (360 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NIPA2_HUMAN
DESCRIPTION: RecName: Full=Magnesium transporter NIPA2; AltName: Full=Non-imprinted in Prader-Willi/Angelman syndrome region protein 2;
FUNCTION: Acts as a selective Mg(2+) transporter (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein (Potential). Early endosome (By similarity). Note=Recruited to the cell membrane in response to low extracellular magnesium (By similarity).
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Belongs to the NIPA family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: NIPA2
Diseases sorted by gene-association score: angelman syndrome (13), prader-willi syndrome (11), childhood absence epilepsy (7), autosomal recessive congenital ichthyosis (4)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.36 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 344.10 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -175.80374-0.470 Picture PostScript Text
3' UTR -390.121537-0.254 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008521 - Mg_trans_NIPA

Pfam Domains:
PF00892 - EamA-like transporter family
PF05653 - Magnesium transporter NIPA

SCOP Domains:
103481 - Multidrug resistance efflux transporter EmrE

ModBase Predicted Comparative 3D Structure on Q8N8Q9
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0015095 magnesium ion transmembrane transporter activity

Biological Process:
GO:0006811 ion transport
GO:0015693 magnesium ion transport
GO:1903830 magnesium ion transmembrane transport

Cellular Component:
GO:0005768 endosome
GO:0005769 early endosome
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  DQ601777 - Homo sapiens piRNA piR-39843, complete sequence.
U90904 - Human clone 23773 mRNA sequence.
BC000957 - Homo sapiens non imprinted in Prader-Willi/Angelman syndrome 2, mRNA (cDNA clone IMAGE:3451448), partial cds.
BC011775 - Homo sapiens non imprinted in Prader-Willi/Angelman syndrome 2, mRNA (cDNA clone MGC:19609 IMAGE:3640970), complete cds.
AY732242 - Homo sapiens hypothetical protein mRNA, complete cds.
AK096305 - Homo sapiens cDNA FLJ38986 fis, clone NT2RI2005814.
JD160037 - Sequence 141061 from Patent EP1572962.
JD422826 - Sequence 403850 from Patent EP1572962.
JD363671 - Sequence 344695 from Patent EP1572962.
JD067589 - Sequence 48613 from Patent EP1572962.
JD190183 - Sequence 171207 from Patent EP1572962.
JD334665 - Sequence 315689 from Patent EP1572962.
JD321666 - Sequence 302690 from Patent EP1572962.
JD386590 - Sequence 367614 from Patent EP1572962.
JD299308 - Sequence 280332 from Patent EP1572962.
JD286370 - Sequence 267394 from Patent EP1572962.
JD084968 - Sequence 65992 from Patent EP1572962.
AK300843 - Homo sapiens cDNA FLJ54940 complete cds, highly similar to Non-imprinted in Prader-Willi/Angelman syndrome region protein 2 homolog.
AK313584 - Homo sapiens cDNA, FLJ94148.
JF432506 - Synthetic construct Homo sapiens clone IMAGE:100073727 non imprinted in Prader-Willi/Angelman syndrome 2 (NIPA2) gene, encodes complete protein.
KJ899681 - Synthetic construct Homo sapiens clone ccsbBroadEn_09075 NIPA2 gene, encodes complete protein.
JD060271 - Sequence 41295 from Patent EP1572962.
JD490278 - Sequence 471302 from Patent EP1572962.
JD283117 - Sequence 264141 from Patent EP1572962.
JD151750 - Sequence 132774 from Patent EP1572962.
JD391549 - Sequence 372573 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8N8Q9 (Reactome details) participates in the following event(s):

R-HSA-5336453 NIPAs transport Mg2+ from extracellular region to cytosol
R-HSA-5223345 Miscellaneous transport and binding events
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: NIPA2_HUMAN, NM_001008892, NP_112184, Q8N8Q9, Q96F03, Q9BVS2
UCSC ID: uc001yuz.3
RefSeq Accession: NM_001008892
Protein: Q8N8Q9 (aka NIPA2_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001008892.2
exon count: 6CDS single in 3' UTR: no RNA size: 2994
ORF size: 1083CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2179.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.