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NIPAL1 Gene

protein-coding   GIFtS: 43
GCID: GC04P047917

NIPA-Like Domain Containing 1


(Previous symbol: NPAL1)
  See NIPAL1-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
NIPA-Like Domain Containing 11 2
NPAL11 2 3
Non-Imprinted In Prader-Willi/Angelman Syndrome Region Protein 32 3
NIPA-Like Protein 12 3
Magnesium Transporter NIPA32
NIPA33

External Ids:    HGNC: 271941   Entrez Gene: 1525192   Ensembl: ENSG000001632937   UniProtKB: Q6NVV33   

Export aliases for NIPAL1 gene to outside databases

Previous GC identifers: GC04P047714 GC04P048018 GC04P047339


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for NIPAL1 Gene:
NIPAL1 (NIPA-like domain containing 1) is a protein-coding gene. Diseases associated with NIPAL1 include angelman syndrome. GO annotations related to this gene include magnesium ion transmembrane transporter activity. An important paralog of this gene is NIPA1.

UniProtKB/Swiss-Prot: NIPA3_HUMAN, Q6NVV3
Function: Acts as a Mg(2+) transporter. Can also transport other divalent cations such as Fe(2+), Sr(2+), Ba(2+),
Mn(2+), Cu(2+) and Co(2+) but to a much less extent than Mg(2+) (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000004.11  NC_018915.2  NT_006238.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the NIPAL1 gene promoter:
         NF-YB   CBF-B   CBF-A   NF-YA   NF-YC   CP1C   CP1A   NF-Y   CBF-C   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNIPAL1 promoter sequence
   Search Chromatin IP Primers for NIPAL1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NIPAL1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4p12   Ensembl cytogenetic band:  4p12   HGNC cytogenetic band: 4p12

NIPAL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NIPAL1 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P047917:  view genomic region     (about GC identifiers)

Start:
47,916,159 bp from pter      End:
48,042,188 bp from pter
Size:
126,030 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NIPA3_HUMAN, Q6NVV3 (See protein sequence)
Recommended Name: Magnesium transporter NIPA3  
Size: 410 amino acids; 44638 Da
Secondary accessions: B3KTB0 Q68DA9

Explore the universe of human proteins at neXtProt for NIPAL1: NX_Q6NVV3

Explore proteomics data for NIPAL1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn25, Asn35, Asn50, Asn55

  • See NIPAL1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_997213.1  
    ENSEMBL proteins: 
     ENSP00000295461   ENSP00000425795   ENSP00000422276  

    NIPAL1 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for NIPAL1

     
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    LSBio Antibodies in human, mouse, rat for NIPAL1

    NIPAL1 Assay Products:

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    Cloud-Clone Corp. ELISAs for NIPAL1
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    Search eBioscience for ELISAs for NIPAL1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR008521 Mg_trans_NIPA

    Graphical View of Domain Structure for InterPro Entry Q6NVV3

    ProtoNet protein and cluster: Q6NVV3

    UniProtKB/Swiss-Prot: NIPA3_HUMAN, Q6NVV3
    Similarity: Belongs to the NIPA family


    Find genes that share domains with NIPAL1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NIPA3_HUMAN, Q6NVV3
    Function: Acts as a Mg(2+) transporter. Can also transport other divalent cations such as Fe(2+), Sr(2+), Ba(2+),
    Mn(2+), Cu(2+) and Co(2+) but to a much less extent than Mg(2+) (By similarity)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015095magnesium ion transmembrane transporter activity IEA--
         
    Find genes that share ontologies with NIPAL1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for NIPAL1:
     Decreased Wnt reporter activit 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NIPAL1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for NIPAL1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for NIPAL1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for NIPAL1

    miRNA
    Products:
        
    miRTarBase miRNAs that target NIPAL1:
    hsa-mir-192-5p (MIRT026452), hsa-mir-331-3p (MIRT043429)

    Block miRNA regulation of human, mouse, rat NIPAL1 using miScript Target Protectors
    7 qRT-PCR Assays for microRNAs that regulate NIPAL1:
    hsa-miR-877* hsa-miR-4303 hsa-miR-607 hsa-miR-4328 hsa-miR-3674 hsa-miR-518f* hsa-miR-1279
    SwitchGear 3'UTR luciferase reporter plasmidNIPAL1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for NIPAL1
    Predesigned siRNA for gene silencing in human, mouse, rat NIPAL1

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for NIPAL1

    Clone
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    GenScript: all cDNA clones in your preferred vector: NIPAL1 (NM_207330)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for NIPAL1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NIPAL1

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for NIPAL1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NIPAL1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    NIPA3_HUMAN, Q6NVV3: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with NIPAL1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NIPAL1
    Interactions:

        Search GeneGlobe Interaction Network for NIPAL1

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015693magnesium ion transport ----

    Find genes that share ontologies with NIPAL1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for NIPAL1 (NIPA3)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for NIPAL1 gene: 
    NM_207330.1  

    Unigene Cluster for NIPAL1:

    NIPA-like domain containing 1
    Hs.134190  [show with all ESTs]
    Unigene Representative Sequence: CR749484
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000513724 ENST00000500571(uc003gxr.1) ENST00000508180 ENST00000295461(uc003gxw.3)
    ENST00000511852 ENST00000511123
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat NIPAL1 using miScript Target Protectors
    7 qRT-PCR Assays for microRNAs that regulate NIPAL1:
    hsa-miR-877* hsa-miR-4303 hsa-miR-607 hsa-miR-4328 hsa-miR-3674 hsa-miR-518f* hsa-miR-1279
    SwitchGear 3'UTR luciferase reporter plasmidNIPAL1 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for NIPAL1
    Predesigned siRNA for gene silencing in human, mouse, rat NIPAL1
    Clone
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    OriGene clones in human, mouse for NIPAL1 (see all 6)
    OriGene ORF clones in mouse, rat for NIPAL1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: NIPAL1 (NM_207330)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for NIPAL1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NIPAL1
    Primer
    Products:
        
    OriGene qSTAR qPCR primer pairs in human, mouse for NIPAL1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NIPAL1
      QuantiTect SYBR Green Assays in human, mouse, rat NIPAL1
      QuantiFast Probe-based Assays in human, mouse, rat NIPAL1

    Additional mRNA sequence: 

    AK023734.1 AK095299.1 AL832997.1 BC041434.1 BC067881.1 CR749484.1 

    4 DOTS entries:

    DT.304216  DT.95217185  DT.121240868  DT.121240869 

    Selected AceView cDNA sequences (see all 35):

    CB241441 AK095299 AL832997 BC067881 NM_207330 AU139993 BG111613 AA385555 
    AA779891 CB960388 CB989993 AI769290 AA005203 BX101076 H80181 CB959577 
    AA005287 AK023734 AI079919 CD104403 CB989636 CR749484 AI813952 BM848123 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for NIPAL1    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7
    SP1:                                                                  
    SP2:                                      -                           
    SP3:              -                                                   
    SP4:                                      -     -     -     -         


    ECgene alternative splicing isoforms for NIPAL1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    NIPAL1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    NIPAL1 Expression
    About this image

    NIPAL1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NIPAL1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.134190
        Custom PCR Arrays for NIPAL1
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NIPAL1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for NIPAL1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nipal11 , 5 NIPA-like domain containing 11, 5 84.96(n)1
    87.07(a)1
      5 (38.44 cM)5
    707011  NM_001081205.11  NP_001074674.11 
     726477965 
    chicken
    (Gallus gallus)
    Aves NIPAL11 NIPA-like domain containing 1 70.99(n)
    70.54(a)
      428783  XM_004936053.1  XP_004936110.1 
    lizard
    (Anolis carolinensis)
    Reptilia NIPAL16
    NIPA-like domain containing 1
    70(a)
    1 ↔ 1
    GL343293.1(633520-648619)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia nipal11 NIPA-like domain containing 1 66.26(n)
    71.25(a)
      100491823  XM_002933460.2  XP_002933506.2 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1015836
    zgc:101583
    62(a)
    many ↔ many
    14(40379105-40386292) ENSDARG00000026682
    fruit fly
    (Drosophila melanogaster)
    Insecta spict6
    spichthyin
    45(a)
    1 → many
    2L(12704725-12706683)
    worm
    (Caenorhabditis elegans)
    Secernentea nipa-16
    Protein NIPA-1, isoform b (nipa-1) mRNA, complete ...
    44(a)
    1 → many
    III(3112487-3127117) WBGene00021820
    rice
    (Oryza sativa)
    Liliopsida Os.61712 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 75.42(n)    AK073285.1 


    ENSEMBL Gene Tree for NIPAL1 (if available)
    TreeFam Gene Tree for NIPAL1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NIPAL1 gene
    NIPA12  NIPAL32  NIPAL22  NIPAL42  NIPA22  
    4 SIMAP similar genes for NIPAL1 using alignment to 3 protein entries:     NIPA3_HUMAN (see all proteins):
    NIPA2    NIPAL4    NIPA1    NIPAL2

    Find genes that share paralogs with NIPAL1           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for NIPAL1
    PGOHUM00000247474


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for NIPAL1 (see all 441)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1404933381,2
    C--48017052(+) TAGCCA/GGGCGT 1 -- us2k10--------
    rs1454813371,2
    --48017056(+) CGGGCA/GTGGTG 1 -- us2k10--------
    rs1818159101,2
    --48017068(+) GGGGCA/GCCTGT 1 -- us2k10--------
    rs3216291,2
    C--48017229(+) AACAAA/GCAAAC 1 -- us2k113Minor allele frequency- G:0.03NA WA CSA EA 375
    rs1163159901,2
    F--48017230(+) ACAAGC/GAAACA 1 -- us2k11Minor allele frequency- G:0.05WA 118
    rs1863580791,2
    --48017568(+) AGGCAC/TCCCAG 1 -- us2k10--------
    rs1472650461,2
    --48017617(+) CCCCAC/TCCCTC 1 -- us2k10--------
    rs601416481,2
    C,F--48017622(+) CCCCTC/TACCTT 1 -- us2k12Minor allele frequency- T:0.10WA 120
    rs786213261,2
    C,F--48017639(+) TCTTGA/GGACAG 1 -- us2k12Minor allele frequency- G:0.13NA EA 240
    rs1880176911,2
    --48017689(+) ATCATA/GTCTCA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for NIPAL1 (47916159 - 48042188 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for NIPAL1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NIPAL1
    DNA2.0 Custom Variant and Variant Library Synthesis for NIPAL1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    1 disease for NIPAL1:    
    About MalaCards
    angelman syndrome


    Find genes that share disorders with NIPAL1           About GenesLikeMe


    Export disorders for NIPAL1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for NIPAL1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with NIPAL1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 152519 HGNC: 27194 AceView: LOC152519 Ensembl:ENSG00000163293 euGenes: HUgn152519
    ECgene: NIPAL1 H-InvDB: NIPAL1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for NIPAL1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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