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Aliases for NIPAL3 Gene

Aliases for NIPAL3 Gene

  • NIPA Like Domain Containing 3 2 3 5
  • NIPA-Like Protein 3 3 4
  • NPAL3 3 4
  • DJ462O23.2 3

External Ids for NIPAL3 Gene

Previous HGNC Symbols for NIPAL3 Gene

  • NPAL3

Previous GeneCards Identifiers for NIPAL3 Gene

  • GC01P024616
  • GC01P024742
  • GC01P022994

Summaries for NIPAL3 Gene

GeneCards Summary for NIPAL3 Gene

NIPAL3 (NIPA Like Domain Containing 3) is a Protein Coding gene. Among its related pathways are Miscellaneous transport and binding events and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include magnesium ion transmembrane transporter activity. An important paralog of this gene is NIPAL2.

Additional gene information for NIPAL3 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NIPAL3 Gene

Genomics for NIPAL3 Gene

GeneHancer (GH) Regulatory Elements for NIPAL3 Gene

Promoters and enhancers for NIPAL3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J024411 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 616.6 +2.1 2085 8.4 SP1 ZFX CC2D1A MNT CBFA2T2 ZNF148 MLLT1 ZNF121 CEBPG GTF2F1 STPG1 NIPAL3 SRRM1 SRSF10 ELOA RCAN3 SYF2 NCMAP ENSG00000261349
GH01J024438 Enhancer 1.2 Ensembl ENCODE dbSUPER 22.9 +24.6 24589 1.7 CBFA2T2 ZNF148 GTF2F1 SMARCA4 DPF2 IKZF1 ZIC2 PHF21A ATF1 REST STPG1 NIPAL3 SRSF10 SRRM1 NCMAP ENSG00000232298 GRHL3 GC01P024477
GH01J024390 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 15.5 -21.1 -21098 3.4 SP1 CC2D1A CTCF SP7 RELA CREM RAD21 IKZF1 RXRA ARID2 STPG1 NIPAL3 IFNLR1 GRHL3 ENSG00000232298 NCMAP GC01P024325
GH01J024501 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.4 +91.4 91409 7.9 ELF3 CBFA2T2 MLLT1 ZNF121 ZNF384 SP7 SP5 EGR1 ZNF639 SMARCA4 RCAN3 NCMAP NIPAL3 STPG1 GRHL3 RUNX3 SRRM1 GC01M024529 RCAN3AS
GH01J024362 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.6 -49.1 -49144 3.6 CREM PRDM1 IKZF1 FOSL2 ZNF600 ZIC2 PKNOX1 ZNF629 CEBPB CHD2 STPG1 NIPAL3 GRHL3 PNRC2 GC01P024325
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NIPAL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NIPAL3 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • E47
  • NF-Y
  • POU3F2
  • Tal-1beta

Genomic Locations for NIPAL3 Gene

Genomic Locations for NIPAL3 Gene
chr1:24,413,674-24,472,983
(GRCh38/hg38)
Size:
59,310 bases
Orientation:
Plus strand
chr1:24,742,245-24,799,473
(GRCh37/hg19)
Size:
57,229 bases
Orientation:
Plus strand

Genomic View for NIPAL3 Gene

Genes around NIPAL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NIPAL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NIPAL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NIPAL3 Gene

Proteins for NIPAL3 Gene

  • Protein details for NIPAL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6P499-NPAL3_HUMAN
    Recommended name:
    NIPA-like protein 3
    Protein Accession:
    Q6P499
    Secondary Accessions:
    • A2A298
    • Q6MZT9
    • Q9BVE6

    Protein attributes for NIPAL3 Gene

    Size:
    406 amino acids
    Molecular mass:
    44742 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for NIPAL3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NIPAL3 Gene

Post-translational modifications for NIPAL3 Gene

  • Glycosylation at isoforms=2, 3166
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NIPAL3 Gene

Domains & Families for NIPAL3 Gene

Gene Families for NIPAL3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for NIPAL3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NIPAL3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ92779 (A2A298_HUMAN)
  • NIPA-like protein 3 (NPAL3_HUMAN)
  • NPAL3 protein (Q96EB9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6P499

UniProtKB/Swiss-Prot:

NPAL3_HUMAN :
  • Belongs to the NIPA family.
Family:
  • Belongs to the NIPA family.
genes like me logo Genes that share domains with NIPAL3: view

Function for NIPAL3 Gene

Phenotypes From GWAS Catalog for NIPAL3 Gene

Gene Ontology (GO) - Molecular Function for NIPAL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0015095 magnesium ion transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with NIPAL3: view
genes like me logo Genes that share phenotypes with NIPAL3: view

Animal Models for NIPAL3 Gene

MGI Knock Outs for NIPAL3:

Animal Model Products

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for NIPAL3 - Now 50% OFF >
  • * NIPAL3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * NIPAL3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NIPAL3 Gene

Localization for NIPAL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NIPAL3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NIPAL3 gene
Compartment Confidence
plasma membrane 3
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NIPAL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NIPAL3: view

Pathways & Interactions for NIPAL3 Gene

genes like me logo Genes that share pathways with NIPAL3: view

Pathways by source for NIPAL3 Gene

Gene Ontology (GO) - Biological Process for NIPAL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015693 magnesium ion transport IBA,IEA 21873635
GO:1903830 magnesium ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with NIPAL3: view

No data available for SIGNOR curated interactions for NIPAL3 Gene

Drugs & Compounds for NIPAL3 Gene

No Compound Related Data Available

Transcripts for NIPAL3 Gene

Unigene Clusters for NIPAL3 Gene

NIPA-like domain containing 3:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for NIPAL3 - Now 50% OFF >
  • * NIPAL3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * NIPAL3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for NIPAL3 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f ^ 3a · 3b · 3c · 3d · 3e · 3f ^ 4 ^ 5a · 5b · 5c · 5d · 5e · 5f ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ·
SP1: - - - - - - - - - - -
SP2: - - - - - - - - - - -
SP3: - - - - - - - - - - - - - - - - - - -
SP4:
SP5: - - - - - - - - - - - - - - - - - - -
SP6:
SP7:
SP8:
SP9: - - - - - - - - - - - - - - - - -
SP10: - - - - - - - - - - - -
SP11: - - - - - - - - - - - - - - - - -
SP12: - - - - - - - - - - - -
SP13: - - - - - - - - - -
SP14: - -
SP15: - - - - - - - - - - - - - - -
SP16: - - - - - - - - -
SP17: - -
SP18: - - - -
SP19: - - - - - - - - - - -
SP20: - - - -
SP21: - - - - - - -
SP22: - - -
SP23: -

ExUns: 9c · 9d ^ 10a · 10b · 10c · 10d · 10e ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16a · 16b · 16c · 16d · 16e ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22 ^
SP1: - - - - -
SP2: -
SP3: - - -
SP4: - -
SP5:
SP6:
SP7: - -
SP8: - - - -
SP9: - - -
SP10:
SP11:
SP12:
SP13:
SP14: -
SP15:
SP16:
SP17:
SP18:
SP19: - - - - - - - - -
SP20:
SP21:
SP22:
SP23:

Relevant External Links for NIPAL3 Gene

GeneLoc Exon Structure for
NIPAL3
ECgene alternative splicing isoforms for
NIPAL3

Expression for NIPAL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NIPAL3 Gene

mRNA differential expression in normal tissues according to GTEx for NIPAL3 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x4.6) and Brain - Cerebellar Hemisphere (x4.3).

Protein differential expression in normal tissues from HIPED for NIPAL3 Gene

This gene is overexpressed in Fetal Brain (35.6), Peripheral blood mononuclear cells (12.2), Kidney (10.8), and Ovary (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NIPAL3 Gene



Protein tissue co-expression partners for NIPAL3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NIPAL3 Gene:

NIPAL3

SOURCE GeneReport for Unigene cluster for NIPAL3 Gene:

Hs.523442

Evidence on tissue expression from TISSUES for NIPAL3 Gene

  • Nervous system(5)
genes like me logo Genes that share expression patterns with NIPAL3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NIPAL3 Gene

Orthologs for NIPAL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NIPAL3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NIPAL3 35 34
  • 99.1 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NIPAL3 35 34
  • 90.39 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NIPAL3 35 34
  • 89 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nipal3 34
  • 86.62 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NIPAL3 35
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nipal3 17 35 34
  • 85.71 (n)
oppossum
(Monodelphis domestica)
Mammalia NIPAL3 35
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves NIPAL3 35 34
  • 74.88 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 24 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia nipal3 34
  • 70.22 (n)
zebrafish
(Danio rerio)
Actinopterygii nipal3 35 34
  • 66.57 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta spict 35
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea nipa-1 35
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 34 (a)
OneToMany
Species where no ortholog for NIPAL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NIPAL3 Gene

ENSEMBL:
Gene Tree for NIPAL3 (if available)
TreeFam:
Gene Tree for NIPAL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NIPAL3: view image

Paralogs for NIPAL3 Gene

Paralogs for NIPAL3 Gene

(3) SIMAP similar genes for NIPAL3 Gene using alignment to 3 proteins:

  • NPAL3_HUMAN
  • A6NN97_HUMAN
  • H0Y4I9_HUMAN
genes like me logo Genes that share paralogs with NIPAL3: view

Variants for NIPAL3 Gene

Sequence variations from dbSNP and Humsavar for NIPAL3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000040109 -- 24,464,281(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000129929 -- 24,437,226(+) T/G intron_variant
rs1000143615 -- 24,438,302(+) C/G intron_variant
rs1000154445 -- 24,459,790(+) T/A genic_downstream_transcript_variant, intron_variant
rs1000183572 -- 24,437,489(+) C/G/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NIPAL3 Gene

Variant ID Type Subtype PubMed ID
dgv26e212 CNV loss 25503493
esv2675642 CNV deletion 23128226
esv3577791 CNV loss 25503493
esv3585501 CNV loss 21293372
esv994910 CNV insertion 20482838
nsv469575 CNV loss 16826518
nsv545805 CNV loss 21841781
nsv6965 CNV deletion 18451855
nsv834447 CNV loss 17160897

Variation tolerance for NIPAL3 Gene

Residual Variation Intolerance Score: 32.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.51; 29.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NIPAL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NIPAL3
Human Gene Mutation Database (HGMD)
NIPAL3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NIPAL3 Gene

Disorders for NIPAL3 Gene

Additional Disease Information for NIPAL3

No disorders were found for NIPAL3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NIPAL3 Gene

Publications for NIPAL3 Gene

  1. Targeted disruption of the mouse Npal3 gene leads to deficits in behavior, increased IgE levels, and impaired lung function. (PMID: 19738379) Grzmil P … Burfeind P (Cytogenetic and genome research 2009) 3 23 58
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Large-scale concatenation cDNA sequencing. (PMID: 9110174) Yu W … Gibbs RA (Genome research 1997) 2 3 58
  5. A "double adaptor" method for improved shotgun library construction. (PMID: 8619474) Andersson B … Gibbs RA (Analytical biochemistry 1996) 2 3 58

Products for NIPAL3 Gene

  • Biorbyt antibodies for NIPAL3

Sources for NIPAL3 Gene

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