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NIPAL3 NIPA like domain containing 3 [ Homo sapiens (human) ]

Gene ID: 57185, updated on 5-Mar-2024

Summary

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Official Symbol
NIPAL3provided by HGNC
Official Full Name
NIPA like domain containing 3provided by HGNC
Primary source
HGNC:HGNC:25233
See related
Ensembl:ENSG00000001461 MIM:620034; AllianceGenome:HGNC:25233
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NPAL3; SLC57A5; DJ462O23.2
Summary
Predicted to enable magnesium ion transmembrane transporter activity. Predicted to be involved in magnesium ion transport. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in brain (RPKM 18.3), prostate (RPKM 16.8) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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See NIPAL3 in Genome Data Viewer
Location:
1p36.11
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (24413524..24472983)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (24251895..24311350)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (24740014..24799473)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24581311-24581877 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24604941-24605442 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24612590-24613188 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24613189-24613787 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24624394-24624641 Neighboring gene Sharpr-MPRA regulatory region 347 Neighboring gene GRHL3 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24648587-24649104 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:24649105-24649620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 432 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:24661406-24662028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24664014-24664642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24664643-24665269 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24669049-24669863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 396 Neighboring gene grainyhead like transcription factor 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:24691307-24692506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 398 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24714266-24714492 Neighboring gene sperm tail PG-rich repeat containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 400 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:24745074-24746273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:24782303-24782815 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:24784099-24784600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 402 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:24828715-24828887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 433 Neighboring gene MPRA-validated peak119 silencer Neighboring gene RCAN3 antisense RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24860519-24861170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24861821-24862472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:24862473-24863122 Neighboring gene RCAN family member 3 Neighboring gene Sharpr-MPRA regulatory region 2491 Neighboring gene NCMAP divergent transcript

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Targeted disruption of the mouse Npal3 gene leads to deficits in behavior, increased IgE levels, and impaired lung function. Grzmil P, et al. Cytogenet Genome Res, 2009. PMID 19738379
  2. Systematic identification of pathological lamin A interactors. Dittmer TA, et al. Mol Biol Cell, 2014 May. PMID 24623722, Free PMC Article
  3. Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane. Hannigan MM, et al. Mol Cell Proteomics, 2020 Nov. PMID 32788342, Free PMC Article
  4. Large-scale concatenation cDNA sequencing. Yu W, et al. Genome Res, 1997 Apr. PMID 9110174, Free PMC Article
  5. A "double adaptor" method for improved shotgun library construction. Andersson B, et al. Anal Biochem, 1996 Apr 5. PMID 8619474

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Study demonstrates that both human NPAL3 and mouse NPAL3 are ubiquitously expressed and encode highly conserved proteins
    Title: Targeted disruption of the mouse Npal3 gene leads to deficits in behavior, increased IgE levels, and impaired lung function.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp686E22155

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables magnesium ion transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in magnesium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in magnesium ion transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
NIPA-like protein 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001322854.2 → NP_001309783.1  NIPA-like protein 3 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Consensus CDS
    CCDS30631.1
    UniProtKB/Swiss-Prot
    A2A298, Q6MZT9, Q6P499, Q9BVE6
    Conserved Domains (1) summary
    cl23754
    Location:32 → 326
    EamA; EamA-like transporter family

  2. NM_001322855.2 → NP_001309784.1  NIPA-like protein 3 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Consensus CDS
    CCDS30631.1
    UniProtKB/Swiss-Prot
    A2A298, Q6MZT9, Q6P499, Q9BVE6
    Conserved Domains (1) summary
    cl23754
    Location:32 → 326
    EamA; EamA-like transporter family

  3. NM_001322856.2 → NP_001309785.1  NIPA-like protein 3 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Consensus CDS
    CCDS30631.1
    UniProtKB/Swiss-Prot
    A2A298, Q6MZT9, Q6P499, Q9BVE6
    Conserved Domains (1) summary
    cl23754
    Location:32 → 326
    EamA; EamA-like transporter family

  4. NM_001322857.1 → NP_001309786.1  NIPA-like protein 3 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Consensus CDS
    CCDS30631.1
    UniProtKB/Swiss-Prot
    A2A298, Q6MZT9, Q6P499, Q9BVE6
    Conserved Domains (1) summary
    cl23754
    Location:32 → 326
    EamA; EamA-like transporter family

  5. NM_001322858.2 → NP_001309787.1  NIPA-like protein 3 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Conserved Domains (1) summary
    cl23754
    Location:4 → 165
    EamA; EamA-like transporter family

  6. NM_001322859.2 → NP_001309788.1  NIPA-like protein 3 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Conserved Domains (1) summary
    cl23754
    Location:4 → 165
    EamA; EamA-like transporter family

  7. NM_001322860.2 → NP_001309789.1  NIPA-like protein 3 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Conserved Domains (1) summary
    cl23754
    Location:4 → 165
    EamA; EamA-like transporter family

  8. NM_001322861.2 → NP_001309790.1  NIPA-like protein 3 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Conserved Domains (1) summary
    cl23754
    Location:4 → 165
    EamA; EamA-like transporter family

  9. NM_001322862.2 → NP_001309791.1  NIPA-like protein 3 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Consensus CDS
    CCDS81282.1
    UniProtKB/Swiss-Prot
    Q6P499
    Related
    ENSP00000003912.3, ENST00000003912.7
    Conserved Domains (1) summary
    cl23754
    Location:1 → 244
    EamA; EamA-like transporter family

  10. NM_001322863.2 → NP_001309792.1  NIPA-like protein 3 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Consensus CDS
    CCDS81282.1
    UniProtKB/Swiss-Prot
    Q6P499
    Conserved Domains (1) summary
    cl23754
    Location:1 → 244
    EamA; EamA-like transporter family

  11. NM_001322864.2 → NP_001309793.1  NIPA-like protein 3 isoform d

    Status: VALIDATED

    Source sequence(s)
    AL031431

  12. NM_001322865.2 → NP_001309794.1  NIPA-like protein 3 isoform e

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Consensus CDS
    CCDS81280.1
    UniProtKB/Swiss-Prot
    Q6P499
    Related
    ENSP00000350722.4, ENST00000358028.8
    Conserved Domains (1) summary
    cl23754
    Location:32 → 201
    EamA; EamA-like transporter family

  13. NM_001322866.2 → NP_001309795.1  NIPA-like protein 3 isoform f

    Status: VALIDATED

    Source sequence(s)
    AL031431

  14. NM_001322868.2 → NP_001309797.1  NIPA-like protein 3 isoform g

    Status: VALIDATED

    Source sequence(s)
    AL031431

  15. NM_001330409.2 → NP_001317338.1  NIPA-like protein 3 isoform h

    Status: VALIDATED

    Source sequence(s)
    AL031431
    Consensus CDS
    CCDS81281.1
    UniProtKB/TrEMBL
    A6NN97, A8MPU6, Q5TH81
    Related
    ENSP00000343549.2, ENST00000339255.2

  16. NM_020448.5 → NP_065181.1  NIPA-like protein 3 isoform a

    See identical proteins and their annotated locations for NP_065181.1

    Status: VALIDATED

    Source sequence(s)
    AL031431, BC063583, DA223169
    Consensus CDS
    CCDS30631.1
    UniProtKB/Swiss-Prot
    A2A298, Q6MZT9, Q6P499, Q9BVE6
    Related
    ENSP00000363520.4, ENST00000374399.9
    Conserved Domains (1) summary
    cl23754
    Location:32 → 326
    EamA; EamA-like transporter family

RNA

  1. NR_136506.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL031431

  2. NR_136507.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL031431

  3. NR_136508.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL031431

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    24413524..24472983
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541808.3 → XP_011540110.1  NIPA-like protein 3 isoform X1

    Conserved Domains (1) summary
    cl23754
    Location:18 → 312
    EamA; EamA-like transporter family

  2. XM_047425988.1 → XP_047281944.1  NIPA-like protein 3 isoform X2

    UniProtKB/TrEMBL
    A6NN97, A8MPU6, Q5TH81

  3. XM_047425991.1 → XP_047281947.1  NIPA-like protein 3 isoform X4

  4. XM_017001868.2 → XP_016857357.1  NIPA-like protein 3 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    24251895..24311350
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337800.1 → XP_054193775.1  NIPA-like protein 3 isoform X1

  2. XM_054337801.1 → XP_054193776.1  NIPA-like protein 3 isoform X2

    UniProtKB/TrEMBL
    A6NN97, A8MPU6, Q5TH81

  3. XM_054337803.1 → XP_054193778.1  NIPA-like protein 3 isoform X4

  4. XM_054337802.1 → XP_054193777.1  NIPA-like protein 3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P499.1 GenPept UniProtKB/Swiss-Prot:Q6P499

Gene LinkOut

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