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

    Gene ID: 57185, updated on 10-Dec-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 active in membrane. [provided by Alliance of Genome Resources, Dec 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (24413524..24472983)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (24251895..24311350)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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, ENST00000003912.8
      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_2024_08

    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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