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NIPAL2 NIPA like domain containing 2 [ Homo sapiens (human) ]

Gene ID: 79815, updated on 27-Nov-2024

Summary

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Official Symbol
NIPAL2provided by HGNC
Official Full Name
NIPA like domain containing 2provided by HGNC
Primary source
HGNC:HGNC:25854
See related
Ensembl:ENSG00000104361 AllianceGenome:HGNC:25854
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
NPAL2; SLC57A4
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, Nov 2024]
Expression
Ubiquitous expression in skin (RPKM 16.1), prostate (RPKM 7.7) and 25 other tissues See more
Orthologs
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Genomic context

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See NIPAL2 in Genome Data Viewer
Location:
8q22.2
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (98189826..98294235, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (99315312..99419709, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (99202054..99306463, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27677 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27678 Neighboring gene tRNA-undetermined (NNN) 2-1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19395 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:99177852-99179051 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:99179424-99180035 Neighboring gene reactive intermediate imine deaminase A homolog Neighboring gene NIPAL2 antisense RNA 1 Neighboring gene POP1 homolog, ribonuclease P/MRP subunit Neighboring gene RNA, U6 small nuclear 914, pseudogene Neighboring gene uncharacterized LOC105375659 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:99271842-99273041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19396 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:99317371-99318570 Neighboring gene NANOG hESC enhancer GRCh37_chr8:99355446-99355947 Neighboring gene Sharpr-MPRA regulatory region 13929 Neighboring gene uncharacterized LOC124901988 Neighboring gene Sharpr-MPRA regulatory region 12621 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:99396932-99397599 Neighboring gene serine/threonine kinase 3 Neighboring gene microRNA 9903

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. Mutations in ichthyin a new gene on chromosome 5q33 in a new form of autosomal recessive congenital ichthyosis. Lefèvre C, et al. Hum Mol Genet, 2004 Oct 15. PMID 15317751
  2. Gene expression profile of human bone marrow stromal cells: high-throughput expressed sequence tag sequencing analysis. Jia L, et al. Genomics, 2002 Jan. PMID 11827452
  3. Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans. Del-Aguila JL, et al. Pharmacogenomics J, 2014 Feb. PMID 23400010, Free PMC Article
  4. Systematic protein-protein interaction mapping for clinically relevant human GPCRs. Sokolina K, et al. Mol Syst Biol, 2017 Mar 15. PMID 28298427, Free PMC Article
  5. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

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

EBI GWAS Catalog

Description
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
EBI GWAS Catalog

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

  • FLJ13955

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables magnesium ion transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
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 2

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_001321635.2 → NP_001308564.1  NIPA-like protein 2 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AI753381, AK024017, AK025015, BC144055, BU677761, DA482369
    Consensus CDS
    CCDS83310.1
    UniProtKB/Swiss-Prot
    A2RTY8, Q9H841
    Related
    ENSP00000407087.2, ENST00000430223.7
    Conserved Domains (1) summary
    cl23754
    Location:45 → 332
    EamA; EamA-like transporter family

  2. NM_001321636.2 → NP_001308565.1  NIPA-like protein 2 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon resultiing in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (c) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    AI753381, AK024017, AK025015, BC144055, BU677761, DA482369
    UniProtKB/Swiss-Prot
    Q9H841
    Conserved Domains (1) summary
    cl23754
    Location:45 → 315
    EamA; EamA-like transporter family

  3. NM_024759.3 → NP_079035.1  NIPA-like protein 2 isoform b

    See identical proteins and their annotated locations for NP_079035.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an additional exon that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    AI753381, AK024017, AK025015, BU677761, DA482369
    Consensus CDS
    CCDS6278.1
    UniProtKB/Swiss-Prot
    Q9H841
    Related
    ENSP00000339256.3, ENST00000341166.3
    Conserved Domains (1) summary
    cl23754
    Location:45 → 332
    EamA; EamA-like transporter family

RNA

  1. NR_135745.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI753381, AK024017, AK025015, AL706246, AW082976, BC144055, BU677761, DA482369

  2. NR_135746.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains two additional internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI753381, AK024017, AK025015, AL706246, AP003439, AW082976, BC144055, BU677761, DA482369

  3. NR_135747.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI753381, AK024017, AK025015, BC144055, BP346328, BU677761, DA184376, DA482369, DC402113

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    98189826..98294235 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011517302.4 → XP_011515604.2  NIPA-like protein 2 isoform X1

    Conserved Domains (1) summary
    cl23754
    Location:45 → 186
    EamA; EamA-like transporter family

  2. XM_047422243.1 → XP_047278199.1  NIPA-like protein 2 isoform X2

RNA

  1. XR_928352.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    99315312..99419709 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361244.1 → XP_054217219.1  NIPA-like protein 2 isoform X1

  2. XM_054361245.1 → XP_054217220.1  NIPA-like protein 2 isoform X2

RNA

  1. XR_008487882.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H841.2 GenPept UniProtKB/Swiss-Prot:Q9H841

Gene LinkOut

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