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    NFATC2IP nuclear factor of activated T cells 2 interacting protein [ Homo sapiens (human) ]

    Gene ID: 84901, updated on 28-Oct-2024

    Summary

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    Official Symbol
    NFATC2IPprovided by HGNC
    Official Full Name
    nuclear factor of activated T cells 2 interacting proteinprovided by HGNC
    Primary source
    HGNC:HGNC:25906
    See related
    Ensembl:ENSG00000176953 MIM:614525; AllianceGenome:HGNC:25906
    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
    ESC2; NIP45; RAD60
    Summary
    Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 11.4), spleen (RPKM 10.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NFATC2IP in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28950937..28967092)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29232053..29248207)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28962258..28978413)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:28917069-28917917 Neighboring gene rabaptin, RAB GTPase binding effector protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7318 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:28937019-28937602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10652 Neighboring gene CD19 molecule Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:28961580-28962114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:28962134-28962634 Neighboring gene NFATC2IP antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:28973628-28973836 Neighboring gene microRNA 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7324 Neighboring gene SPNS lysolipid transporter 1, lysophospholipid Neighboring gene linker for activation of T cells

    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 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. NFATC2IP is a mediator of SUMO-dependent genome integrity. Cho T, et al. Genes Dev, 2024 Apr 17. PMID 38503515, Free PMC Article
    2. Genetic, epigenetic and transcriptional variations at NFATC2IP locus with weight loss in response to diet interventions: The POUNDS Lost Trial. Sun D, et al. Diabetes Obes Metab, 2018 Sep. PMID 29693310, Free PMC Article
    3. Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. Novatchkova M, et al. BMC Bioinformatics, 2005 Feb 7. PMID 15698469, Free PMC Article
    4. Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. Benita Y, et al. Blood, 2010 Jul 1. PMID 20410506, Free PMC Article
    5. Calcium channel TRPV6 promotes breast cancer metastasis by NFATC2IP. Xu X, et al. Cancer Lett, 2021 Oct 28. PMID 34265397

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NFATC2IP is a mediator of SUMO-dependent genome integrity.
      Title: NFATC2IP is a mediator of SUMO-dependent genome integrity.
    2. Calcium channel TRPV6 promotes breast cancer metastasis by NFATC2IP.
      Title: Calcium channel TRPV6 promotes breast cancer metastasis by NFATC2IP.
    3. Targeted deletion of NFAT-Interacting-Protein-(NIP) 45 resolves experimental asthma by inhibiting Innate Lymphoid Cells group 2 (ILC2).
      Title: Targeted deletion of NFAT-Interacting-Protein-(NIP) 45 resolves experimental asthma by inhibiting Innate Lymphoid Cells group 2 (ILC2).
    4. interactions of fat intake with the genetic (rs11150675) and transcriptional (ILMN_1725441) variations at the NFATC2IP locus on 2-year weight change. cis-DNA methylation at cg26663590 of the NFATC2IP locus showed an opposite impact on weight-loss in response to high-fat vs low-fat diet. baseline methylation at cg26663590 causally mediated 52.8% of the effect of rs11150675 on 2-year weight-loss in the high-fat diet group
      Title: Genetic, epigenetic and transcriptional variations at NFATC2IP locus with weight loss in response to diet interventions: The POUNDS Lost Trial.
    5. ZBTB25 functions as a negative regulator of nuclear factor of activated T cells (NF-AT) activation, such that RNA interference mediated knockdown resulted in enhanced activation of target genes.
      Title: Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor.
    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

    EBI GWAS Catalog

    Description
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    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)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14639, MGC126790, MGC138387

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein sumoylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    NFATC2-interacting protein
    Names
    45 kDa NF-AT-interacting protein
    45 kDa NFAT-interacting protein
    nuclear factor of activated T-cells, cytoplasmic 2-interacting protein
    nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein

    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_001394784.1 → NP_001381713.1  NFATC2-interacting protein isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC109460
      Conserved Domains (2) summary
      cd17078
      Location:236 → 309
      Ubl_SLD1_NFATC2ip; SUMO-like domain 1 (SLD1), structurally similar to a beta-grasp ubiquitin-like fold, found in nuclear factor of activated T-cells 2 interacting protein (NFATC2ip) and similar proteins
      cd17079
      Location:319 → 391
      Ubl_SLD2_NFATC2ip; SUMO-like domain 2 (SLD2), structurally similar to a beta-grasp ubiquitin-like fold, found in nuclear factor of activated T-cells 2 interacting protein (NFATC2ip) and similar proteins

    2. NM_001394785.1 → NP_001381714.1  NFATC2-interacting protein isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC109460
      Conserved Domains (1) summary
      cl28922
      Location:278 → 333
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    3. NM_001394786.1 → NP_001381715.1  NFATC2-interacting protein isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC109460
      Conserved Domains (1) summary
      cd17079
      Location:169 → 241
      Ubl_SLD2_NFATC2ip; SUMO-like domain 2 (SLD2), structurally similar to a beta-grasp ubiquitin-like fold, found in nuclear factor of activated T-cells 2 interacting protein (NFATC2ip) and similar proteins

    4. NM_032815.4 → NP_116204.3  NFATC2-interacting protein isoform 1

      See identical proteins and their annotated locations for NP_116204.3

      Status: VALIDATED

      Source sequence(s)
      AC109460
      Consensus CDS
      CCDS10645.1
      UniProtKB/Swiss-Prot
      B7Z4G5, Q66K34, Q6NVK1, Q8NCF5, Q8NFR2, Q96ST9
      Related
      ENSP00000324792.4, ENST00000320805.9
      Conserved Domains (2) summary
      smart00213
      Location:265 → 334
      UBQ; Ubiquitin homologues
      pfam11976
      Location:348 → 417
      Rad60-SLD; Ubiquitin-2 like Rad60 SUMO-like

    RNA

    1. NR_172207.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC109460

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      28950937..28967092
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      29232053..29248207
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NCF5.1 GenPept UniProtKB/Swiss-Prot:Q8NCF5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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