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

Gene ID: 84901, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in lymph node (RPKM 11.4), spleen (RPKM 10.6) and 25 other tissues See more
Orthologs
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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)

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.

Chemical Information
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