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    NPAT nuclear protein, coactivator of histone transcription [ Homo sapiens (human) ]

    Gene ID: 4863, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NPATprovided by HGNC
    Official Full Name
    nuclear protein, coactivator of histone transcriptionprovided by HGNC
    Primary source
    HGNC:HGNC:7896
    See related
    Ensembl:ENSG00000149308 MIM:601448; AllianceGenome:HGNC:7896
    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
    E14; p220; E14/NPAT
    Summary
    Enables transcription coactivator activity and transcription corepressor activity. Involved in cell cycle G1/S phase transition and positive regulation of transcription by RNA polymerase II. Located in Cajal body; Gemini of coiled bodies; and cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 6.0), spleen (RPKM 3.9) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See NPAT in Genome Data Viewer
    Location:
    11q22.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (108157215..108222638, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (108164767..108230180, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (108027942..108093365, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902748 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:107991956-107992494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5482 Neighboring gene MPRA-validated peak1447 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr11:108021496-108021664 Neighboring gene acetyl-CoA acetyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3877 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108047982 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108089151 Neighboring gene NANOG hESC enhancer GRCh37_chr11:108089784-108090285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5487 Neighboring gene MPRA-validated peak1450 silencer Neighboring gene MPRA-validated peak1449 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108140516 Neighboring gene ATM serine/threonine kinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:108147863-108148662 Neighboring gene chromosome 11 open reading frame 65 Neighboring gene MPRA-validated peak1451 silencer Neighboring gene MPRA-validated peak1452 silencer Neighboring gene MPRA-validated peak1453 silencer Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108273376 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108294773 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108301322 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108309656 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108323261 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108333620 Neighboring gene Sharpr-MPRA regulatory region 13200 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:108337475-108338327 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:108344264 Neighboring gene uncharacterized LOC124902749 Neighboring gene protein O-glucosyltransferase 3

    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. Identification and characterization of a new gene physically linked to the ATM gene. Imai T, et al. Genome Res, 1996 May. PMID 8743993
    2. Exome sequencing reveals germline NPAT mutation as a candidate risk factor for Hodgkin lymphoma. Saarinen S, et al. Blood, 2011 Jul 21. PMID 21562039
    3. Germline NPAT inactivating variants as cause of hereditary colorectal cancer. Terradas M, et al. Eur J Hum Genet, 2024 Jul. PMID 38778081,
    4. The cyclin E/Cdk2 substrate and Cajal body component p220(NPAT) activates histone transcription through a novel LisH-like domain. Wei Y, et al. Mol Cell Biol, 2003 May. PMID 12724424, Free PMC Article
    5. Characterization of functional regions for nuclear localization of NPAT. Sagara M, et al. J Biochem, 2002 Dec. PMID 12473189

    See all (60) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Germline NPAT inactivating variants as cause of hereditary colorectal cancer.
      Title: Germline NPAT inactivating variants as cause of hereditary colorectal cancer.
    2. The genetic association of the transcription factor NPAT with glycemic response to metformin involves regulation of fuel selection.
      Title: The genetic association of the transcription factor NPAT with glycemic response to metformin involves regulation of fuel selection.
    3. Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations.
      Title: Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations.
    4. Cpn10 has a role in the spatial regulation of NPAT signaling
      Title: Interaction of Heat Shock Protein Cpn10 with the Cyclin E/Cdk2 Substrate Nuclear Protein Ataxia-Telangiectasia (NPAT) Is Involved in Regulating Histone Transcription.
    5. The conserved C-terminal domain shared by FLASH, YARP, and Mute recognizes the C-terminal sequence of NPAT orthologues, thus acting as a signal targeting proteins to histone locus bodies.
      Title: A conserved interaction that is essential for the biogenesis of histone locus bodies.
    6. Genetic variants of NPAT-ATM and AURKA are associated with an individual early adverse reaction in the gastrointestinal tract of patients with cervical cancer treated with pelvic radiation therapy
      Title: Genetic variants of NPAT-ATM and AURKA are associated with an early adverse reaction in the gastrointestinal tract of patients with cervical cancer treated with pelvic radiation therapy.
    7. NPAT is thus far the first gene implicated in nodular lymphocyte predominant Hodgkin lymphoma predisposition.
      Title: Exome sequencing reveals germline NPAT mutation as a candidate risk factor for Hodgkin lymphoma.
    8. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    9. NPAT is essential for histone mRNA 3' end processing and recruits CDK9 to replication-dependent histone genes.
      Title: Induced G1 cell-cycle arrest controls replication-dependent histone mRNA 3' end processing through p21, NPAT and CDK9.
    10. Cyclin D2 and the CDK substrate p220(NPAT) are required for self-renewal of human embryonic stem cells.
      Title: Cyclin D2 and the CDK substrate p220(NPAT) are required for self-renewal of human embryonic stem cells.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    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)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription corepressor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell cycle G1/S phase transition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Cajal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Gemini of coiled bodies IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein NPAT
    Names
    nuclear protein of the ATM locus
    nuclear protein of the ataxia telangiectasia mutated locus
    nuclear protein, ataxia-telangiectasia locus
    nuclear protein, co-activator of histone transcription

    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_001321307.1 → NP_001308236.1  protein NPAT isoform 1

      Status: VALIDATED

      Source sequence(s)
      AP001925, AP002433
      UniProtKB/TrEMBL
      B9EG70
      Conserved Domains (2) summary
      pfam09528
      Location:244 → 857
      Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)
      pfam15712
      Location:759 → 1434
      NPAT_C; NPAT C terminus

    2. NM_002519.3 → NP_002510.2  protein NPAT isoform 2

      See identical proteins and their annotated locations for NP_002510.2

      Status: VALIDATED

      Source sequence(s)
      AP002433, BC050561, BC094769, DA338219, X97186
      Consensus CDS
      CCDS41710.1
      UniProtKB/Swiss-Prot
      A8K1V5, A8K6M2, Q13632, Q14207, Q14967, Q16580, Q86W55, Q8IWE9
      UniProtKB/TrEMBL
      B9EG70
      Related
      ENSP00000278612.8, ENST00000278612.9
      Conserved Domains (2) summary
      pfam09528
      Location:244 → 857
      Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)
      pfam15712
      Location:759 → 1427
      NPAT_C; NPAT C terminus

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      108157215..108222638 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011542854.3 → XP_011541156.1  protein NPAT isoform X1

      UniProtKB/TrEMBL
      B9EG70
      Conserved Domains (2) summary
      pfam09528
      Location:244 → 857
      Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)
      pfam15712
      Location:759 → 1436
      NPAT_C; NPAT C terminus

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      108164767..108230180 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054368884.1 → XP_054224859.1  protein NPAT isoform X1

      UniProtKB/TrEMBL
      B9EG70
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14207.3 GenPept UniProtKB/Swiss-Prot:Q14207

    Gene LinkOut

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

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