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

Gene ID: 4863, updated on 2-Nov-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, Nov 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 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)

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

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

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

Gene LinkOut

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