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PML PML nuclear body scaffold [ Homo sapiens (human) ]

Gene ID: 5371, updated on 4-Oct-2020

Summary

Official Symbol
PMLprovided by HGNC
Official Full Name
PML nuclear body scaffoldprovided by HGNC
Primary source
HGNC:HGNC:9113
See related
Ensembl:ENSG00000140464 MIM:102578
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MYL; RNF71; PP8675; TRIM19
Summary
The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in fat (RPKM 11.8), spleen (RPKM 8.1) and 25 other tissues See more
Orthologs

Genomic context

See PML in Genome Data Viewer
Location:
15q24.1
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (73994716..74047827)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74287014..74340160)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene LOXL1 antisense RNA 1 Neighboring gene lysyl oxidase like 1 Neighboring gene stomatin like 1 Neighboring gene dynamin 1 pseudogene 33 Neighboring gene RNA, 7SL, cytoplasmic 429, pseudogene Neighboring gene golgin A6 family member A

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
GeneReviews: Not available
Genome-wide association identifies three new susceptibility loci for Paget's disease of bone.
GeneReviews: Not available
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
GeneReviews: Not available

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of PML enhances HIV-1 infectivity and reverse transcription in primary human foreskin fibroblast cells, but not in various T or myeloid cell lines PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env PML, TopBP1, NBS1 or ATM-induced activation of phosphorylation of Chk2 participates in the DNA damage-elicited pro-apoptotic cascade that leads to the demise of Env-elicited syncytia PubMed
env Interactions between tumor suppressor protein PML, TopBP1 and ATM exhibit in HIV-1 Env-elicited syncytia PubMed
env Tumor suppressor protein PML is required for the activating phosphorylation of ATM, p38 MAPK, and p53 in HIV-1 Env-elicited syncytia PubMed
Tat tat Data suggests that PML proteins regulate Tat-mediated transcriptional activation by modulating the availability of cyclin T1 and other essential cofactors to the transcription machinery PubMed
integrase gag-pol HIV-1 preintegration complexes containing HIV-1 integrase induce the cytoplasmic recruitment of integrase interactor 1 (INI1, hSNF5) and PML and associate with these cellular proteins before migrating to the nucleus PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
SMAD binding IEA
Inferred from Electronic Annotation
more info
 
SUMO binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
sumo-dependent protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin-protein transferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest ISS
Inferred from Sequence or Structural Similarity
more info
 
PML body organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
PML body organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
activation of cysteine-type endopeptidase activity involved in apoptotic process IEA
Inferred from Electronic Annotation
more info
 
branching involved in mammary gland duct morphogenesis IEA
Inferred from Electronic Annotation
more info
 
cell cycle arrest IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell fate commitment IEA
Inferred from Electronic Annotation
more info
 
cellular response to interleukin-4 IEA
Inferred from Electronic Annotation
more info
 
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
cellular senescence IDA
Inferred from Direct Assay
more info
PubMed 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
common-partner SMAD protein phosphorylation IEA
Inferred from Electronic Annotation
more info
 
defense response to virus IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum calcium ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
entrainment of circadian clock by photoperiod ISS
Inferred from Sequence or Structural Similarity
more info
 
extrinsic apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
 
fibroblast migration IEA
Inferred from Electronic Annotation
more info
 
innate immune response IDA
Inferred from Direct Assay
more info
PubMed 
interferon-gamma-mediated signaling pathway TAS
Traceable Author Statement
more info
 
intrinsic apoptotic signaling pathway in response to DNA damage IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator ISS
Inferred from Sequence or Structural Similarity
more info
 
intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress IEA
Inferred from Electronic Annotation
more info
 
intrinsic apoptotic signaling pathway in response to oxidative stress IEA
Inferred from Electronic Annotation
more info
 
maintenance of protein location in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
myeloid cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell growth IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of viral release from host cell IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of extrinsic apoptotic signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of fibroblast proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
protein import into nucleus IEA
Inferred from Electronic Annotation
more info
 
protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
regulation of calcium ion transport into cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell adhesion IEA
Inferred from Electronic Annotation
more info
 
regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of double-strand break repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to UV IEA
Inferred from Electronic Annotation
more info
 
response to cytokine IDA
Inferred from Direct Assay
more info
PubMed 
response to gamma radiation IEA
Inferred from Electronic Annotation
more info
 
response to hypoxia IDA
Inferred from Direct Assay
more info
PubMed 
retinoic acid receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transforming growth factor beta receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
PML body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
PML body IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with PML body IDA
Inferred from Direct Assay
more info
PubMed 
PML body TAS
Traceable Author Statement
more info
PubMed 
chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 
early endosome membrane IEA
Inferred from Electronic Annotation
more info
 
extrinsic component of endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
heterochromatin IEA
Inferred from Electronic Annotation
more info
 
nuclear chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
nuclear matrix IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
protein PML
Names
PML/RARA fusion
RING finger protein 71
probable transcription factor PML
promyelocytic leukemia protein
promyelocytic leukemia, inducer of
tripartite motif protein TRIM19
tripartite motif-containing protein 19

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029036.1 RefSeqGene

    Range
    5044..58155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002675.4NP_002666.1  protein PML isoform 6

    See identical proteins and their annotated locations for NP_002666.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 3' UTR and the 3' coding region compared to variant 1. The resulting isoform (6, also known as PML-IV, PML-X and TRIM19zeta) contains a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BF510860, X63131
    Consensus CDS
    CCDS45297.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000378567.3, ENST00000395135.7
    Conserved Domains (4) summary
    smart00336
    Location:124166
    BBOX; B-Box-type zinc finger
    pfam00097
    Location:5791
    zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
    pfam12126
    Location:240570
    DUF3583; Protein of unknown function (DUF3583)
    pfam14197
    Location:231293
    Cep57_CLD_2; Centrosome localization domain of PPC89
  2. NM_033238.3NP_150241.2  protein PML isoform 1

    See identical proteins and their annotated locations for NP_150241.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (1, also known as TRIM19alpha).
    Source sequence(s)
    AB209411, AC013486, M79462, X63131
    Consensus CDS
    CCDS10255.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000268058.3, ENST00000268058.8
    Conserved Domains (5) summary
    smart00336
    Location:124166
    BBOX; B-Box-type zinc finger
    pfam00097
    Location:5791
    zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
    pfam12126
    Location:240570
    DUF3583; Protein of unknown function (DUF3583)
    pfam14197
    Location:231293
    Cep57_CLD_2; Centrosome localization domain of PPC89
    cl10012
    Location:610758
    DnaQ_like_exo; DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily
  3. NM_033239.3NP_150242.1  protein PML isoform 9

    See identical proteins and their annotated locations for NP_150242.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) differs in the 3' UTR and the 3' coding region compared to variant 1. The resulting isoform (9, also known as PML-II and TRIM19kappa) contains a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC034251, X63131
    Consensus CDS
    CCDS10257.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000268059.6, ENST00000268059.10
    Conserved Domains (5) summary
    smart00336
    Location:124166
    BBOX; B-Box-type zinc finger
    pfam00097
    Location:5791
    zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
    pfam06484
    Location:509640
    Ten_N; Teneurin Intracellular Region
    pfam12126
    Location:240570
    DUF3583; Protein of unknown function (DUF3583)
    pfam14197
    Location:231293
    Cep57_CLD_2; Centrosome localization domain of PPC89
  4. NM_033240.3NP_150243.2  protein PML isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and the 3' coding region compared to variant 1. The resulting isoform (2, also known PML-2, PML-V and TRIM19beta) contains a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BX647287, X63131
    Consensus CDS
    CCDS45298.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000395576.2, ENST00000435786.6
    Conserved Domains (4) summary
    smart00336
    Location:124166
    BBOX; B-Box-type zinc finger
    pfam00097
    Location:5791
    zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
    pfam12126
    Location:240570
    DUF3583; Protein of unknown function (DUF3583)
    pfam14197
    Location:231293
    Cep57_CLD_2; Centrosome localization domain of PPC89
  5. NM_033244.4NP_150247.2  protein PML isoform 5

    See identical proteins and their annotated locations for NP_150247.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 3' UTR and the 3' coding region compared to variant 1. The resulting isoform (5, also known as PML-3B, PML-VI and TRIM19epsilon) contains a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AF230405, BC034251, X63131
    Consensus CDS
    CCDS45299.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000394642.3, ENST00000436891.7
    Conserved Domains (5) summary
    TIGR00599
    Location:53125
    rad18; DNA repair protein rad18
    cd16449
    Location:5791
    RING-HC; HC subclass of RING (RING-HC) finger and its variants
    pfam12126
    Location:240552
    DUF3583; Protein of unknown function (DUF3583)
    cd19770
    Location:187237
    Bbox2_TRIM19_C-V; B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called promyelocytic leukemia protein (PML), and similar proteins
    cd19804
    Location:126168
    Bbox1_TRIM19_C-V; B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins
  6. NM_033246.3NP_150249.1  protein PML isoform 7

    See identical proteins and their annotated locations for NP_150249.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) has multiple differences in the coding region compared to variant 1, one of which results in translational frame-shift. The resulting isoform (7, also known as PML-6B, PML-VIB, TRIM19eta and TRIM19iota) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BF510860, X63131
    Consensus CDS
    CCDS45300.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000353004.4, ENST00000359928.8
    Conserved Domains (4) summary
    smart00336
    Location:124166
    BBOX; B-Box-type zinc finger
    pfam00097
    Location:5791
    zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
    pfam12126
    Location:240418
    DUF3583; Protein of unknown function (DUF3583)
    pfam14197
    Location:231293
    Cep57_CLD_2; Centrosome localization domain of PPC89
  7. NM_033247.3NP_150250.2  protein PML isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) has multiple differences in the coding region compared to variant 1, one of which results in translational frame-shift. The resulting isoform (8, also known as PML-VII and TRIM19theta) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC034251, X63131
    Consensus CDS
    CCDS10256.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000378564.2, ENST00000395132.6
    Conserved Domains (4) summary
    smart00336
    Location:124166
    BBOX; B-Box-type zinc finger
    pfam00097
    Location:5791
    zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
    pfam12126
    Location:240418
    DUF3583; Protein of unknown function (DUF3583)
    pfam14197
    Location:231293
    Cep57_CLD_2; Centrosome localization domain of PPC89
  8. NM_033249.3NP_150252.1  protein PML isoform 10

    See identical proteins and their annotated locations for NP_150252.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) has multiple differences in the coding region compared to variant 1, one of which results in translational frame-shift. The resulting isoform (10, also known as PML-4A, PML-IVA and TRIM19lambda) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BF510860, X63131
    Consensus CDS
    CCDS58386.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000457023.1, ENST00000564428.5
    Conserved Domains (4) summary
    smart00336
    Location:124166
    BBOX; B-Box-type zinc finger
    pfam00097
    Location:5791
    zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
    pfam12126
    Location:240522
    DUF3583; Protein of unknown function (DUF3583)
    pfam14197
    Location:231293
    Cep57_CLD_2; Centrosome localization domain of PPC89
  9. NM_033250.3NP_150253.2  protein PML isoform 11

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) has multiple differences in the coding region compared to variant 1, one of which results in translational frame-shift. The resulting isoform (11, also known as PML-2A and PML-IIA) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC034251, X63131
    Consensus CDS
    CCDS10258.1
    UniProtKB/Swiss-Prot
    P29590
    Related
    ENSP00000315434.8, ENST00000354026.10
    Conserved Domains (5) summary
    smart00336
    Location:124166
    BBOX; B-Box-type zinc finger
    pfam00097
    Location:5791
    zf-C3HC4; Zinc finger, C3HC4 type (RING finger)
    pfam06484
    Location:461592
    Ten_N; Teneurin Intracellular Region
    pfam12126
    Location:240522
    DUF3583; Protein of unknown function (DUF3583)
    pfam14197
    Location:231293
    Cep57_CLD_2; Centrosome localization domain of PPC89

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    73994716..74047827
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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