PML (PML nuclear body scaffold) - Rat Genome Database

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Pathways
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Gene: PML (PML nuclear body scaffold) Sus scrofa
Analyze
Symbol: PML
Name: PML nuclear body scaffold
RGD ID: 13911106
Description: ENCODES a protein that exhibits cobalt ion binding (ortholog); identical protein binding (ortholog); protein heterodimerization activity (ortholog); INVOLVED IN apoptotic process (ortholog); branching involved in mammary gland duct morphogenesis (ortholog); cell fate commitment (ortholog); PARTICIPATES IN mTOR signaling pathway; transforming growth factor-beta Smad dependent signaling pathway; ASSOCIATED WITH acute promyelocytic leukemia (ortholog); Bardet-Biedl syndrome (ortholog); Bloom syndrome (ortholog); FOUND IN nuclear membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: promyelocytic leukemia; protein PML
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl759,405,053 - 59,450,105 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1759,405,044 - 59,450,155 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2764,023,286 - 64,071,578 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
apoptotic process  (ISO)
branching involved in mammary gland duct morphogenesis  (IEA,ISO)
cell fate commitment  (IEA,ISO)
cellular response to interleukin-4  (IEA,ISO)
cellular response to leukemia inhibitory factor  (IEA,ISO)
cellular senescence  (IEA)
chromatin remodeling  (ISO)
circadian regulation of gene expression  (IEA)
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest  (IEA)
endoplasmic reticulum calcium ion homeostasis  (IEA)
entrainment of circadian clock by photoperiod  (IEA)
extrinsic apoptotic signaling pathway  (IEA,ISO)
fibroblast migration  (IEA)
innate immune response  (IBA,IEA)
intrinsic apoptotic signaling pathway by p53 class mediator  (IEA,ISO)
intrinsic apoptotic signaling pathway in response to DNA damage  (IBA,IEA,ISO)
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  (IEA)
intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress  (IEA,ISO)
intrinsic apoptotic signaling pathway in response to oxidative stress  (IEA,ISO)
maintenance of protein location in nucleus  (IEA,ISO)
myeloid cell differentiation  (IEA,ISO)
negative regulation of angiogenesis  (IEA,ISO)
negative regulation of cell growth  (IEA)
negative regulation of cell population proliferation  (IEA,ISO)
negative regulation of DNA-templated transcription  (IEA)
negative regulation of interleukin-1 beta production  (IEA)
negative regulation of interleukin-1 production  (IEA)
negative regulation of mitotic cell cycle  (ISO)
negative regulation of telomere maintenance via telomerase  (ISO)
negative regulation of translation in response to oxidative stress  (ISO)
negative regulation of ubiquitin-dependent protein catabolic process  (IEA)
oncogene-induced cell senescence  (IEA)
PML body organization  (IEA,ISO)
positive regulation of apoptotic process involved in mammary gland involution  (ISO)
positive regulation of apoptotic signaling pathway  (IEA,ISO)
positive regulation of defense response to virus by host  (ISO)
positive regulation of extrinsic apoptotic signaling pathway  (IEA)
positive regulation of fibroblast proliferation  (IEA)
positive regulation of peptidyl-lysine acetylation  (IEA)
positive regulation of protein localization to chromosome, telomeric region  (ISO)
positive regulation of signal transduction by p53 class mediator  (IEA)
positive regulation of telomere maintenance  (IEA)
proteasome-mediated ubiquitin-dependent protein catabolic process  (IEA)
protein import into nucleus  (IEA,ISO)
protein monoubiquitination  (IEA)
protein stabilization  (ISO)
protein targeting  (ISO)
protein-containing complex assembly  (IEA)
protein-containing complex localization  (IEA,ISO)
regulation of calcium ion transport into cytosol  (IEA)
regulation of cell adhesion  (IEA)
regulation of cell cycle  (ISO)
regulation of circadian rhythm  (IEA)
regulation of DNA-templated transcription  (IEA)
regulation of double-strand break repair  (IEA)
response to cytokine  (IEA)
response to gamma radiation  (IEA,ISO)
response to hypoxia  (IEA,ISO)
response to UV  (IEA,ISO)
retinoic acid receptor signaling pathway  (IEA,ISO)
SMAD protein signal transduction  (IEA,ISO)
suppression of viral release by host  (IBA,IEA)
transforming growth factor beta receptor signaling pathway  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:22301074   PMID:30032202   PMID:32641476  


Genomics

Comparative Map Data
PML
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl759,405,053 - 59,450,105 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1759,405,044 - 59,450,155 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2764,023,286 - 64,071,578 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PML
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381573,994,716 - 74,047,827 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1573,994,673 - 74,047,827 (+)EnsemblGRCh38hg38GRCh38
GRCh371574,287,057 - 74,340,168 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361572,074,067 - 72,127,213 (+)NCBINCBI36Build 36hg18NCBI36
Build 341572,074,066 - 72,115,787NCBI
Celera1551,164,334 - 51,230,308 (+)NCBICelera
Cytogenetic Map15q24.1NCBI
HuRef1551,118,849 - 51,172,183 (+)NCBIHuRef
CHM1_11574,404,975 - 74,458,114 (+)NCBICHM1_1
T2T-CHM13v2.01571,812,061 - 71,865,194 (+)NCBIT2T-CHM13v2.0
Pml
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39958,125,359 - 58,157,077 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl958,125,359 - 58,157,069 (-)EnsemblGRCm39 Ensembl
GRCm38958,217,179 - 58,249,796 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl958,218,076 - 58,249,786 (-)EnsemblGRCm38mm10GRCm38
MGSCv37958,064,986 - 58,097,593 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36958,016,679 - 58,047,923 (-)NCBIMGSCv36mm8
Celera955,451,359 - 55,484,054 (-)NCBICelera
Cytogenetic Map9BNCBI
cM Map931.63NCBI
Pml
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8867,523,164 - 67,557,801 (-)NCBIGRCr8
mRatBN7.2858,627,347 - 58,661,927 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl858,628,837 - 58,658,971 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0863,002,515 - 63,034,310 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl863,004,870 - 63,034,226 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0862,778,563 - 62,810,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4862,020,438 - 62,051,927 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera858,089,954 - 58,121,691 (-)NCBICelera
Cytogenetic Map8q24NCBI
Pml
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554503,656,498 - 3,692,406 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554503,654,854 - 3,692,057 (-)NCBIChiLan1.0ChiLan1.0
PML
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21663,217,504 - 63,269,639 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11567,381,987 - 67,433,255 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01552,903,874 - 52,955,151 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11571,658,884 - 71,710,883 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1571,658,884 - 71,710,883 (+)Ensemblpanpan1.1panPan2
PML
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13037,232,337 - 37,278,434 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3037,232,306 - 37,277,741 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3037,167,830 - 37,214,029 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03037,439,424 - 37,485,481 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3037,439,414 - 37,485,559 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13037,391,257 - 37,437,382 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03037,417,163 - 37,463,467 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03037,673,462 - 37,719,075 (+)NCBIUU_Cfam_GSD_1.0
Pml
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640115,287,097 - 115,329,964 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647133,135,164 - 33,177,666 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647133,135,186 - 33,173,218 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PML
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1269,441,998 - 9,494,949 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl269,451,112 - 9,494,931 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666048132,120,299 - 132,175,245 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pml
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624781464,658 - 497,775 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624781464,858 - 498,146 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in PML
741 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 1 2
Low 10 3 3 4 2 22 2 3 1
Below cutoff 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000002141   ⟹   ENSSSCP00000002091
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl759,417,297 - 59,450,105 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000038698   ⟹   ENSSSCP00000039115
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl759,405,053 - 59,450,105 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000040910   ⟹   ENSSSCP00000049665
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl759,405,054 - 59,450,070 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000081527   ⟹   ENSSSCP00000062386
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl759,413,600 - 59,450,131 (-)Ensembl
RefSeq Acc Id: XM_001925572   ⟹   XP_001925607
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1759,405,044 - 59,450,155 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_001925607   ⟸   XM_001925572
- UniProtKB: A0A8D1ERL5 (UniProtKB/TrEMBL),   M3UZA5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000049665   ⟸   ENSSSCT00000040910
RefSeq Acc Id: ENSSSCP00000002091   ⟸   ENSSSCT00000002141
RefSeq Acc Id: ENSSSCP00000062386   ⟸   ENSSSCT00000081527
RefSeq Acc Id: ENSSSCP00000039115   ⟸   ENSSSCT00000038698
Protein Domains
B box-type   RING-type


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000001912 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00015046524 UniProtKB/TrEMBL
  ENSSSCG00025050479 UniProtKB/TrEMBL
  ENSSSCG00030017360 UniProtKB/TrEMBL
  ENSSSCG00035021541 UniProtKB/TrEMBL
  ENSSSCG00040045197 UniProtKB/TrEMBL
  ENSSSCG00045020816 UniProtKB/TrEMBL
  ENSSSCG00050030680 UniProtKB/TrEMBL
  ENSSSCG00055015485 UniProtKB/TrEMBL
  ENSSSCG00060072020 UniProtKB/TrEMBL
  ENSSSCG00065045946 UniProtKB/TrEMBL
  ENSSSCG00070010189 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000002141.5 UniProtKB/TrEMBL
  ENSSSCT00000038698.3 UniProtKB/TrEMBL
  ENSSSCT00000040910 ENTREZGENE
  ENSSSCT00000040910.2 UniProtKB/TrEMBL
  ENSSSCT00015062362.1 UniProtKB/TrEMBL
  ENSSSCT00015062550.1 UniProtKB/TrEMBL
  ENSSSCT00015062818.1 UniProtKB/TrEMBL
  ENSSSCT00015062960.1 UniProtKB/TrEMBL
  ENSSSCT00015063237.1 UniProtKB/TrEMBL
  ENSSSCT00025068939.1 UniProtKB/TrEMBL
  ENSSSCT00025069237.1 UniProtKB/TrEMBL
  ENSSSCT00025069317.1 UniProtKB/TrEMBL
  ENSSSCT00025069513.1 UniProtKB/TrEMBL
  ENSSSCT00030024002.1 UniProtKB/TrEMBL
  ENSSSCT00030024014.1 UniProtKB/TrEMBL
  ENSSSCT00030024026.1 UniProtKB/TrEMBL
  ENSSSCT00030024044.1 UniProtKB/TrEMBL
  ENSSSCT00030024053.1 UniProtKB/TrEMBL
  ENSSSCT00035028089.1 UniProtKB/TrEMBL
  ENSSSCT00035028094.1 UniProtKB/TrEMBL
  ENSSSCT00035028104.1 UniProtKB/TrEMBL
  ENSSSCT00035028120.1 UniProtKB/TrEMBL
  ENSSSCT00035028131.1 UniProtKB/TrEMBL
  ENSSSCT00040060635.1 UniProtKB/TrEMBL
  ENSSSCT00040060747.1 UniProtKB/TrEMBL
  ENSSSCT00040060897.1 UniProtKB/TrEMBL
  ENSSSCT00040061089.1 UniProtKB/TrEMBL
  ENSSSCT00040061189.1 UniProtKB/TrEMBL
  ENSSSCT00045036498.1 UniProtKB/TrEMBL
  ENSSSCT00045036574.1 UniProtKB/TrEMBL
  ENSSSCT00045036783.1 UniProtKB/TrEMBL
  ENSSSCT00050041247.1 UniProtKB/TrEMBL
  ENSSSCT00050041253.1 UniProtKB/TrEMBL
  ENSSSCT00050041257.1 UniProtKB/TrEMBL
  ENSSSCT00050041270.1 UniProtKB/TrEMBL
  ENSSSCT00050041278.1 UniProtKB/TrEMBL
  ENSSSCT00055030454.1 UniProtKB/TrEMBL
  ENSSSCT00055030542.1 UniProtKB/TrEMBL
  ENSSSCT00055030678.1 UniProtKB/TrEMBL
  ENSSSCT00055030788.1 UniProtKB/TrEMBL
  ENSSSCT00055030917.1 UniProtKB/TrEMBL
  ENSSSCT00060098390.1 UniProtKB/TrEMBL
  ENSSSCT00060098415.1 UniProtKB/TrEMBL
  ENSSSCT00060098422.1 UniProtKB/TrEMBL
  ENSSSCT00060098550.1 UniProtKB/TrEMBL
  ENSSSCT00065062836.1 UniProtKB/TrEMBL
  ENSSSCT00065062846.1 UniProtKB/TrEMBL
  ENSSSCT00065062857.1 UniProtKB/TrEMBL
  ENSSSCT00065062889.1 UniProtKB/TrEMBL
  ENSSSCT00065062899.1 UniProtKB/TrEMBL
  ENSSSCT00070019885.1 UniProtKB/TrEMBL
  ENSSSCT00070019923.1 UniProtKB/TrEMBL
  ENSSSCT00070019941.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro DUF3583 UniProtKB/TrEMBL
  TRIM45/56/19 UniProtKB/TrEMBL
  Znf_B-box UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/TrEMBL
KEGG Report ssc:100157336 UniProtKB/TrEMBL
NCBI Gene PML ENTREZGENE
PANTHER BONUS, ISOFORM C-RELATED UniProtKB/TrEMBL
  PROTEIN PML UniProtKB/TrEMBL
Pfam DUF3583 UniProtKB/TrEMBL
  zf-B_box UniProtKB/TrEMBL
PROSITE ZF_BBOX UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART BBOX UniProtKB/TrEMBL
Superfamily-SCOP B-box zinc-binding domain UniProtKB/TrEMBL
  RING/U-box UniProtKB/TrEMBL
UniProt A0A287A573_PIG UniProtKB/TrEMBL
  A0A287AZS0_PIG UniProtKB/TrEMBL
  A0A480JXC7_PIG UniProtKB/TrEMBL
  A0A4X1TKF4_PIG UniProtKB/TrEMBL
  A0A4X1TKG3_PIG UniProtKB/TrEMBL
  A0A4X1TMU5_PIG UniProtKB/TrEMBL
  A0A8D0NXV7_PIG UniProtKB/TrEMBL
  A0A8D0P2B3_PIG UniProtKB/TrEMBL
  A0A8D1EP25_PIG UniProtKB/TrEMBL
  A0A8D1ERL5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1QXE1_PIG UniProtKB/TrEMBL
  A0A8D1TCG2_PIG UniProtKB/TrEMBL
  A0A8K1K0K0_PIG UniProtKB/TrEMBL
  A0A8K1K0R2_PIG UniProtKB/TrEMBL
  A0A8K1K0X1_PIG UniProtKB/TrEMBL
  A0A8K1K264_PIG UniProtKB/TrEMBL
  F1SID1_PIG UniProtKB/TrEMBL
  M3UZA5 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A5G2QCS0 UniProtKB/TrEMBL
VGNC ID VGNC:99296 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-04-14 PML  PML nuclear body scaffold  PML  promyelocytic leukemia  Symbol and/or name change 5135510 APPROVED