Pcgf3 (polycomb group ring finger 3) - Rat Genome Database

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Gene: Pcgf3 (polycomb group ring finger 3) Rattus norvegicus
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Symbol: Pcgf3
Name: polycomb group ring finger 3
RGD ID: 1311479
Description: Predicted to enable histone H2AK119 ubiquitin ligase activity. Predicted to be involved in random inactivation of X chromosome and regulation of transcription by RNA polymerase II. Predicted to be located in X chromosome and nucleus. Predicted to be part of PRC1 complex. Orthologous to human PCGF3 (polycomb group ring finger 3); PARTICIPATES IN histone modification pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC305624; polycomb group RING finger protein 3; ring finger protein 3; Rnf3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly; Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8141,381,976 - 1,436,709 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl141,381,380 - 1,436,912 (-)EnsemblGRCr8
mRatBN7.2141,237,594 - 1,291,717 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl141,233,947 - 1,291,793 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx141,136,329 - 1,173,467 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0142,438,091 - 2,475,222 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0141,134,803 - 1,171,901 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0142,247,805 - 2,297,155 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl142,247,808 - 2,297,155 (-)Ensemblrn6Rnor6.0
Rnor_5.0142,242,206 - 2,295,509 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4141,824,819 - 1,839,263 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera141,276,942 - 1,313,583 (-)NCBICelera
RGSC_v3.1141,784,275 - 1,835,105 (-)NCBI
Cytogenetic Map14p22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO)
PcG protein complex  (IEA,ISO)
PRC1 complex  (IBA)
X chromosome  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. PRC1 complex diversity: where is it taking us? Gil J and O'Loghlen A, Trends Cell Biol. 2014 Jul 22. pii: S0962-8924(14)00102-0. doi: 10.1016/j.tcb.2014.06.005.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
5. Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Simon JA and Kingston RE, Mol Cell. 2013 Mar 7;49(5):808-24. doi: 10.1016/j.molcel.2013.02.013.
Additional References at PubMed
PMID:12477932   PMID:21282530   PMID:28596365  


Genomics

Comparative Map Data
Pcgf3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8141,381,976 - 1,436,709 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl141,381,380 - 1,436,912 (-)EnsemblGRCr8
mRatBN7.2141,237,594 - 1,291,717 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl141,233,947 - 1,291,793 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx141,136,329 - 1,173,467 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0142,438,091 - 2,475,222 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0141,134,803 - 1,171,901 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0142,247,805 - 2,297,155 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl142,247,808 - 2,297,155 (-)Ensemblrn6Rnor6.0
Rnor_5.0142,242,206 - 2,295,509 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4141,824,819 - 1,839,263 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera141,276,942 - 1,313,583 (-)NCBICelera
RGSC_v3.1141,784,275 - 1,835,105 (-)NCBI
Cytogenetic Map14p22NCBI
PCGF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384705,832 - 770,089 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4705,748 - 770,089 (+)Ensemblhg38GRCh38
GRCh374699,621 - 763,877 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364689,573 - 754,428 (+)NCBIBuild 36Build 36hg18NCBI36
Build 344689,572 - 754,255NCBI
Celera4654,586 - 701,073 (+)NCBICelera
Cytogenetic Map4p16.3NCBI
HuRef4674,466 - 735,220 (+)NCBIHuRef
CHM1_14699,353 - 761,389 (+)NCBICHM1_1
T2T-CHM13v2.04705,458 - 767,880 (+)NCBIT2T-CHM13v2.0
Pcgf3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395108,609,082 - 108,654,842 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5108,609,098 - 108,654,842 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm385108,461,259 - 108,506,976 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5108,461,232 - 108,506,976 (+)Ensemblmm10GRCm38
MGSCv375108,890,351 - 108,932,118 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv365108,701,634 - 108,743,401 (+)NCBIMGSCv36mm8
Celera5105,582,876 - 105,624,630 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map553.13NCBI
Pcgf3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955514307,332 - 350,039 (+)Ensembl
ChiLan1.0NW_004955514307,331 - 350,039 (+)NCBIChiLan1.0ChiLan1.0
PCGF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v231,015,288 - 1,086,487 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14973,254 - 1,043,017 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04802,990 - 874,063 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14746,147 - 805,443 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4746,137 - 805,443 (+)EnsemblpanPan2panpan1.1
PCGF3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1391,673,424 - 91,708,751 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl391,676,496 - 91,708,754 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha394,138,937 - 94,187,941 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0392,673,047 - 92,722,052 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl392,673,047 - 92,722,019 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1391,844,192 - 91,893,180 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0391,900,171 - 91,949,129 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0392,281,790 - 92,330,796 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pcgf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528568,647,474 - 68,671,564 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647722,349,171 - 22,373,393 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647722,349,166 - 22,373,256 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCGF3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8140,446 - 182,261 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.18140,435 - 189,796 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2880,086 - 128,768 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCGF3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12748,015,976 - 48,077,688 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2748,020,010 - 48,053,520 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660514,401,028 - 4,463,055 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcgf3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475526,294,689 - 26,326,318 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475526,294,675 - 26,344,864 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pcgf3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11118,240,320 - 18,283,484 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pcgf3
235 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:51
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000000071
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14111334906Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14117877928Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14131893212Rat

Markers in Region
D14Got2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2141,241,910 - 1,242,083 (+)MAPPERmRatBN7.2
Rnor_6.0142,252,122 - 2,252,294NCBIRnor6.0
Rnor_5.0142,246,750 - 2,246,922UniSTSRnor5.0
RGSC_v3.4141,788,683 - 1,788,856RGDRGSC3.4
RGSC_v3.4141,788,684 - 1,788,856UniSTSRGSC3.4
Celera141,281,259 - 1,281,431UniSTS
RGSC_v3.1141,788,683 - 1,788,856RGD
RH 2.0 Map147.8RGD
Cytogenetic Map14p22UniSTS
AU049720  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2141,242,240 - 1,242,375 (+)MAPPERmRatBN7.2
Rnor_6.0142,252,453 - 2,252,587NCBIRnor6.0
Rnor_5.0142,247,081 - 2,247,215UniSTSRnor5.0
RGSC_v3.4141,789,015 - 1,789,149UniSTSRGSC3.4
Celera141,281,591 - 1,281,725UniSTS
Cytogenetic Map14p22UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 162 91 90 59 91 59 6 355 191 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000000071   ⟹   ENSRNOP00000000071
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl141,381,380 - 1,436,912 (-)Ensembl
mRatBN7.2 Ensembl141,233,947 - 1,291,793 (-)Ensembl
Rnor_6.0 Ensembl142,247,808 - 2,297,155 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108544   ⟹   ENSRNOP00000084689
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl141,248,150 - 1,291,777 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000111567   ⟹   ENSRNOP00000084631
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl141,233,947 - 1,279,698 (-)Ensembl
RefSeq Acc Id: NM_001107245   ⟹   NP_001100715
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8141,381,976 - 1,436,709 (-)NCBI
mRatBN7.2141,237,594 - 1,291,717 (-)NCBI
Rnor_6.0142,247,805 - 2,297,155 (-)NCBI
Rnor_5.0142,242,206 - 2,295,509 (-)NCBI
RGSC_v3.4141,824,819 - 1,839,263 (-)RGD
Celera141,276,942 - 1,313,583 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100715 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI67000 (Get FASTA)   NCBI Sequence Viewer  
  EDL84012 (Get FASTA)   NCBI Sequence Viewer  
  EDL84013 (Get FASTA)   NCBI Sequence Viewer  
  EDL84014 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000071.6
RefSeq Acc Id: NP_001100715   ⟸   NM_001107245
- UniProtKB: B2RZ26 (UniProtKB/TrEMBL),   F7EV63 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000000071   ⟸   ENSRNOT00000000071
Ensembl Acc Id: ENSRNOP00000084631   ⟸   ENSRNOT00000111567
Ensembl Acc Id: ENSRNOP00000084689   ⟸   ENSRNOT00000108544
Protein Domains
RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2RZ26-F1-model_v2 AlphaFold B2RZ26 1-241 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699150
Promoter ID:EPDNEW_R9674
Type:initiation region
Name:Pcgf3_1
Description:polycomb group ring finger 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0142,297,206 - 2,297,266EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311479 AgrOrtholog
BioCyc Gene G2FUF-16677 BioCyc
Ensembl Genes ENSRNOG00000000062 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000071.6 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
  Phosphatidylinositol 3-kinase Catalytic Subunit, Chain A, domain 1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9031673 IMAGE-MGC_LOAD
InterPro PcG_RING_finger UniProtKB/TrEMBL
  RAWUL UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/TrEMBL
KEGG Report rno:305624 UniProtKB/TrEMBL
MGC_CLONE MGC:189162 IMAGE-MGC_LOAD
NCBI Gene 305624 ENTREZGENE
PANTHER POLYCOMB GROUP RING FINGER PROTEIN UniProtKB/TrEMBL
Pfam RAWUL UniProtKB/TrEMBL
  zf-C3HC4_2 UniProtKB/TrEMBL
PhenoGen Pcgf3 PhenoGen
PROSITE ZF_RING_1 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000062 RatGTEx
SMART RING UniProtKB/TrEMBL
Superfamily-SCOP RING/U-box UniProtKB/TrEMBL
UniProt B2RZ26 ENTREZGENE, UniProtKB/TrEMBL
  F7EV63 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Pcgf3  polycomb group ring finger 3  Rnf3_predicted  ring finger protein 3 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Rnf3_predicted  ring finger protein 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED