Prdm8 (PR/SET domain 8) - Rat Genome Database

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Gene: Prdm8 (PR/SET domain 8) Rattus norvegicus
Analyze
Symbol: Prdm8
Name: PR/SET domain 8
RGD ID: 1311628
Description: Predicted to enable chromatin binding activity; histone H3K9 methyltransferase activity; and transcription corepressor activity. Predicted to be involved in oligodendrocyte development and regulation of DNA-templated transcription. Predicted to act upstream of or within corpus callosum morphogenesis; corticospinal tract morphogenesis; and negative regulation of DNA-templated transcription. Predicted to be located in nuclear body. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in progressive myoclonus epilepsy 10. Orthologous to human PRDM8 (PR/SET domain 8); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC305198; PR domain 8; PR domain containing 8; PR domain zinc finger protein 8
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
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81411,708,477 - 11,728,111 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1411,708,269 - 11,715,125 (-)EnsemblGRCr8
mRatBN7.21411,403,202 - 11,424,059 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1411,404,407 - 11,410,993 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1411,368,547 - 11,375,146 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01412,668,380 - 12,674,979 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01411,365,871 - 11,372,466 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01413,052,776 - 13,073,583 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1413,054,771 - 13,058,172 (-)Ensemblrn6Rnor6.0
Rnor_5.01412,997,401 - 13,016,208 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41412,792,168 - 12,800,272 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1411,478,154 - 11,498,957 (-)NCBICelera
RGSC_v3.11412,794,475 - 12,847,649 (-)NCBI
Cytogenetic Map14p22NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nuclear body  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
2. 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.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:19050759   PMID:19646955   PMID:22284184   PMID:22961547  


Genomics

Comparative Map Data
Prdm8
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81411,708,477 - 11,728,111 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1411,708,269 - 11,715,125 (-)EnsemblGRCr8
mRatBN7.21411,403,202 - 11,424,059 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1411,404,407 - 11,410,993 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1411,368,547 - 11,375,146 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01412,668,380 - 12,674,979 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01411,365,871 - 11,372,466 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01413,052,776 - 13,073,583 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1413,054,771 - 13,058,172 (-)Ensemblrn6Rnor6.0
Rnor_5.01412,997,401 - 13,016,208 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41412,792,168 - 12,800,272 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1411,478,154 - 11,498,957 (-)NCBICelera
RGSC_v3.11412,794,475 - 12,847,649 (-)NCBI
Cytogenetic Map14p22NCBI
PRDM8
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38480,185,270 - 80,204,329 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl480,183,879 - 80,204,329 (+)Ensemblhg38GRCh38
GRCh37481,106,424 - 81,125,483 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36481,325,448 - 81,344,507 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34481,462,617 - 81,482,659NCBI
Celera478,399,921 - 78,418,995 (+)NCBICelera
Cytogenetic Map4q21.21NCBI
HuRef476,850,375 - 76,869,478 (+)NCBIHuRef
CHM1_1481,082,918 - 81,101,978 (+)NCBICHM1_1
T2T-CHM13v2.0483,515,641 - 83,534,739 (+)NCBIT2T-CHM13v2.0
Prdm8
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39598,315,241 - 98,335,313 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl598,315,057 - 98,336,850 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38598,167,203 - 98,187,454 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl598,167,198 - 98,188,991 (+)Ensemblmm10GRCm38
MGSCv37598,609,888 - 98,616,467 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36598,421,280 - 98,427,639 (+)NCBIMGSCv36mm8
Celera595,512,228 - 95,518,646 (+)NCBICelera
Cytogenetic Map5E3NCBI
cM Map547.77NCBI
Prdm8
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554334,459,669 - 4,462,928 (+)Ensembl
ChiLan1.0NW_0049554334,443,339 - 4,463,687 (+)NCBIChiLan1.0ChiLan1.0
PRDM8
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2349,862,396 - 49,883,002 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1450,050,770 - 50,071,517 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0443,993,635 - 44,014,430 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1449,838,610 - 49,861,862 (-)NCBIPanPan1.1PanPan1.1panPan2
PRDM8
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1324,435,693 - 4,451,500 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl324,443,289 - 4,451,036 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3237,429,971 - 37,450,384 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0324,455,166 - 4,475,675 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl324,467,514 - 4,475,233 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1324,507,428 - 4,514,597 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0324,391,796 - 4,412,184 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03235,552,459 - 35,572,911 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Prdm8
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244052857,896,244 - 7,902,942 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367491,820,235 - 1,823,714 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367491,819,491 - 1,827,440 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRDM8
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8137,605,600 - 137,612,651 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.18137,604,805 - 137,611,389 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28146,777,885 - 146,840,639 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRDM8
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1728,610,166 - 28,631,712 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl728,626,265 - 28,629,707 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660377,060,539 - 7,080,848 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prdm8
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475710,802,406 - 10,805,704 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475710,801,701 - 10,809,887 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Prdm8
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1118,432,999 - 8,453,046 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Prdm8
84 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:72
Count of miRNA genes:37
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000002746, ENSRNOT00000071706
Prediction methods:Miranda, Rnahybrid
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
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14395787821572472Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14395787818558812Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14939329839411170Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141133490630674469Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141133471628389666Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14395787831121464Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14117877928Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14862139853621398Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14395787824886169Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14131893212Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14862139853621398Rat

Markers in Region
PRDM8_8072  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21411,404,505 - 11,405,424 (+)MAPPERmRatBN7.2
Rnor_6.01413,054,077 - 13,054,995NCBIRnor6.0
Rnor_5.01412,996,807 - 12,997,725UniSTSRnor5.0
RGSC_v3.41412,793,778 - 12,794,696UniSTSRGSC3.4
Celera1411,479,455 - 11,480,373UniSTS
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 56 163 66 65 37 30 37 6 216 119 11 142 36 91 28 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000002746   ⟹   ENSRNOP00000002746
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1411,708,477 - 11,715,125 (-)Ensembl
mRatBN7.2 Ensembl1411,404,407 - 11,410,993 (-)Ensembl
Rnor_6.0 Ensembl1413,054,771 - 13,058,172 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000071706   ⟹   ENSRNOP00000066439
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1413,054,775 - 13,058,172 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000173510   ⟹   ENSRNOP00000099430
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1411,708,269 - 11,715,062 (-)Ensembl
RefSeq Acc Id: NM_001371967   ⟹   NP_001358896
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81411,708,477 - 11,715,062 (-)NCBI
mRatBN7.21411,404,407 - 11,410,993 (-)NCBI
RefSeq Acc Id: XM_017599430   ⟹   XP_017454919
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81411,708,521 - 11,728,111 (-)NCBI
mRatBN7.21411,403,202 - 11,424,059 (-)NCBI
Rnor_6.01413,052,776 - 13,073,583 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063273053   ⟹   XP_063129123
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81411,708,521 - 11,715,456 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001358896 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454919 (Get FASTA)   NCBI Sequence Viewer  
  XP_063129123 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99620 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002746
  ENSRNOP00000002746.4
  ENSRNOP00000099430
  ENSRNOP00000099430.1
RefSeq Acc Id: XP_017454919   ⟸   XM_017599430
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000002746   ⟸   ENSRNOT00000002746
Ensembl Acc Id: ENSRNOP00000066439   ⟸   ENSRNOT00000071706
RefSeq Acc Id: NP_001358896   ⟸   NM_001371967
- UniProtKB: D4A123 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063129123   ⟸   XM_063273053
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000099430   ⟸   ENSRNOT00000173510

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A123-F1-model_v2 AlphaFold D4A123 1-689 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311628 AgrOrtholog
BioCyc Gene G2FUF-16359 BioCyc
Ensembl Genes ENSRNOG00000002004 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002746 ENTREZGENE
  ENSRNOT00000002746.8 UniProtKB/TrEMBL
  ENSRNOT00000173510 ENTREZGENE
  ENSRNOT00000173510.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro PRDM8_PR/SET UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/TrEMBL
  TR-Histone_Methyltrans UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
NCBI Gene 305198 ENTREZGENE
PANTHER AGAP007109-PA UniProtKB/TrEMBL
  PR DOMAIN ZINC FINGER PROTEIN 8 UniProtKB/TrEMBL
Pfam PRDM2_PR UniProtKB/TrEMBL
  zf-C2H2_4 UniProtKB/TrEMBL
PhenoGen Prdm8 PhenoGen
PROSITE SET UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002004 RatGTEx
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0ABK0LDB5_RAT UniProtKB/TrEMBL
  D4A123 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Prdm8  PR/SET domain 8  Prdm8  PR domain 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Prdm8  PR domain 8  Prdm8  PR domain containing 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Prdm8  PR domain containing 8   Prdm8_predicted  PR domain containing 8 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Prdm8_predicted  PR domain containing 8 (predicted)      Symbol and Name status set to approved 70820 APPROVED