Prdm12 (PR/SET domain 12) - Rat Genome Database

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Gene: Prdm12 (PR/SET domain 12) Rattus norvegicus
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Symbol: Prdm12
Name: PR/SET domain 12
RGD ID: 1586401
Description: Predicted to enable histone chaperone activity and histone methyltransferase binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II and neurogenesis. Predicted to act upstream of or within detection of temperature stimulus involved in sensory perception of pain and neuron projection development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in hereditary sensory and autonomic neuropathy type 8. Orthologous to human PRDM12 (PR/SET domain 12); INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC688699; PR domain 12; PR domain containing 12; PR domain zinc finger protein 12; similar to PR domain containing 12
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8335,322,962 - 35,341,878 (+)NCBIGRCr8
mRatBN7.2314,928,651 - 14,943,341 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl314,928,628 - 14,943,331 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0310,181,104 - 10,199,185 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl310,181,924 - 10,196,626 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0315,540,492 - 15,556,510 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4310,752,644 - 10,767,390 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera39,677,191 - 9,695,307 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

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

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19050759   PMID:26005867   PMID:26443638  


Genomics

Comparative Map Data
Prdm12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8335,322,962 - 35,341,878 (+)NCBIGRCr8
mRatBN7.2314,928,651 - 14,943,341 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl314,928,628 - 14,943,331 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0310,181,104 - 10,199,185 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl310,181,924 - 10,196,626 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0315,540,492 - 15,556,510 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4310,752,644 - 10,767,390 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera39,677,191 - 9,695,307 (+)NCBICelera
Cytogenetic Map3p12NCBI
PRDM12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389130,664,594 - 130,682,983 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9130,664,594 - 130,682,986 (+)EnsemblGRCh38hg38GRCh38
GRCh379133,539,981 - 133,558,370 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369132,529,802 - 132,548,205 (+)NCBINCBI36Build 36hg18NCBI36
Build 349130,569,534 - 130,587,938NCBI
Celera9104,078,514 - 104,096,917 (+)NCBICelera
Cytogenetic Map9q34.12NCBI
HuRef9103,027,137 - 103,045,252 (+)NCBIHuRef
CHM1_19133,688,996 - 133,707,405 (+)NCBICHM1_1
T2T-CHM13v2.09142,869,556 - 142,887,937 (+)NCBIT2T-CHM13v2.0
Prdm12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39231,526,767 - 31,545,798 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl231,530,049 - 31,545,807 (+)EnsemblGRCm39 Ensembl
GRCm38231,635,026 - 31,655,795 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl231,640,037 - 31,655,795 (+)EnsemblGRCm38mm10GRCm38
MGSCv37231,495,557 - 31,511,315 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36231,461,730 - 31,476,506 (+)NCBIMGSCv36mm8
Celera231,340,637 - 31,356,608 (+)NCBICelera
Cytogenetic Map2BNCBI
cM Map221.85NCBI
Prdm12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955513612,566 - 627,323 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955513612,566 - 627,848 (+)NCBIChiLan1.0ChiLan1.0
PRDM12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2118,667,002 - 8,687,551 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan198,669,344 - 8,689,893 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09101,786,052 - 101,803,287 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19130,436,273 - 130,463,441 (+)NCBIpanpan1.1PanPan1.1panPan2
PRDM12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1953,284,455 - 53,300,951 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl953,284,455 - 53,299,312 (-)NCBICanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl953,284,455 - 53,299,312 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha952,483,776 - 52,498,082 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0954,184,262 - 54,198,358 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl954,183,297 - 54,198,358 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1952,961,799 - 52,975,893 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0953,282,589 - 53,296,693 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0953,375,614 - 53,389,929 (-)NCBIUU_Cfam_GSD_1.0
Prdm12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947197,884,498 - 197,901,547 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648717,656,311 - 17,670,477 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648717,656,311 - 17,670,074 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRDM12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1270,723,681 - 270,739,468 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11270,723,880 - 270,739,468 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21304,646,521 - 304,662,114 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRDM12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1127,460,614 - 7,477,453 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl127,462,142 - 7,477,403 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660797,986,033 - 8,003,810 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prdm12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247605,049,666 - 5,063,161 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247605,048,760 - 5,063,504 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prdm12
98 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:43
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000012234
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat

Markers in Region
D3Rat55  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2314,937,621 - 14,937,759 (-)MAPPERmRatBN7.2
Rnor_6.0310,187,496 - 10,187,633NCBIRnor6.0
Rnor_5.0315,546,858 - 15,546,995UniSTSRnor5.0
RGSC_v3.4310,761,680 - 10,761,818RGDRGSC3.4
RGSC_v3.4310,761,681 - 10,761,818UniSTSRGSC3.4
RGSC_v3.1310,656,176 - 10,656,313RGD
Celera39,688,743 - 9,688,880UniSTS
RH 3.4 Map359.5UniSTS
RH 3.4 Map359.5RGD
RH 2.0 Map30.0RGD
Cytogenetic Map3p12UniSTS


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

endocrine system exocrine system hepatobiliary system nervous system reproductive system respiratory system
High
Medium 12
Low 37 4
Below cutoff 3 3 3 18 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012234   ⟹   ENSRNOP00000012234
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl314,928,628 - 14,943,331 (+)Ensembl
Rnor_6.0 Ensembl310,181,924 - 10,196,626 (-)Ensembl
RefSeq Acc Id: NM_001427360   ⟹   NP_001414289
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8335,326,008 - 35,341,878 (+)NCBI
RefSeq Acc Id: NM_001427361   ⟹   NP_001414290
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8335,322,962 - 35,341,878 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414289 (Get FASTA)   NCBI Sequence Viewer  
  NP_001414290 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012234.3
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000012234   ⟸   ENSRNOT00000012234
RefSeq Acc Id: NP_001414290   ⟸   NM_001427361
- UniProtKB: D3ZEJ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001414289   ⟸   NM_001427360
- UniProtKB: D3ZEJ0 (UniProtKB/TrEMBL)
Protein Domains
C2H2-type   SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZEJ0-F1-model_v2 AlphaFold D3ZEJ0 1-365 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:1586401 AgrOrtholog
BioCyc Gene G2FUF-50174 BioCyc
Ensembl Genes ENSRNOG00000009218 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012234.5 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro PRDM12_PR/SET UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
  Znf_PRDM12 UniProtKB/TrEMBL
KEGG Report rno:688699 UniProtKB/TrEMBL
NCBI Gene 688699 ENTREZGENE
PANTHER PR DOMAIN ZINC FINGER PROTEIN UniProtKB/TrEMBL
  PR DOMAIN ZINC FINGER PROTEIN 12 UniProtKB/TrEMBL
Pfam PRDM2_PR UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
PhenoGen Prdm12 PhenoGen
PIRSF PRDM12 UniProtKB/TrEMBL
PROSITE SET UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009218 RatGTEx
SMART SET UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
  SSF82199 UniProtKB/TrEMBL
UniProt D3ZEJ0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Prdm12  PR/SET domain 12  Prdm12  PR domain 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Prdm12  PR domain 12  Prdm12  PR domain containing 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Prdm12  PR domain containing 12  LOC688699  similar to PR domain containing 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC688699  similar to PR domain containing 12  LOC687700  similar to PR domain containing 12  Data merged from RGD:1597584 1643240 APPROVED
2006-11-20 LOC687700  similar to PR domain containing 12      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC688699  similar to PR domain containing 12      Symbol and Name status set to provisional 70820 PROVISIONAL