Prdm2 (PR/SET domain 2) - Rat Genome Database

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Gene: Prdm2 (PR/SET domain 2) Rattus norvegicus
Analyze
Symbol: Prdm2
Name: PR/SET domain 2
RGD ID: 1594531
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in response to estradiol. Located in nucleus. Orthologous to human PRDM2 (PR/SET domain 2); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: PR domain 2; PR domain containing 2, with ZNF domain; PR domain containing 2, with ZNF domain (mapped); PR domain zinc finger protein 2; PR domain-containing protein 2; Prdm2_mapped; retinoblastoma interacting zinc finger protein; retinoblastoma protein-binding zinc finger protein; retinoblastoma protein-interacting zinc finger protein; Riz; zinc finger protein RIZ
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25155,421,066 - 155,531,884 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5155,422,134 - 155,531,825 (-)Ensembl
Rnor_6.05161,769,587 - 161,879,150 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5161,770,653 - 161,879,133 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05165,468,778 - 165,578,775 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45161,962,929 - 162,072,519 (-)NCBIRGSC3.4rn4RGSC3.4
Celera5153,753,320 - 153,860,334 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
cadmium dichloride  (EXP)
CGP 52608  (ISO)
chlordecone  (ISO)
ciguatoxin CTX1B  (ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
fenthion  (ISO)
fenvalerate  (EXP)
fonofos  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gentamycin  (EXP)
glyphosate  (EXP)
indometacin  (ISO)
methamphetamine  (ISO)
methidathion  (ISO)
methotrexate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
nitric oxide  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
parathion  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
potassium dichromate  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
succimer  (ISO)
tamibarotene  (ISO)
terbufos  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. The retinoblastoma-interacting zinc-finger protein RIZ is a downstream effector of estrogen action. Abbondanza C, etal., Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3130-5.
2. 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.
3. The retinoblastoma protein binds to RIZ, a zinc-finger protein that shares an epitope with the adenovirus E1A protein. Buyse IM, etal., Proc Natl Acad Sci U S A. 1995 May 9;92(10):4467-71.
4. 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.
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8654390   PMID:9334209   PMID:11544182   PMID:27573876  


Genomics

Comparative Map Data
Prdm2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25155,421,066 - 155,531,884 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5155,422,134 - 155,531,825 (-)Ensembl
Rnor_6.05161,769,587 - 161,879,150 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5161,770,653 - 161,879,133 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05165,468,778 - 165,578,775 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45161,962,929 - 162,072,519 (-)NCBIRGSC3.4rn4RGSC3.4
Celera5153,753,320 - 153,860,334 (-)NCBICelera
Cytogenetic Map5q36NCBI
PRDM2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38113,700,188 - 13,825,079 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl113,700,188 - 13,825,079 (+)EnsemblGRCh38hg38GRCh38
GRCh37114,026,683 - 14,151,574 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36113,903,937 - 14,024,162 (+)NCBINCBI36hg18NCBI36
Build 34113,776,655 - 13,859,875NCBI
Celera112,508,705 - 12,633,526 (+)NCBI
Cytogenetic Map1p36.21NCBI
HuRef112,544,696 - 12,669,465 (+)NCBIHuRef
CHM1_1113,825,064 - 13,950,026 (+)NCBICHM1_1
T2T-CHM13v2.0113,142,270 - 13,267,189 (+)NCBI
Prdm2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394142,833,961 - 142,939,560 (-)NCBIGRCm39mm39
GRCm39 Ensembl4142,833,961 - 142,939,565 (-)Ensembl
GRCm384143,107,391 - 143,212,769 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4143,107,391 - 143,212,995 (-)EnsemblGRCm38mm10GRCm38
MGSCv374142,697,294 - 142,802,612 (-)NCBIGRCm37mm9NCBIm37
MGSCv364142,394,156 - 142,479,396 (-)NCBImm8
Celera4144,915,482 - 145,028,265 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map476.84NCBI
Prdm2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555274,012,332 - 4,105,311 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555274,005,410 - 4,105,376 (-)NCBIChiLan1.0ChiLan1.0
PRDM2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1113,853,829 - 13,910,800 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl113,853,895 - 13,961,610 (+)Ensemblpanpan1.1panPan2
PanPan1.1 Ensembl113,853,895 - 13,961,610 (+)NCBIpanpan1.1panPan2
Mhudiblu_PPA_v0112,838,201 - 12,963,735 (+)NCBIMhudiblu_PPA_v0panPan3
PRDM2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1283,381,021 - 83,429,640 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl283,382,552 - 83,465,687 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha279,917,102 - 80,036,570 (-)NCBI
ROS_Cfam_1.0284,031,028 - 84,150,815 (-)NCBI
ROS_Cfam_1.0 Ensembl284,031,037 - 84,150,473 (-)Ensembl
UMICH_Zoey_3.1280,784,169 - 80,888,460 (-)NCBI
UNSW_CanFamBas_1.0281,802,556 - 81,922,434 (-)NCBI
UU_Cfam_GSD_1.0282,869,382 - 82,989,085 (-)NCBI
Prdm2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505836,081,381 - 36,129,727 (+)NCBI
SpeTri2.0NW_0049364741,910,026 - 1,924,900 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRDM2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl673,118,177 - 73,239,423 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1673,135,872 - 73,240,271 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2667,387,475 - 67,455,877 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRDM2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120118,437,171 - 118,565,554 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl20118,436,717 - 118,550,461 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605422,166,785 - 22,295,971 (-)NCBIVero_WHO_p1.0
Prdm2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624764276,893 - 384,270 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_004624764261,451 - 384,270 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D5Got96  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25155,532,103 - 155,532,450 (+)MAPPERmRatBN7.2
Rnor_6.05161,879,412 - 161,879,758NCBIRnor6.0
Rnor_5.05165,578,603 - 165,578,949UniSTSRnor5.0
RGSC_v3.45162,072,797 - 162,073,144RGDRGSC3.4
RGSC_v3.45162,072,798 - 162,073,144UniSTSRGSC3.4
RGSC_v3.15162,082,986 - 162,083,332RGD
Celera5153,860,613 - 153,860,959UniSTS
RH 3.4 Map51058.6UniSTS
RH 3.4 Map51058.6RGD
RH 2.0 Map51091.8RGD
Cytogenetic Map5q36UniSTS
42.MMHAP20FRF12.seq  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25155,499,161 - 155,499,335 (+)MAPPERmRatBN7.2
Rnor_6.05161,847,761 - 161,847,934NCBIRnor6.0
Rnor_5.05165,546,952 - 165,547,125UniSTSRnor5.0
RGSC_v3.45162,040,518 - 162,040,691UniSTSRGSC3.4
Celera5153,830,112 - 153,830,285UniSTS
Cytogenetic Map5q36UniSTS
BE120443  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25155,446,444 - 155,446,597 (+)MAPPERmRatBN7.2
Rnor_6.05161,794,757 - 161,794,909NCBIRnor6.0
Rnor_5.05165,493,948 - 165,494,100UniSTSRnor5.0
RGSC_v3.45161,987,221 - 161,987,373UniSTSRGSC3.4
Celera5153,777,437 - 153,777,589UniSTS
RH 3.4 Map51057.9UniSTS
Cytogenetic Map5q36UniSTS
RH135296  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25155,422,169 - 155,422,381 (+)MAPPERmRatBN7.2
Rnor_6.05161,770,689 - 161,770,900NCBIRnor6.0
Rnor_5.05165,469,880 - 165,470,091UniSTSRnor5.0
RGSC_v3.45161,962,965 - 161,963,176UniSTSRGSC3.4
Celera5153,753,356 - 153,753,567UniSTS
RH 3.4 Map51058.2UniSTS
Cytogenetic Map5q36UniSTS
ksks160  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25155,447,866 - 155,448,175 (+)MAPPERmRatBN7.2
Rnor_6.05161,796,179 - 161,796,487NCBIRnor6.0
Rnor_5.05165,495,370 - 165,495,678UniSTSRnor5.0
RGSC_v3.45161,988,643 - 161,988,951UniSTSRGSC3.4
Celera5153,778,859 - 153,779,167UniSTS
Cytogenetic Map5q36UniSTS
PMC312773P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25155,479,438 - 155,479,558 (+)MAPPERmRatBN7.2
Rnor_6.05161,827,987 - 161,828,106NCBIRnor6.0
Rnor_5.05165,527,178 - 165,527,297UniSTSRnor5.0
RGSC_v3.45162,020,799 - 162,020,918UniSTSRGSC3.4
Celera5153,810,393 - 153,810,512UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5143799107158428037Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5151006154161165494Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5151113452164465185Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:91
Count of miRNA genes:82
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000041175
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.


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 29 23 8 19 8 1 73 34 41 11
Low 14 34 33 33 8 10 1 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041175   ⟹   ENSRNOP00000046011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5155,422,134 - 155,531,825 (-)Ensembl
Rnor_6.0 Ensembl5161,770,653 - 161,879,133 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078237   ⟹   ENSRNOP00000072686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5161,773,758 - 161,875,362 (-)Ensembl
RefSeq Acc Id: NM_001077648   ⟹   NP_001071116
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,422,134 - 155,531,825 (-)NCBI
Rnor_6.05161,770,653 - 161,879,133 (-)NCBI
Rnor_5.05165,468,778 - 165,578,775 (-)NCBI
RGSC_v3.45161,962,929 - 162,072,519 (-)RGD
Celera5153,753,320 - 153,860,334 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239337   ⟹   XP_006239399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,421,066 - 155,497,595 (-)NCBI
Rnor_6.05161,769,587 - 161,846,165 (-)NCBI
Rnor_5.05165,468,778 - 165,578,775 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593426   ⟹   XP_017448915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,421,066 - 155,531,852 (-)NCBI
Rnor_6.05161,769,587 - 161,879,138 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110087   ⟹   XP_038966015
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,421,066 - 155,531,852 (-)NCBI
RefSeq Acc Id: XM_039110088   ⟹   XP_038966016
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,421,066 - 155,495,927 (-)NCBI
RefSeq Acc Id: XM_039110089   ⟹   XP_038966017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,442,380 - 155,531,884 (-)NCBI
RefSeq Acc Id: XM_039110090   ⟹   XP_038966018
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,421,066 - 155,459,327 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001071116   ⟸   NM_001077648
- Sequence:
RefSeq Acc Id: XP_006239399   ⟸   XM_006239337
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017448915   ⟸   XM_017593426
- Peptide Label: isoform X1
- UniProtKB: F1LQ66 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000046011   ⟸   ENSRNOT00000041175
RefSeq Acc Id: ENSRNOP00000072686   ⟸   ENSRNOT00000078237
RefSeq Acc Id: XP_038966015   ⟸   XM_039110087
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038966016   ⟸   XM_039110088
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966018   ⟸   XM_039110090
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038966017   ⟸   XM_039110089
- Peptide Label: isoform X3
Protein Domains
SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63755-F1-model_v2 AlphaFold Q63755 1-1706 view protein structure

Transcriptome

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

Promoters
RGD ID:13694240
Promoter ID:EPDNEW_R4765
Type:multiple initiation site
Name:Prdm2_1
Description:PR/SET domain 2
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_6.05161,879,146 - 161,879,206EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1594531 AgrOrtholog
BioCyc Gene G2FUF-39304 BioCyc
Ensembl Genes ENSRNOG00000033522 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046011 ENTREZGENE
  ENSRNOP00000046011.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041175 ENTREZGENE
  ENSRNOT00000041175.5 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PRDM2_PR-SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RIZ_retinblastoma-bd_prot UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SET_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:313678 UniProtKB/Swiss-Prot
NCBI Gene 313678 ENTREZGENE
Pfam SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PRDM2 RGD
PhenoGen Prdm2 PhenoGen
PIRSF RIZ_SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF82199 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LQ66 ENTREZGENE, UniProtKB/TrEMBL
  PRDM2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Prdm2  PR/SET domain 2  Prdm2  PR domain 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Prdm2  PR domain 2  Prdm2  PR domain containing 2, with ZNF domain  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-13   PR domain containing 2, with ZNF domain  Prdm2  PR domain containing 2, with ZNF domain (mapped)  Name updated 737654 APPROVED
2007-04-12 Prdm2  PR domain containing 2, with ZNF domain (mapped)  Prdm2_mapped  PR domain containing 2, with ZNF domain (mapped)  Data Merged 737654 APPROVED
2006-11-20 Prdm2  PR domain containing 2, with ZNF domain (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Prdm2_mapped  PR domain containing 2, with ZNF domain (mapped)  Prdm2  PR domain containing 2, with ZNF domain  Symbol and Name updated 1556543 APPROVED
2001-11-30 Prdm2  PR domain containing 2, with ZNF domain      Symbol and Name updated to reflect Human and Mouse nomenclature 68913 APPROVED
2001-11-30 Riz  Retinoblastoma interacting zinc finger protein      Symbol and Name withdrawn 68913 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_product member of the PR domain family, a subset of Kr├╝ppel-like zinc finger genes 1300403