PRDM2 (PR/SET domain 2) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: PRDM2 (PR/SET domain 2) Chlorocebus sabaeus
Analyze
Symbol: PRDM2
Name: PR/SET domain 2
RGD ID: 18761018
Description: ENCODES a protein that exhibits DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); DNA-binding transcription repressor activity, RNA polymerase II-specific (inferred); INVOLVED IN determination of adult lifespan (ortholog); response to estradiol (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH amphetamine abuse (ortholog); chromosome 1p36 deletion syndrome (ortholog); Contracture (ortholog); FOUND IN Golgi apparatus (inferred); nucleoplasm (inferred); nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC103225564; PR domain zinc finger protein 2; uncharacterized LOC103225564
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120118,437,171 - 118,565,554 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20118,436,717 - 118,550,461 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605422,166,785 - 22,295,971 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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


Genomics

Comparative Map Data
PRDM2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120118,437,171 - 118,565,554 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20118,436,717 - 118,550,461 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605422,166,785 - 22,295,971 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
PRDM2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38113,700,188 - 13,825,079 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl113,700,188 - 13,825,079 (+)EnsemblGRCh38hg38GRCh38
GRCh37114,026,683 - 14,151,574 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36113,903,937 - 14,024,162 (+)NCBINCBI36Build 36hg18NCBI36
Build 34113,776,655 - 13,859,875NCBI
Celera112,508,705 - 12,633,526 (+)NCBICelera
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 (+)NCBIT2T-CHM13v2.0
Prdm2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394142,833,961 - 142,939,560 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4142,833,961 - 142,939,565 (-)EnsemblGRCm39 Ensembl
GRCm384143,107,391 - 143,212,769 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4143,107,391 - 143,212,995 (-)EnsemblGRCm38mm10GRCm38
MGSCv374142,697,294 - 142,802,612 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364142,394,156 - 142,479,396 (-)NCBIMGSCv36mm8
Celera4144,915,482 - 145,028,265 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map476.84NCBI
Prdm2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85160,704,396 - 160,815,184 (-)NCBIGRCr8
mRatBN7.25155,421,066 - 155,531,884 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5155,422,134 - 155,531,825 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5158,106,645 - 158,216,138 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05159,879,929 - 159,989,430 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05159,861,245 - 159,970,147 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5153,753,320 - 153,860,334 (-)NCBICelera
Cytogenetic Map5q36NCBI
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
NHGRI_mPanPan1-v21213,094,678 - 213,224,420 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11212,342,327 - 212,472,168 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0112,838,201 - 12,963,735 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0284,031,028 - 84,150,815 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl284,031,037 - 84,150,473 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1280,784,169 - 80,888,460 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0281,802,556 - 81,922,434 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0282,869,382 - 82,989,085 (-)NCBIUU_Cfam_GSD_1.0
Prdm2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505836,081,381 - 36,129,727 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364741,862,898 - 1,949,500 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624764276,893 - 384,270 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624764261,451 - 384,270 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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 hemolymphoid system nervous system
High
Medium 24 58
Low 12 20 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000017709   ⟹   ENSCSAP00000017181
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl20118,436,717 - 118,550,461 (-)Ensembl
RefSeq Acc Id: XM_007980472   ⟹   XP_007978663
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.120118,439,015 - 118,565,534 (-)NCBI
Vero_WHO_p1.0NW_02366605422,166,785 - 22,295,969 (-)NCBI
Sequence:
RefSeq Acc Id: XM_007980475   ⟹   XP_007978666
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.120118,437,171 - 118,564,495 (-)NCBI
Vero_WHO_p1.0NW_02366605422,166,785 - 22,295,970 (-)NCBI
Sequence:
RefSeq Acc Id: XM_037985012   ⟹   XP_037840940
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605422,166,785 - 22,295,971 (-)NCBI
RefSeq Acc Id: XM_037985013   ⟹   XP_037840941
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605422,166,785 - 22,283,193 (-)NCBI
RefSeq Acc Id: XM_037985014   ⟹   XP_037840942
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605422,203,206 - 22,295,971 (-)NCBI
RefSeq Acc Id: XM_037985015   ⟹   XP_037840943
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605422,204,056 - 22,295,970 (-)NCBI
RefSeq Acc Id: XM_037985016   ⟹   XP_037840944
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605422,166,785 - 22,251,550 (-)NCBI
RefSeq Acc Id: XM_037985017   ⟹   XP_037840945
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605422,204,475 - 22,251,550 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_007978666   ⟸   XM_007980475
- Peptide Label: isoform X3
- UniProtKB: A0A0D9S8J2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007978663   ⟸   XM_007980472
- Peptide Label: isoform X5
RefSeq Acc Id: ENSCSAP00000017181   ⟸   ENSCSAT00000017709
RefSeq Acc Id: XP_037840940   ⟸   XM_037985012
- Peptide Label: isoform X1
RefSeq Acc Id: XP_037840941   ⟸   XM_037985013
- Peptide Label: isoform X1
RefSeq Acc Id: XP_037840944   ⟸   XM_037985016
- Peptide Label: isoform X6
RefSeq Acc Id: XP_037840942   ⟸   XM_037985014
- Peptide Label: isoform X2
RefSeq Acc Id: XP_037840943   ⟸   XM_037985015
- Peptide Label: isoform X4
RefSeq Acc Id: XP_037840945   ⟸   XM_037985017
- Peptide Label: isoform X7


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000000824 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000017709.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro PRDM2_PR-SET UniProtKB/TrEMBL
  RIZ_retinblastoma-bd_prot UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/TrEMBL
NCBI Gene PRDM2 ENTREZGENE
PANTHER PR DOMAIN ZINC FINGER PROTEIN UniProtKB/TrEMBL
  PR DOMAIN ZINC FINGER PROTEIN 2 UniProtKB/TrEMBL
Pfam PRDM2_PR UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
  zf-C2H2_6 UniProtKB/TrEMBL
PIRSF RIZ_SET UniProtKB/TrEMBL
PROSITE SET UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART SET UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
  SSF82199 UniProtKB/TrEMBL
UniProt A0A0D9S8J2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-12-03 PRDM2  PR/SET domain 2  LOC103225564  uncharacterized LOC103225564  Data merged from RGD:18783518 737654 PROVISIONAL