Prdm13 (PR/SET domain 13) - 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 Behavioral & Substance Use Disorder 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 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
Advanced Search (OLGA)
Gene: Prdm13 (PR/SET domain 13) Rattus norvegicus
Analyze
Symbol: Prdm13
Name: PR/SET domain 13
RGD ID: 1589883
Description: Predicted to enable RNA polymerase II-specific DNA-binding transcription factor binding activity; chromatin binding activity; and histone methyltransferase activity. Predicted to be involved in GABAergic neuron differentiation; hypothalamus cell differentiation; and regulation of gene expression. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and neurogenesis. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia. Orthologous to human PRDM13 (PR/SET domain 13); INTERACTS WITH acrylamide; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC689695; PR domain 13; PR domain containing 13; PR domain zinc finger protein 13; similar to PR domain containing 13
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
GRCr8540,017,607 - 40,029,658 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl540,017,607 - 40,038,207 (-)EnsemblGRCr8
mRatBN7.2535,220,815 - 35,232,866 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl535,225,435 - 35,232,881 (-)EnsemblmRatBN7.2
Rnor_6.0535,821,023 - 35,831,897 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl535,823,983 - 35,831,712 (-)Ensemblrn6Rnor6.0
Rnor_5.0540,479,940 - 40,520,016 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4536,422,405 - 36,429,851 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera534,241,250 - 34,249,988 (-)NCBICelera
Cytogenetic Map5q21NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IEA,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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19050759   PMID:23639443   PMID:24370451  


Genomics

Comparative Map Data
Prdm13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8540,017,607 - 40,029,658 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl540,017,607 - 40,038,207 (-)EnsemblGRCr8
mRatBN7.2535,220,815 - 35,232,866 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl535,225,435 - 35,232,881 (-)EnsemblmRatBN7.2
Rnor_6.0535,821,023 - 35,831,897 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl535,823,983 - 35,831,712 (-)Ensemblrn6Rnor6.0
Rnor_5.0540,479,940 - 40,520,016 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4536,422,405 - 36,429,851 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera534,241,250 - 34,249,988 (-)NCBICelera
Cytogenetic Map5q21NCBI
PRDM13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38699,606,833 - 99,615,562 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl699,606,774 - 99,615,578 (+)Ensemblhg38GRCh38
GRCh376100,054,709 - 100,063,438 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366100,161,371 - 100,170,175 (+)NCBIBuild 36Build 36hg18NCBI36
Build 346100,161,370 - 100,170,175NCBI
Celera6100,698,764 - 100,707,568 (+)NCBICelera
Cytogenetic Map6q16.2ENTREZGENE
HuRef697,494,031 - 97,502,835 (+)NCBIHuRef
CHM1_16100,316,733 - 100,325,537 (+)NCBICHM1_1
T2T-CHM13v2.06100,780,286 - 100,789,017 (+)NCBIT2T-CHM13v2.0
Prdm13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39421,675,865 - 21,685,963 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl421,677,480 - 21,685,963 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38421,675,865 - 21,685,963 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl421,677,480 - 21,685,963 (-)Ensemblmm10GRCm38
MGSCv37421,604,627 - 21,613,110 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36421,768,102 - 21,776,798 (-)NCBIMGSCv36mm8
Celera421,422,449 - 21,430,966 (-)NCBICelera
Cytogenetic Map4A3NCBI
cM Map48.78NCBI
Prdm13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541125,481,741 - 25,489,049 (+)Ensembl
ChiLan1.0NW_00495541125,481,601 - 25,489,049 (+)NCBIChiLan1.0ChiLan1.0
PRDM13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25119,653,430 - 119,662,153 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16117,534,566 - 117,543,309 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0697,447,729 - 97,456,541 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16101,329,818 - 101,337,368 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6101,329,818 - 101,337,368 (+)EnsemblpanPan2panpan1.1
PRDM13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11257,803,068 - 57,811,592 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1257,562,568 - 57,570,210 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01258,627,167 - 58,634,809 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1258,627,167 - 58,634,809 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11257,983,496 - 57,991,136 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01257,830,521 - 57,838,171 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01258,076,316 - 58,083,973 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Prdm13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494692,744,529 - 92,753,274 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366511,200,089 - 1,207,872 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366511,199,928 - 1,208,697 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRDM13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl166,538,862 - 66,546,409 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1166,539,061 - 66,546,506 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2175,215,375 - 75,223,674 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRDM13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11374,267,245 - 74,280,131 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1374,267,329 - 74,275,085 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604046,596,092 - 46,604,842 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prdm13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248105,421,522 - 5,428,848 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248105,421,231 - 5,428,863 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Prdm13
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11121,653,699 - 121,661,212 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Prdm13
60 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:49
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000010126
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
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53801167083011670Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)51373115343590997Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)53275164977751649Rat
6907115Mcs29Mammary carcinoma susceptibility QTL 29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)53800433183004331Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)538207390136631402Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)52367149379046465Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5862723052665523Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51757663362576633Rat
1578774Tcas8Tongue tumor susceptibility QTL 83.47tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)51570745160707451Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53801167083011670Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53801167083011670Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)539019942102105896Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)53331167378311673Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)53275164977751649Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)53113042148841739Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)51748608062486080Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5862723053627230Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)53998594884985948Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5692228281330203Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53331167378311673Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)53952692484526924Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51460607859606078Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906491770353Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)536460764136631402Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5706553574335773Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51748608062486080Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906487027358Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52602321171023211Rat
2303577Gluco47Glucose level QTL 473blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51652001961520019Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)52367149368671493Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
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
5 3 88 12 7 4 11 4 2 39 22 2 80 8 45 3 15 15

Sequence


Ensembl Acc Id: ENSRNOT00000010126   ⟹   ENSRNOP00000010126
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl535,225,435 - 35,232,881 (-)Ensembl
Rnor_6.0 Ensembl535,823,983 - 35,831,712 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000136642   ⟹   ENSRNOP00000100927
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl540,017,607 - 40,038,207 (-)Ensembl
RefSeq Acc Id: NM_001191098   ⟹   NP_001178027
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8540,017,607 - 40,029,658 (-)NCBI
mRatBN7.2535,220,815 - 35,232,866 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001178027 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL98510 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000100927
  ENSRNOP00000100927.1
Ensembl Acc Id: ENSRNOP00000010126   ⟸   ENSRNOT00000010126
RefSeq Acc Id: NP_001178027   ⟸   NM_001191098
- UniProtKB: A6IID9 (UniProtKB/TrEMBL),   D3ZKY4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000100927   ⟸   ENSRNOT00000136642
Protein Domains
C2H2-type   SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKY4-F1-model_v2 AlphaFold D3ZKY4 1-757 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:1589883 AgrOrtholog
BioCyc Gene G2FUF-41819 BioCyc
Ensembl Genes ENSRNOG00000007683 Ensembl
  ENSRNOG00000083626 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000136642 ENTREZGENE
  ENSRNOT00000136642.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro PRDM13_PR/SET UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/TrEMBL
  Zinc_finger UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
NCBI Gene 689695 ENTREZGENE
PANTHER PR DOMAIN ZINC FINGER PROTEIN UniProtKB/TrEMBL
  PR DOMAIN ZINC FINGER PROTEIN 13 UniProtKB/TrEMBL
Pfam PRDM2_PR UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
PhenoGen Prdm13 PhenoGen
PROSITE SET UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007683 RatGTEx
  ENSRNOG00000083626 RatGTEx
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
  SSF82199 UniProtKB/TrEMBL
UniProt A0ABK0LHZ5_RAT UniProtKB/TrEMBL
  A6IID9 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKY4 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Prdm13  PR/SET domain 13  Prdm13  PR domain 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Prdm13  PR domain 13  Prdm13  PR domain containing 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Prdm13  PR domain containing 13  LOC689695  similar to PR domain containing 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC689695  similar to PR domain containing 13  LOC681862  similar to PR domain containing 13  Data merged from RGD:1590501 1643240 APPROVED
2006-11-20 LOC689695  similar to PR domain containing 13      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC681862  similar to PR domain containing 13      Symbol and Name status set to provisional 70820 PROVISIONAL