Prdm14 (PR/SET domain 14) - Rat Genome Database

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Gene: Prdm14 (PR/SET domain 14) Rattus norvegicus
Analyze
Symbol: Prdm14
Name: PR/SET domain 14
RGD ID: 2319590
Description: Predicted to enable RNA binding activity; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and chromatin DNA binding activity. Predicted to be involved in positive regulation of flagellated sperm motility; positive regulation of stem cell population maintenance; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including embryo implantation; inner cell mass cell fate commitment; and negative regulation of macromolecule biosynthetic process. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human PRDM14 (PR/SET domain 14); PARTICIPATES IN DNA modification pathway; INTERACTS WITH 4,4'-sulfonyldiphenol (ortholog); 5-fluorouracil (ortholog); aflatoxin B1 (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100365184; PR domain 14; PR domain containing 14; PR domain containing 14-like; PR domain zinc finger protein 14
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Prdm14em10Nips   Prdm14tm1(H2BVenus)Nips  
Genetic Models: WI;WDB-Prdm14tm1(H2BVenus)Nips WI-Prdm14em10Nips
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8510,864,137 - 10,876,666 (+)NCBIGRCr8
mRatBN7.256,082,163 - 6,092,712 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl56,082,442 - 6,092,712 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.055,710,076 - 5,730,560 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl55,710,392 - 5,730,560 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0510,550,222 - 10,570,255 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera55,665,056 - 5,674,368 (+)NCBICelera
Cytogenetic Map5q11NCBI
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

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Integrating DNA methylation and microRNA biomarkers in sputum for lung cancer detection. Su Y, etal., Clin Epigenetics. 2016 Oct 19;8:109. doi: 10.1186/s13148-016-0275-5. eCollection 2016.
5. High expression of PRDM14 correlates with cell differentiation and is a novel prognostic marker in resected non-small cell lung cancer. Zhang T, etal., Med Oncol. 2013;30(3):605. doi: 10.1007/s12032-013-0605-9. Epub 2013 May 21.
Additional References at PubMed
PMID:18622394   PMID:21183938   PMID:22482507   PMID:23670199   PMID:24183668   PMID:24268575   PMID:26523391   PMID:27281218   PMID:32001439   PMID:33637711  


Genomics

Comparative Map Data
Prdm14
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8510,864,137 - 10,876,666 (+)NCBIGRCr8
mRatBN7.256,082,163 - 6,092,712 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl56,082,442 - 6,092,712 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.055,710,076 - 5,730,560 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl55,710,392 - 5,730,560 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0510,550,222 - 10,570,255 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera55,665,056 - 5,674,368 (+)NCBICelera
Cytogenetic Map5q11NCBI
PRDM14
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38870,051,651 - 70,071,252 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl870,051,651 - 70,071,693 (-)EnsemblGRCh38hg38GRCh38
GRCh37870,963,886 - 70,983,487 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36871,126,575 - 71,146,116 (-)NCBINCBI36Build 36hg18NCBI36
Build 34871,126,578 - 71,146,116NCBI
Celera866,961,694 - 66,981,231 (-)NCBICelera
Cytogenetic Map8q13.3NCBI
HuRef866,457,068 - 66,476,744 (-)NCBIHuRef
CHM1_1871,019,399 - 71,039,074 (-)NCBICHM1_1
T2T-CHM13v2.0870,481,509 - 70,501,107 (-)NCBIT2T-CHM13v2.0
Prdm14
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39113,183,649 - 13,197,467 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl113,183,681 - 13,197,387 (-)EnsemblGRCm39 Ensembl
GRCm38113,113,428 - 13,127,163 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl113,113,457 - 13,127,163 (-)EnsemblGRCm38mm10GRCm38
MGSCv37113,103,509 - 13,117,244 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36113,098,642 - 13,112,377 (-)NCBIMGSCv36mm8
MGSCv36113,198,671 - 13,212,167 (-)NCBIMGSCv36mm8
Celera113,077,505 - 13,091,214 (-)NCBICelera
Cytogenetic Map1A3NCBI
cM Map14.1NCBI
Prdm14
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554449,612,059 - 9,626,817 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554449,606,310 - 9,626,772 (+)NCBIChiLan1.0ChiLan1.0
PRDM14
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2785,784,874 - 85,806,252 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1861,414,702 - 61,436,088 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0866,578,674 - 66,599,360 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1868,240,111 - 68,261,039 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl868,240,741 - 68,260,263 (-)Ensemblpanpan1.1panPan2
PRDM14
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12919,203,798 - 19,220,149 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2919,203,807 - 19,220,518 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2919,420,735 - 19,479,950 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02919,300,801 - 19,317,150 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2919,300,810 - 19,317,144 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12919,340,296 - 19,356,663 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02919,406,772 - 19,423,122 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02919,687,457 - 19,703,818 (-)NCBIUU_Cfam_GSD_1.0
Prdm14
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530359,964,384 - 59,979,219 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649614,806,928 - 14,820,967 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649614,789,443 - 14,820,967 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRDM14
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl465,271,315 - 65,295,178 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1465,273,988 - 65,295,362 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2470,938,499 - 70,962,240 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRDM14
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1865,800,454 - 65,820,190 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl865,800,923 - 65,819,456 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603975,620,953 - 75,642,095 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prdm14
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474421,104,798 - 21,120,591 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474421,092,091 - 21,121,313 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prdm14
60 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:22
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000034525
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
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)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat


Genetic Models
This gene Prdm14 is modified in the following models/strains:
WI;WDB-Prdm14tm1(H2BVenus)Nips     WI-Prdm14em10Nips    


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 reproductive system respiratory system
High
Medium
Low 13
Below cutoff 1 2 12 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034525   ⟹   ENSRNOP00000032955
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl56,082,442 - 6,092,712 (+)Ensembl
Rnor_6.0 Ensembl55,710,392 - 5,730,560 (+)Ensembl
RefSeq Acc Id: NM_001427157   ⟹   NP_001414086
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8510,864,137 - 10,876,666 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414086 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032955.5
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000032955   ⟸   ENSRNOT00000034525
RefSeq Acc Id: NP_001414086   ⟸   NM_001427157
- UniProtKB: D3ZI87 (UniProtKB/TrEMBL)
Protein Domains
C2H2-type   SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZI87-F1-model_v2 AlphaFold D3ZI87 1-559 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:2319590 AgrOrtholog
BioCyc Gene G2FUF-42244 BioCyc
Ensembl Genes ENSRNOG00000021792 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034525.6 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro PRDM14_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
NCBI Gene 100365184 ENTREZGENE
PANTHER PR DOMAIN ZINC FINGER PROTEIN UniProtKB/TrEMBL
  PR DOMAIN ZINC FINGER PROTEIN 14 UniProtKB/TrEMBL
Pfam PRDM2_PR UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
PhenoGen Prdm14 PhenoGen
PROSITE SET UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021792 RatGTEx
SMART SET UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
  SSF82199 UniProtKB/TrEMBL
UniProt D3ZI87 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Prdm14  PR/SET domain 14  Prdm14  PR domain 14  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Prdm14  PR domain 14  Prdm14  PR domain containing 14  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-11-07 Prdm14  PR domain containing 14  LOC100365184  PR domain containing 14-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100365184  PR domain containing 14-like      Symbol and Name status set to provisional 70820 PROVISIONAL