Prdm4 (PR/SET domain 4) - Rat Genome Database

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Gene: Prdm4 (PR/SET domain 4) Rattus norvegicus
Analyze
Symbol: Prdm4
Name: PR/SET domain 4
RGD ID: 619929
Description: Enables death receptor binding activity. Involved in several processes, including cellular response to nutrient; negative regulation of cell growth; and regulation of stem cell differentiation. Located in cytoplasm and nucleus. Orthologous to human PRDM4 (PR/SET domain 4); PARTICIPATES IN neurotrophic factor signaling pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: PR domain 4; PR domain containing 4; PR domain zinc finger protein 4; PR domain-containing protein 4; SC-1
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
mRatBN7.2717,953,832 - 17,980,489 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl717,954,019 - 17,980,489 (+)Ensembl
Rnor_6.0723,959,932 - 23,986,535 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl723,960,378 - 23,985,525 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0724,109,460 - 24,136,615 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4720,096,859 - 20,117,628 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1720,110,929 - 20,131,701 (+)NCBI
Celera715,190,862 - 15,211,498 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:15051733   PMID:23918801   PMID:27125459  


Genomics

Comparative Map Data
Prdm4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2717,953,832 - 17,980,489 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl717,954,019 - 17,980,489 (+)Ensembl
Rnor_6.0723,959,932 - 23,986,535 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl723,960,378 - 23,985,525 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0724,109,460 - 24,136,615 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4720,096,859 - 20,117,628 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1720,110,929 - 20,131,701 (+)NCBI
Celera715,190,862 - 15,211,498 (+)NCBICelera
Cytogenetic Map7q13NCBI
PRDM4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812107,732,871 - 107,761,137 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12107,732,871 - 107,761,272 (-)EnsemblGRCh38hg38GRCh38
GRCh3712108,126,648 - 108,154,914 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612106,650,773 - 106,679,044 (-)NCBINCBI36hg18NCBI36
Build 3412106,629,110 - 106,657,381NCBI
Celera12107,792,201 - 107,820,465 (-)NCBI
Cytogenetic Map12q23.3NCBI
HuRef12105,186,879 - 105,215,475 (-)NCBIHuRef
CHM1_112108,092,594 - 108,120,863 (-)NCBICHM1_1
T2T-CHM13v2.012107,696,363 - 107,724,628 (-)NCBI
Prdm4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391085,727,828 - 85,752,958 (-)NCBIGRCm39mm39
GRCm39 Ensembl1085,727,830 - 85,753,006 (-)Ensembl
GRCm381085,891,964 - 85,917,152 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1085,891,966 - 85,917,142 (-)EnsemblGRCm38mm10GRCm38
MGSCv371085,354,711 - 85,379,690 (-)NCBIGRCm37mm9NCBIm37
MGSCv361085,321,765 - 85,346,744 (-)NCBImm8
Celera1087,866,535 - 87,891,563 (-)NCBICelera
Cytogenetic Map10C1NCBI
Prdm4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540541,336,199 - 41,353,261 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540541,335,019 - 41,354,625 (-)NCBIChiLan1.0ChiLan1.0
PRDM4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112108,699,444 - 108,727,444 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12108,699,444 - 108,727,304 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012105,303,009 - 105,331,305 (-)NCBIMhudiblu_PPA_v0panPan3
PRDM4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11031,071,998 - 31,100,008 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1031,072,297 - 31,098,636 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1031,056,699 - 31,084,641 (+)NCBI
ROS_Cfam_1.01031,916,430 - 31,944,338 (+)NCBI
ROS_Cfam_1.0 Ensembl1031,916,780 - 31,944,338 (+)Ensembl
UMICH_Zoey_3.11031,655,923 - 31,683,803 (+)NCBI
UNSW_CanFamBas_1.01031,945,006 - 31,972,913 (+)NCBI
UU_Cfam_GSD_1.01032,131,601 - 32,159,592 (+)NCBI
Prdm4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494514,381,658 - 14,407,064 (+)NCBI
SpeTri2.0NW_0049364927,392,072 - 7,417,478 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRDM4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl512,638,488 - 12,668,878 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1512,638,335 - 12,668,890 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2512,424,617 - 12,455,111 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRDM4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111102,952,123 - 102,980,500 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl11102,953,480 - 102,980,173 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037142,093,057 - 142,121,392 (+)NCBIVero_WHO_p1.0
Prdm4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247502,076,466 - 2,097,766 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247502,077,130 - 2,106,331 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:37
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000006886
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.


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 2 35 32 16 19 16 1 2 74 33 41 11 1
Low 1 8 25 25 25 7 9 2 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006886   ⟹   ENSRNOP00000006886
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl717,954,019 - 17,980,489 (+)Ensembl
Rnor_6.0 Ensembl723,960,378 - 23,985,525 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100599   ⟹   ENSRNOP00000090471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl717,954,090 - 17,964,535 (+)Ensembl
RefSeq Acc Id: NM_133312   ⟹   NP_579846
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,958,666 - 17,979,439 (+)NCBI
Rnor_6.0723,964,716 - 23,985,485 (+)NCBI
Rnor_5.0724,109,460 - 24,136,615 (+)NCBI
RGSC_v3.4720,096,859 - 20,117,628 (+)RGD
Celera715,190,862 - 15,211,498 (+)RGD
Sequence:
RefSeq Acc Id: XM_006241160   ⟹   XP_006241222
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,953,886 - 17,980,489 (+)NCBI
Rnor_6.0723,959,935 - 23,986,535 (+)NCBI
Rnor_5.0724,109,460 - 24,136,615 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241161   ⟹   XP_006241223
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,953,886 - 17,980,489 (+)NCBI
Rnor_6.0723,959,935 - 23,985,485 (+)NCBI
Rnor_5.0724,109,460 - 24,136,615 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078328   ⟹   XP_038934256
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,953,832 - 17,980,489 (+)NCBI
RefSeq Acc Id: XM_039078330   ⟹   XP_038934258
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,953,886 - 17,970,070 (+)NCBI
RefSeq Acc Id: XM_039078331   ⟹   XP_038934259
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,953,886 - 17,970,070 (+)NCBI
RefSeq Acc Id: XR_005486542
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,953,886 - 17,979,598 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_579846   ⟸   NM_133312
- Sequence:
RefSeq Acc Id: XP_006241222   ⟸   XM_006241160
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006241223   ⟸   XM_006241161
- Peptide Label: isoform X2
- UniProtKB: F1LPR7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006886   ⟸   ENSRNOT00000006886
RefSeq Acc Id: XP_038934256   ⟸   XM_039078328
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934258   ⟸   XM_039078330
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934259   ⟸   XM_039078331
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000090471   ⟸   ENSRNOT00000100599
Protein Domains
C2H2-type   SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9QZP2-F1-model_v2 AlphaFold Q9QZP2 1-798 view protein structure

Transcriptome

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

Promoters
RGD ID:13695094
Promoter ID:EPDNEW_R5619
Type:single initiation site
Name:Prdm4_1
Description:PR/SET domain 4
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_6.0723,960,443 - 23,960,503EPDNEW

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)
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
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)
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
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)
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
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)
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
HXB31/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
HXB4/IpcvMcwi (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
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)
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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
LEXF2B/Stm (2019)
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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
LEXF3/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
LEXF4/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
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)
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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
LN/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
M520/N (2020)
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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)
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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)
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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
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)
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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
WKY/N (2020)
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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)
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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
WN/N (2020)
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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:619929 AgrOrtholog
BioCyc Gene G2FUF-34635 BioCyc
Ensembl Genes ENSRNOG00000004962 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006886 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006886 ENTREZGENE, UniProtKB/TrEMBL
InterPro PRDM4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PRDM4_PR/SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PRDM4_Znf_knuckle UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SET_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:170820 UniProtKB/Swiss-Prot
NCBI Gene 170820 ENTREZGENE
Pfam zf-C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf_PR_Knuckle UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prdm4 PhenoGen
PIRSF PRDM4 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 ZnF_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LPR7 ENTREZGENE, UniProtKB/TrEMBL
  PRDM4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Prdm4  PR/SET domain 4  Prdm4  PR domain 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Prdm4  PR domain 4  Prdm4  PR domain containing 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Prdm4  PR domain containing 4      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Prdm4  PR domain containing 4      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization change in subcellular localization from cytoplasm to the nucleus is associated with p75 neurotrophin receptor binding as well as with serum starvation 633619