Prdm1 (PR/SET domain 1) - Rat Genome Database

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Gene: Prdm1 (PR/SET domain 1) Rattus norvegicus
Analyze
Symbol: Prdm1
Name: PR/SET domain 1
RGD ID: 1311765
Description: Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; histone methyltransferase binding activity; and promoter-specific chromatin binding activity. Predicted to be involved in several processes, including peptidyl-arginine methylation; regulation of lymphocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including circulatory system development; eye morphogenesis; and regulation of gene expression. Predicted to be located in nucleolus and nucleoplasm. Predicted to be active in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in hepatocellular carcinoma and lung adenocarcinoma. Orthologous to human PRDM1 (PR/SET domain 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; acrolein.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC309871; PR domain 1; PR domain containing 1, with ZNF domain; PR domain zinc finger protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82049,542,465 - 49,564,088 (-)NCBIGRCr8
mRatBN7.22047,959,858 - 47,981,488 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2047,959,858 - 47,981,488 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2049,700,158 - 49,721,766 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02049,350,052 - 49,371,661 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02050,033,672 - 50,055,300 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02049,464,921 - 49,556,623 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2049,464,919 - 49,556,518 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02051,096,616 - 51,118,240 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42048,438,224 - 48,459,848 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12048,469,384 - 48,488,777 (-)NCBI
Celera2052,026,331 - 52,047,919 (+)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,4-phenylenediamine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
3,4-dichloroaniline  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
acrolein  (EXP)
acrylamide  (EXP)
adefovir pivoxil  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-naphthoflavone  (ISO)
amitrole  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-lapachone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buta-1,3-diene  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlordecone  (ISO)
chloroacetaldehyde  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
coumarin  (ISO)
crocidolite asbestos  (ISO)
DDE  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
diethyl phthalate  (ISO)
diethylstilbestrol  (EXP,ISO)
diisobutyl phthalate  (ISO)
diisononyl phthalate  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
hydroquinone  (ISO)
hydroxychloroquine  (ISO)
ibrutinib  (ISO)
ifosfamide  (ISO)
indinavir  (ISO)
ketoconazole  (EXP)
L-methionine  (ISO)
lamivudine  (ISO)
lipopolysaccharide  (ISO)
mercury dibromide  (ISO)
metformin  (ISO)
methamphetamine  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
niclosamide  (ISO)
okadaic acid  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (EXP)
PD 0325901  (ISO)
phenylmercury acetate  (ISO)
phosgene  (ISO)
potassium chromate  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
saquinavir  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
sulfasalazine  (ISO)
sulforaphane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
troglitazone  (ISO)
trovafloxacin  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
zidovudine  (ISO)
zinc oxide  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,IEA,ISO)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. PRDM1 rs1010273 polymorphism is associated with overall survival of patients with hepatitis B virus-related hepatocellular carcinoma. Li N, etal., Immunol Lett. 2019 Sep;213:39-45. doi: 10.1016/j.imlet.2019.07.007. Epub 2019 Jul 31.
4. PRDM1 levels are associated with clinical diseases in chronic HBV infection and survival of patients with HBV-related hepatocellular carcinoma. Li N, etal., Int Immunopharmacol. 2019 Aug;73:156-162. doi: 10.1016/j.intimp.2019.05.012. Epub 2019 May 14.
5. The downregulation of PRDM1/Blimp-1 is associated with aberrant expression of miR-223 in extranodal NK/T-cell lymphoma, nasal type. Liang L, etal., J Exp Clin Cancer Res. 2014 Jan 17;33:7. doi: 10.1186/1756-9966-33-7.
6. Bcl-2 and BLIMP-1 expression predict worse prognosis in gastric diffuse large B cell lymphoma (DLCBL) while other markers for nodal DLBCL are not useful. Martin-Arruti M, etal., Histopathology. 2012 Apr;60(5):785-92. doi: 10.1111/j.1365-2559.2011.04160.x. Epub 2012 Feb 9.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Effect of 50-Hz Magnetic Fields on Serum IL-1β and IL-23 and Expression of BLIMP-1, XBP-1, and IRF-4. Molaei S, etal., Inflammation. 2019 Oct;42(5):1800-1807. doi: 10.1007/s10753-019-01042-w.
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Expression of immune checkpoints and T cell exhaustion markers in early and advanced stages of colorectal cancer. Saleh R, etal., Cancer Immunol Immunother. 2020 Oct;69(10):1989-1999. doi: 10.1007/s00262-020-02593-w. Epub 2020 May 11.
12. Downregulation of PRDM1 promotes cellular invasion and lung cancer metastasis. Zhu Z, etal., Tumour Biol. 2017 Apr;39(4):1010428317695929. doi: 10.1177/1010428317695929.
Additional References at PubMed
PMID:1851123   PMID:15750184   PMID:15937476   PMID:16901790   PMID:18622394   PMID:18845144   PMID:19578360   PMID:20463215   PMID:21421998   PMID:21670299   PMID:22987638   PMID:24821700  
PMID:25807483   PMID:27102484  


Genomics

Comparative Map Data
Prdm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82049,542,465 - 49,564,088 (-)NCBIGRCr8
mRatBN7.22047,959,858 - 47,981,488 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2047,959,858 - 47,981,488 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2049,700,158 - 49,721,766 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02049,350,052 - 49,371,661 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02050,033,672 - 50,055,300 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02049,464,921 - 49,556,623 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2049,464,919 - 49,556,518 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02051,096,616 - 51,118,240 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42048,438,224 - 48,459,848 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12048,469,384 - 48,488,777 (-)NCBI
Celera2052,026,331 - 52,047,919 (+)NCBICelera
Cytogenetic Map20q13NCBI
PRDM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386105,992,690 - 106,109,938 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6105,993,463 - 106,109,939 (+)EnsemblGRCh38hg38GRCh38
GRCh376106,534,211 - 106,557,813 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366106,640,888 - 106,664,506 (+)NCBINCBI36Build 36hg18NCBI36
Build 346106,653,507 - 106,664,502NCBI
Celera6107,155,767 - 107,179,390 (+)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6103,981,166 - 104,004,788 (+)NCBIHuRef
CHM1_16106,796,630 - 106,820,250 (+)NCBICHM1_1
T2T-CHM13v2.06107,168,603 - 107,285,801 (+)NCBIT2T-CHM13v2.0
Prdm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391044,313,170 - 44,404,579 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1044,313,173 - 44,404,497 (-)EnsemblGRCm39 Ensembl
GRCm381044,437,174 - 44,528,558 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1044,437,177 - 44,528,501 (-)EnsemblGRCm38mm10GRCm38
MGSCv371044,156,981 - 44,178,493 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361044,125,592 - 44,147,163 (-)NCBIMGSCv36mm8
Celera1045,310,489 - 45,332,012 (-)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1023.24NCBI
Prdm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541131,434,503 - 31,456,056 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541131,434,503 - 31,455,995 (+)NCBIChiLan1.0ChiLan1.0
PRDM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25126,104,593 - 126,129,008 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16123,992,333 - 124,013,831 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06103,899,410 - 103,923,389 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16107,773,229 - 107,796,815 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6107,773,229 - 107,796,815 (+)Ensemblpanpan1.1panPan2
PRDM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11263,454,242 - 63,495,278 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1263,470,974 - 63,495,579 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1263,258,691 - 63,282,613 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01264,316,675 - 64,340,623 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1264,315,991 - 64,339,167 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11263,676,388 - 63,700,298 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01263,518,620 - 63,542,363 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01263,792,179 - 63,816,021 (+)NCBIUU_Cfam_GSD_1.0
Prdm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494698,318,952 - 98,415,844 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365642,667,660 - 2,690,683 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365642,594,362 - 2,690,680 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRDM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl172,311,880 - 72,335,466 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1172,309,096 - 72,335,474 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2181,574,968 - 81,601,267 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRDM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11367,695,436 - 67,719,487 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1367,695,309 - 67,718,931 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604040,029,983 - 40,053,594 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prdm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478016,204,838 - 16,227,390 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478016,205,056 - 16,227,382 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prdm1
118 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:344
Count of miRNA genes:200
Interacting mature miRNAs:256
Transcripts:ENSRNOT00000048270
Prediction methods:Miranda, 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
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat

Markers in Region
RH128684  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr82049,542,571 - 49,542,778 (+)Marker Load Pipeline
mRatBN7.22047,959,964 - 47,960,172 (+)MAPPERmRatBN7.2
Rnor_6.02049,465,028 - 49,465,235NCBIRnor6.0
Rnor_5.02051,096,723 - 51,096,930UniSTSRnor5.0
RGSC_v3.42048,438,331 - 48,438,538UniSTSRGSC3.4
Celera2052,047,605 - 52,047,812UniSTS
RH 3.4 Map20497.91UniSTS
Cytogenetic Map20q13UniSTS
BI295453  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr82049,544,082 - 49,544,299 (+)Marker Load Pipeline
mRatBN7.22047,961,475 - 47,961,693 (+)MAPPERmRatBN7.2
Rnor_6.02049,466,539 - 49,466,756NCBIRnor6.0
Rnor_5.02051,098,234 - 51,098,451UniSTSRnor5.0
RGSC_v3.42048,439,842 - 48,440,059UniSTSRGSC3.4
Celera2052,046,084 - 52,046,301UniSTS
RH 3.4 Map20497.91UniSTS
Cytogenetic Map20q13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 112 91 90 59 25 59 6 218 97 92 45 59 31

Sequence


Ensembl Acc Id: ENSRNOT00000048270   ⟹   ENSRNOP00000040939
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2047,959,858 - 47,981,488 (-)Ensembl
Rnor_6.0 Ensembl2049,464,919 - 49,486,550 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000075979
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2049,474,316 - 49,556,518 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076541   ⟹   ENSRNOP00000068267
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2047,959,858 - 47,981,288 (-)Ensembl
Rnor_6.0 Ensembl2049,464,919 - 49,486,552 (-)Ensembl
RefSeq Acc Id: NM_001107639   ⟹   NP_001101109
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82049,542,465 - 49,564,088 (-)NCBI
mRatBN7.22047,959,858 - 47,981,488 (-)NCBI
Rnor_6.02049,464,921 - 49,486,545 (-)NCBI
Rnor_5.02051,096,616 - 51,118,240 (-)NCBI
RGSC_v3.42048,438,224 - 48,459,848 (-)RGD
Celera2052,026,331 - 52,047,919 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098772   ⟹   XP_038954700
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82049,542,465 - 49,555,245 (-)NCBI
mRatBN7.22047,959,858 - 47,972,648 (-)NCBI
RefSeq Acc Id: XM_063279179   ⟹   XP_063135249
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82049,542,465 - 49,563,888 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001101109 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954700 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135249 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99677 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000040939
  ENSRNOP00000040939.3
  ENSRNOP00000068267
  ENSRNOP00000068267.1
RefSeq Acc Id: NP_001101109   ⟸   NM_001107639
- UniProtKB: D4A1S2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000040939   ⟸   ENSRNOT00000048270
Ensembl Acc Id: ENSRNOP00000068267   ⟸   ENSRNOT00000076541
RefSeq Acc Id: XP_038954700   ⟸   XM_039098772
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135249   ⟸   XM_063279179
- Peptide Label: isoform X2
- UniProtKB: A0A096MJU6 (UniProtKB/TrEMBL),   A6K6V8 (UniProtKB/TrEMBL)
Protein Domains
C2H2-type   SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MJU6-F1-model_v2 AlphaFold A0A096MJU6 1-857 view protein structure

Transcriptome

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

Promoters
RGD ID:13701682
Promoter ID:EPDNEW_R12206
Type:single initiation site
Name:Prdm1_2
Description:PR/SET domain 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12207  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02049,486,394 - 49,486,454EPDNEW
RGD ID:13701683
Promoter ID:EPDNEW_R12207
Type:multiple initiation site
Name:Prdm1_1
Description:PR/SET domain 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12206  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02049,486,548 - 49,486,608EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311765 AgrOrtholog
BioCyc Gene G2FUF-3292 BioCyc
Ensembl Genes ENSRNOG00000000323 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048270 ENTREZGENE
  ENSRNOT00000048270.6 UniProtKB/TrEMBL
  ENSRNOT00000076541 ENTREZGENE
  ENSRNOT00000076541.2 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro PRDM1 UniProtKB/TrEMBL
  PRDM1_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
KEGG Report rno:309871 UniProtKB/TrEMBL
NCBI Gene 309871 ENTREZGENE
PANTHER PR DOMAIN ZINC FINGER PROTEIN UniProtKB/TrEMBL
  PR DOMAIN ZINC FINGER PROTEIN 1 UniProtKB/TrEMBL
Pfam PRDM2_PR UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
PhenoGen Prdm1 PhenoGen
PIRSF PRDM1 UniProtKB/TrEMBL
PROSITE SET UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000323 RatGTEx
SMART SET UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
  SSF82199 UniProtKB/TrEMBL
UniProt A0A096MJU6 ENTREZGENE, UniProtKB/TrEMBL
  A6K6V8 ENTREZGENE, UniProtKB/TrEMBL
  D4A1S2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Prdm1  PR/SET domain 1  Prdm1  PR domain 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Prdm1  PR domain 1  Prdm1  PR domain containing 1, with ZNF domain  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Prdm1  PR domain containing 1, with ZNF domain   Prdm1_predicted  PR domain containing 1, with ZNF domain (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Prdm1_predicted  PR domain containing 1, with ZNF domain (predicted)      Symbol and Name status set to approved 70820 APPROVED