PRDM1 (PR/SET domain 1) - Rat Genome Database
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Gene: PRDM1 (PR/SET domain 1) Homo sapiens
Analyze
Symbol: PRDM1
Name: PR/SET domain 1
RGD ID: 1323391
HGNC Page HGNC
Description: Exhibits DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Localizes to cytoplasm and nucleus.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: B-lymphocyte-induced maturation protein 1; beta-interferon gene positive regulatory domain I-binding factor; beta-interferon gene positive-regulatory domain I binding factor; BLIMP-1; BLIMP1; MGC118922; MGC118923; MGC118924; MGC118925; positive regulatory domain I-binding factor 1; PR domain 1; PR domain containing 1, with ZNF domain; PR domain zinc finger protein 1; PR domain-containing protein 1; PR-domain zinc finger protein 1; PRDI-BF1; PRDI-binding factor 1; PRDI-binding factor-1
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6105,993,463 - 106,109,939 (+)EnsemblGRCh38hg38GRCh38
GRCh386106,046,729 - 106,109,938 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376106,534,195 - 106,557,814 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366106,640,888 - 106,664,506 (+)NCBINCBI36hg18NCBI36
Build 346106,653,507 - 106,664,502NCBI
Celera6107,155,767 - 107,179,390 (+)NCBI
Cytogenetic Map6q21NCBI
HuRef6103,981,166 - 104,004,788 (+)NCBIHuRef
CHM1_16106,796,630 - 106,820,250 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,4-phenylenediamine  (EXP)
1-chloro-2,4-dinitrobenzene  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-dichloroaniline  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxynon-2-enal  (EXP)
5-aza-2'-deoxycytidine  (EXP)
7,12-dimethyltetraphene  (EXP)
acetamide  (ISO)
acrylamide  (ISO)
adefovir pivoxil  (EXP)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP)
alpha-naphthoflavone  (EXP)
arsane  (EXP)
arsenic atom  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (EXP)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (ISO)
bisphenol F  (ISO)
buta-1,3-diene  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroacetaldehyde  (EXP)
choline  (ISO)
cidofovir anhydrous  (EXP)
cisplatin  (EXP)
clodronic acid  (EXP)
crocidolite asbestos  (EXP)
dioxygen  (EXP,ISO)
disodium selenite  (EXP)
diuron  (EXP)
dorsomorphin  (EXP)
endosulfan  (ISO)
folic acid  (ISO)
formaldehyde  (EXP)
hydroquinone  (EXP)
hydroxychloroquine  (EXP)
ibrutinib  (EXP)
ifosfamide  (EXP)
indinavir  (ISO)
L-methionine  (ISO)
lamivudine  (ISO)
lipopolysaccharide  (ISO)
mercury dibromide  (EXP)
metformin  (EXP)
methamphetamine  (ISO)
methotrexate  (EXP)
methylisothiazolinone  (EXP)
methylmercury chloride  (EXP,ISO)
nickel atom  (EXP)
nickel sulfate  (EXP)
p-chloromercuribenzoic acid  (EXP)
paclitaxel  (EXP)
panobinostat  (EXP)
PD 0325901  (EXP)
phenylmercury acetate  (EXP)
phosgene  (ISO)
potassium chromate  (EXP)
saquinavir  (ISO)
SB 431542  (EXP)
serpentine asbestos  (EXP)
silicon dioxide  (EXP)
sodium arsenate  (EXP)
sodium arsenite  (EXP)
succimer  (EXP)
sulfasalazine  (EXP)
sulforaphane  (EXP,ISO)
titanium dioxide  (ISO)
trichostatin A  (EXP)
troglitazone  (EXP)
valproic acid  (EXP)
vanadyl sulfate  (EXP)
zidovudine  (ISO)
zoledronic acid  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,IDA,IEA)
nucleoplasm  (TAS)
nucleus  (IBA,IDA,IEA)

References

Additional References at PubMed
PMID:1851123   PMID:8033216   PMID:8168136   PMID:8921366   PMID:9887105   PMID:10713181   PMID:11067898   PMID:11342629   PMID:11877292   PMID:12150891   PMID:12165517   PMID:12453881  
PMID:12477932   PMID:12626569   PMID:14985713   PMID:16002735   PMID:16424392   PMID:16492805   PMID:16547239   PMID:16585013   PMID:16713569   PMID:16765445   PMID:16849320   PMID:17043021  
PMID:17213024   PMID:17264218   PMID:17379744   PMID:17682124   PMID:17877160   PMID:18071884   PMID:18089822   PMID:18192112   PMID:18235046   PMID:18256039   PMID:18354204   PMID:18370921  
PMID:18400362   PMID:18552212   PMID:18583325   PMID:18596541   PMID:18604866   PMID:18845144   PMID:18992153   PMID:19047678   PMID:19124609   PMID:19194464   PMID:19234190   PMID:19269192  
PMID:19274049   PMID:19322201   PMID:19433448   PMID:19460752   PMID:19530237   PMID:19563034   PMID:19717648   PMID:19735688   PMID:19760754   PMID:19788443   PMID:19828629   PMID:19828640  
PMID:19838193   PMID:19838195   PMID:19898481   PMID:19915048   PMID:20047096   PMID:20379614   PMID:20530581   PMID:20800019   PMID:20859709   PMID:20944005   PMID:20966935   PMID:21102463  
PMID:21103670   PMID:21216962   PMID:21411757   PMID:21421998   PMID:21622776   PMID:21690554   PMID:21722313   PMID:21722636   PMID:21785431   PMID:21873635   PMID:22020966   PMID:22040493  
PMID:22143801   PMID:22167754   PMID:22278826   PMID:22438909   PMID:22555612   PMID:22580854   PMID:22585398   PMID:22593617   PMID:22634616   PMID:22733990   PMID:22851713   PMID:22939624  
PMID:23028907   PMID:23129528   PMID:23273568   PMID:23348703   PMID:23624108   PMID:23648065   PMID:23911415   PMID:23977359   PMID:24004669   PMID:24009228   PMID:24306881   PMID:24438193  
PMID:24527393   PMID:24637363   PMID:24796719   PMID:24804861   PMID:24841128   PMID:25263394   PMID:25265234   PMID:25280345   PMID:25382611   PMID:25410866   PMID:25487076   PMID:25710909  
PMID:25713110   PMID:25826676   PMID:26054109   PMID:26146066   PMID:26206802   PMID:26212250   PMID:26221594   PMID:26310579   PMID:26431332   PMID:26475096   PMID:26530011   PMID:26823144  
PMID:26976045   PMID:27132888   PMID:27181361   PMID:27363279   PMID:27568520   PMID:27613090   PMID:27687004   PMID:27704586   PMID:27924626   PMID:28097234   PMID:28300844   PMID:28314753  
PMID:28378641   PMID:28442738   PMID:28468592   PMID:28473536   PMID:28494239   PMID:28514442   PMID:28629373   PMID:28790031   PMID:28842558   PMID:29416540   PMID:29507755   PMID:29713018  
PMID:29760071   PMID:30051906   PMID:30096391   PMID:30197274   PMID:30654767   PMID:30687317   PMID:30793688   PMID:31002364   PMID:31100710   PMID:31376415   PMID:31618572   PMID:31900314  
PMID:32417234   PMID:32533097   PMID:32562448   PMID:32798401   PMID:32985591  


Genomics

Comparative Map Data
PRDM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6105,993,463 - 106,109,939 (+)EnsemblGRCh38hg38GRCh38
GRCh386106,046,729 - 106,109,938 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376106,534,195 - 106,557,814 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366106,640,888 - 106,664,506 (+)NCBINCBI36hg18NCBI36
Build 346106,653,507 - 106,664,502NCBI
Celera6107,155,767 - 107,179,390 (+)NCBI
Cytogenetic Map6q21NCBI
HuRef6103,981,166 - 104,004,788 (+)NCBIHuRef
CHM1_16106,796,630 - 106,820,250 (+)NCBICHM1_1
Prdm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391044,313,170 - 44,404,548 (-)NCBIGRCm39mm39
GRCm381044,437,174 - 44,528,558 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1044,437,177 - 44,528,501 (-)EnsemblGRCm38mm10GRCm38
MGSCv371044,156,981 - 44,178,493 (-)NCBIGRCm37mm9NCBIm37
MGSCv361044,125,592 - 44,147,163 (-)NCBImm8
Celera1045,310,489 - 45,332,012 (-)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1023.24NCBI
Prdm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12048,469,384 - 48,488,777 (-)NCBI
Celera2052,026,331 - 52,047,919 (+)NCBICelera
Cytogenetic Map20q13NCBI
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
PanPan1.16107,773,229 - 107,796,815 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6107,773,229 - 107,796,815 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06103,899,410 - 103,923,389 (+)NCBIMhudiblu_PPA_v0panPan3
PRDM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1263,470,974 - 63,495,579 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11263,454,242 - 63,495,278 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Prdm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11367,695,436 - 67,719,487 (-)NCBI
ChlSab1.1 Ensembl1367,695,309 - 67,718,931 (-)Ensembl
Prdm1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478016,205,056 - 16,227,382 (-)NCBI

Position Markers
PRDM1_1073  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376106,556,088 - 106,556,956UniSTSGRCh37
Build 366106,662,781 - 106,663,649RGDNCBI36
Celera6107,177,663 - 107,178,532RGD
HuRef6104,003,060 - 104,003,929UniSTS
D6S1410  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376106,557,609 - 106,557,784UniSTSGRCh37
Build 366106,664,302 - 106,664,477RGDNCBI36
Celera6107,179,185 - 107,179,360RGD
Cytogenetic Map6q21UniSTS
HuRef6104,004,583 - 104,004,758UniSTS
GeneMap99-GB4 RH Map6458.29UniSTS
Whitehead-YAC Contig Map6 UniSTS
NCBI RH Map61406.9UniSTS
D6S1217E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh376106,556,705 - 106,556,793UniSTSGRCh37
Build 366106,663,398 - 106,663,486RGDNCBI36
Celera6107,178,281 - 107,178,369RGD
Cytogenetic Map6q21UniSTS
HuRef6104,003,678 - 104,003,766UniSTS
GeneMap99-GB4 RH Map6460.07UniSTS

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR30Ahsa-miR-30a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI23348703
MIRLET7Bhsa-let-7b-5pMirtarbaseexternal_infoImmunohistochemistry//Luciferase reporter assay//qFunctional MTI20651244
MIRLET7Bhsa-let-7b-5pOncomiRDBexternal_infoNANA20651244
MIR127hsa-miR-127-3pMirtarbaseexternal_infoqRT-PCR//Luciferase reporter assay//Western blotFunctional MTI19530237
MIR127hsa-miR-127-3pMirecordsexternal_info{changed}NA19530237
MIR127hsa-miR-127-3pOncomiRDBexternal_infoNANA19530237
MIR125B1hsa-miR-125b-5pMirtarbaseexternal_infoqRT-PCR//Luciferase reporter assayFunctional MTI20497960
MIRLET7F1hsa-let-7f-5pMirtarbaseexternal_infoImmunohistochemistry//Luciferase reporter assay//qFunctional MTI20651244
MIRLET7F2hsa-let-7f-5pMirtarbaseexternal_infoImmunohistochemistry//Luciferase reporter assay//qFunctional MTI20651244
MIRLET7A2hsa-let-7a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI18583325
MIRLET7A2hsa-let-7a-5pMirtarbaseexternal_infoImmunohistochemistry//Luciferase reporter assay//qFunctional MTI20651244
MIR125B2hsa-miR-125b-5pMirtarbaseexternal_infoqRT-PCR//Luciferase reporter assayFunctional MTI20497960
MIRLET7A1hsa-let-7a-5pMirtarbaseexternal_infoLuciferase reporter assayFunctional MTI18583325
MIRLET7A1hsa-let-7a-5pMirtarbaseexternal_infoImmunohistochemistry//Luciferase reporter assay//qFunctional MTI20651244

Predicted Target Of
Summary Value
Count of predictions:3014
Count of miRNA genes:1007
Interacting mature miRNAs:1199
Transcripts:ENST00000369089, ENST00000369091, ENST00000369096, ENST00000424894, ENST00000450060, ENST00000481163, ENST00000489365
Prediction methods:Microtar, 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 sensory system visual system adipose tissue appendage entire extraembryonic component
High
Medium 304 330 401 60 1112 11 871 10 35 71 273 864 52 173 464 1
Low 2079 2278 1196 476 796 367 2805 1427 3100 309 1140 675 119 1031 1722 1
Below cutoff 47 377 122 81 40 82 677 744 572 35 36 51 2 1 602 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_029115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_182907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006715550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011536062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011536063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011536064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017011187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF084199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK129768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK289556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK301341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL022067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL358952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL672292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL832963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY198414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY198415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC103832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC103833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC103834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC103835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF064715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF151143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000369089   ⟹   ENSP00000358085
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,098,940 - 106,109,939 (+)Ensembl
RefSeq Acc Id: ENST00000369091   ⟹   ENSP00000358087
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,086,320 - 106,107,508 (+)Ensembl
RefSeq Acc Id: ENST00000369096   ⟹   ENSP00000358092
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,086,336 - 106,109,938 (+)Ensembl
RefSeq Acc Id: ENST00000424894   ⟹   ENSP00000395566
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,087,580 - 106,095,620 (+)Ensembl
RefSeq Acc Id: ENST00000450060   ⟹   ENSP00000399772
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,098,606 - 106,105,038 (+)Ensembl
RefSeq Acc Id: ENST00000481163
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,098,925 - 106,099,709 (+)Ensembl
RefSeq Acc Id: ENST00000489365
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,088,354 - 106,096,167 (+)Ensembl
RefSeq Acc Id: ENST00000648754   ⟹   ENSP00000498029
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,087,587 - 106,108,282 (+)Ensembl
RefSeq Acc Id: ENST00000651185   ⟹   ENSP00000498716
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6106,048,534 - 106,109,939 (+)Ensembl
RefSeq Acc Id: ENST00000652320   ⟹   ENSP00000498580
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl6105,993,463 - 106,109,939 (+)Ensembl
RefSeq Acc Id: NM_001198   ⟹   NP_001189
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,086,336 - 106,109,938 (+)NCBI
GRCh376106,534,195 - 106,557,814 (+)NCBI
Build 366106,640,888 - 106,664,506 (+)NCBI Archive
HuRef6103,981,166 - 104,004,788 (+)ENTREZGENE
CHM1_16106,796,630 - 106,820,250 (+)NCBI
Sequence:
RefSeq Acc Id: NM_182907   ⟹   NP_878911
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,098,941 - 106,109,938 (+)NCBI
GRCh376106,534,195 - 106,557,814 (+)ENTREZGENE
Build 366106,653,508 - 106,664,506 (+)NCBI Archive
HuRef6103,981,166 - 104,004,788 (+)ENTREZGENE
CHM1_16106,809,171 - 106,820,250 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006715550   ⟹   XP_006715613
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,086,677 - 106,109,934 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011536062   ⟹   XP_011534364
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,086,680 - 106,109,934 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011536063   ⟹   XP_011534365
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,087,580 - 106,109,934 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011536064   ⟹   XP_011534366
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,096,415 - 106,109,934 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017011187   ⟹   XP_016866676
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,046,729 - 106,109,934 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001189   ⟸   NM_001198
- Peptide Label: isoform 1
- UniProtKB: O75626 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_878911   ⟸   NM_182907
- Peptide Label: isoform 2
- UniProtKB: O75626 (UniProtKB/Swiss-Prot),   B4DW27 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006715613   ⟸   XM_006715550
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_011534365   ⟸   XM_011536063
- Peptide Label: isoform X3
- UniProtKB: O75626 (UniProtKB/Swiss-Prot),   Q5T4E8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011534364   ⟸   XM_011536062
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_011534366   ⟸   XM_011536064
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_016866676   ⟸   XM_017011187
- Peptide Label: isoform X3
- UniProtKB: O75626 (UniProtKB/Swiss-Prot),   Q5T4E8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000498029   ⟸   ENST00000648754
RefSeq Acc Id: ENSP00000395566   ⟸   ENST00000424894
RefSeq Acc Id: ENSP00000399772   ⟸   ENST00000450060
RefSeq Acc Id: ENSP00000498716   ⟸   ENST00000651185
RefSeq Acc Id: ENSP00000498580   ⟸   ENST00000652320
RefSeq Acc Id: ENSP00000358092   ⟸   ENST00000369096
RefSeq Acc Id: ENSP00000358087   ⟸   ENST00000369091
RefSeq Acc Id: ENSP00000358085   ⟸   ENST00000369089
Protein Domains
C2H2-type   SET

Promoters
RGD ID:7208793
Promoter ID:EPDNEW_H10142
Type:initiation region
Name:PRDM1_4
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_H10141  EPDNEW_H10143  EPDNEW_H10144  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,046,663 - 106,046,723EPDNEW
RGD ID:7208795
Promoter ID:EPDNEW_H10143
Type:initiation region
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_H10141  EPDNEW_H10142  EPDNEW_H10144  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,086,336 - 106,086,396EPDNEW
RGD ID:7208799
Promoter ID:EPDNEW_H10144
Type:initiation region
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_H10141  EPDNEW_H10142  EPDNEW_H10143  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh386106,098,941 - 106,099,001EPDNEW
RGD ID:6803991
Promoter ID:HG_KWN:54489
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000369091,   NM_001198
Position:
Human AssemblyChrPosition (strand)Source
Build 366106,640,061 - 106,640,967 (+)MPROMDB
RGD ID:6804562
Promoter ID:HG_KWN:54490
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   HeLa_S3,   Lymphoblastoid
Transcripts:OTTHUMT00000327266,   OTTHUMT00000327267
Position:
Human AssemblyChrPosition (strand)Source
Build 366106,642,216 - 106,642,967 (+)MPROMDB
RGD ID:6804563
Promoter ID:HG_KWN:54491
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000041662,   OTTHUMT00000041663,   OTTHUMT00000327268
Position:
Human AssemblyChrPosition (strand)Source
Build 366106,652,316 - 106,653,557 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001198.3(PRDM1):c.2278C>T (p.Leu760=) single nucleotide variant Malignant melanoma [RCV000061289] Chr6:106107286 [GRCh38]
Chr6:106555161 [GRCh37]
Chr6:106661854 [NCBI36]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.220G>A (p.Gly74Ser) single nucleotide variant not specified [RCV000121863] Chr6:106088378 [GRCh38]
Chr6:106536253 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.502C>G (p.Pro168Ala) single nucleotide variant not specified [RCV000121864] Chr6:106099390 [GRCh38]
Chr6:106547265 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.609C>G (p.Asp203Glu) single nucleotide variant not specified [RCV000121865] Chr6:106099497 [GRCh38]
Chr6:106547372 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.448G>A (p.Gly150Ser) single nucleotide variant not specified [RCV000121866] Chr6:106099336 [GRCh38]
Chr6:106547211 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.811A>G (p.Ile271Val) single nucleotide variant not provided [RCV000917033]|not specified [RCV000121867] Chr6:106104971 [GRCh38]
Chr6:106552846 [GRCh37]
Chr6:6q21
benign|not provided
NM_001198.4(PRDM1):c.1147A>G (p.Thr383Ala) single nucleotide variant not specified [RCV000121868] Chr6:106105307 [GRCh38]
Chr6:106553182 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.1306A>G (p.Asn436Asp) single nucleotide variant not specified [RCV000121869] Chr6:106105466 [GRCh38]
Chr6:106553341 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.1100C>T (p.Ser367Phe) single nucleotide variant not specified [RCV000121870] Chr6:106105260 [GRCh38]
Chr6:106553135 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.1148C>T (p.Thr383Met) single nucleotide variant not specified [RCV000121871] Chr6:106105308 [GRCh38]
Chr6:106553183 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.1348C>T (p.Leu450Phe) single nucleotide variant not specified [RCV000121872] Chr6:106105508 [GRCh38]
Chr6:106553383 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.1400C>T (p.Pro467Leu) single nucleotide variant not specified [RCV000121873] Chr6:106105560 [GRCh38]
Chr6:106553435 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.857G>C (p.Arg286Pro) single nucleotide variant not provided [RCV000952532]|not specified [RCV000121874] Chr6:106105017 [GRCh38]
Chr6:106552892 [GRCh37]
Chr6:6q21
benign|not provided
NM_001198.4(PRDM1):c.1061G>A (p.Ser354Asn) single nucleotide variant not specified [RCV000121875] Chr6:106105221 [GRCh38]
Chr6:106553096 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.1222G>C (p.Ala408Pro) single nucleotide variant not specified [RCV000121876] Chr6:106105382 [GRCh38]
Chr6:106553257 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.1141T>C (p.Tyr381His) single nucleotide variant not specified [RCV000121877] Chr6:106105301 [GRCh38]
Chr6:106553176 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.2464C>A (p.Pro822Thr) single nucleotide variant not provided [RCV000889812]|not specified [RCV000121878] Chr6:106107472 [GRCh38]
Chr6:106555347 [GRCh37]
Chr6:6q21
likely benign|not provided
NM_001198.4(PRDM1):c.2233G>A (p.Val745Met) single nucleotide variant not specified [RCV000121879] Chr6:106107241 [GRCh38]
Chr6:106555116 [GRCh37]
Chr6:6q21
not provided
NM_001198.4(PRDM1):c.2312G>A (p.Gly771Asp) single nucleotide variant not specified [RCV000121880] Chr6:106107320 [GRCh38]
Chr6:106555195 [GRCh37]
Chr6:6q21
not provided
GRCh38/hg38 6q16.3-21(chr6:102356502-111049879)x1 copy number loss See cases [RCV000134806] Chr6:102356502..111049879 [GRCh38]
Chr6:102804377..111371082 [GRCh37]
Chr6:102911070..111477775 [NCBI36]
Chr6:6q16.3-21
pathogenic
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3 copy number gain See cases [RCV000139729] Chr6:74382807..142040500 [GRCh38]
Chr6:75092523..142361637 [GRCh37]
Chr6:75149243..142403330 [NCBI36]
Chr6:6q13-24.1
pathogenic
GRCh38/hg38 6q16.1-22.31(chr6:96609994-122161548)x1 copy number loss See cases [RCV000139465] Chr6:96609994..122161548 [GRCh38]
Chr6:97057870..122482694 [GRCh37]
Chr6:97164591..122524393 [NCBI36]
Chr6:6q16.1-22.31
pathogenic
GRCh38/hg38 6q16.3-21(chr6:103279465-113934239)x1 copy number loss See cases [RCV000142287] Chr6:103279465..113934239 [GRCh38]
Chr6:103727340..114255403 [GRCh37]
Chr6:103834033..114362096 [NCBI36]
Chr6:6q16.3-21
pathogenic
GRCh38/hg38 6q21(chr6:105922825-106683920)x3 copy number gain See cases [RCV000143107] Chr6:105922825..106683920 [GRCh38]
Chr6:106370700..107131795 [GRCh37]
Chr6:106477393..107238488 [NCBI36]
Chr6:6q21
uncertain significance
GRCh38/hg38 6q16.3-22.31(chr6:100054889-120488154)x1 copy number loss See cases [RCV000143227] Chr6:100054889..120488154 [GRCh38]
Chr6:100502765..120809300 [GRCh37]
Chr6:100609486..120850999 [NCBI36]
Chr6:6q16.3-22.31
pathogenic
GRCh38/hg38 6q21(chr6:105833853-106582592)x3 copy number gain See cases [RCV000143257] Chr6:105833853..106582592 [GRCh38]
Chr6:106281728..107030467 [GRCh37]
Chr6:106388421..107137160 [NCBI36]
Chr6:6q21
uncertain significance
GRCh37/hg19 6q21(chr6:106281728-107019722)x3 copy number gain See cases [RCV000240329] Chr6:106281728..107019722 [GRCh37]
Chr6:6q21
uncertain significance
GRCh37/hg19 6q21(chr6:105930050-107970442)x1 copy number loss See cases [RCV000446119] Chr6:105930050..107970442 [GRCh37]
Chr6:6q21
uncertain significance
GRCh37/hg19 6q14.3-22.31(chr6:85988428-120548687)x1 copy number loss See cases [RCV000445666] Chr6:85988428..120548687 [GRCh37]
Chr6:6q14.3-22.31
pathogenic
GRCh37/hg19 6q21(chr6:106394584-107635657)x1 copy number loss See cases [RCV000445829] Chr6:106394584..107635657 [GRCh37]
Chr6:6q21
uncertain significance
GRCh37/hg19 6q21(chr6:105550491-107378236)x1 copy number loss See cases [RCV000448307] Chr6:105550491..107378236 [GRCh37]
Chr6:6q21
uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6q16.1-21(chr6:97384446-110247755)x1 copy number loss See cases [RCV000510703] Chr6:97384446..110247755 [GRCh37]
Chr6:6q16.1-21
pathogenic
GRCh37/hg19 6q16.1-21(chr6:94202605-109878834)x1 copy number loss See cases [RCV000512470] Chr6:94202605..109878834 [GRCh37]
Chr6:6q16.1-21
pathogenic
GRCh37/hg19 6q16.1-22.1(chr6:95549951-116684929)x1 copy number loss not provided [RCV000682693] Chr6:95549951..116684929 [GRCh37]
Chr6:6q16.1-22.1
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27
pathogenic
NM_001198.4(PRDM1):c.387C>T (p.Asn129=) single nucleotide variant not provided [RCV000888723] Chr6:106095710 [GRCh38]
Chr6:106543585 [GRCh37]
Chr6:6q21
benign
NM_001198.4(PRDM1):c.281del (p.Asn94fs) deletion not specified [RCV000825441] Chr6:106088438 [GRCh38]
Chr6:106536313 [GRCh37]
Chr6:6q21
uncertain significance
NM_001198.4(PRDM1):c.1881A>G (p.Gly627=) single nucleotide variant not provided [RCV000925816] Chr6:106106478 [GRCh38]
Chr6:106554353 [GRCh37]
Chr6:6q21
likely benign
GRCh37/hg19 6q21(chr6:106427169-106641115)x3 copy number gain not provided [RCV001007554] Chr6:106427169..106641115 [GRCh37]
Chr6:6q21
uncertain significance
GRCh37/hg19 6q16.3-22.1(chr6:101296547-117004249)x3 copy number gain Microcephaly [RCV001251053] Chr6:101296547..117004249 [GRCh37]
Chr6:6q16.3-22.1
pathogenic
GRCh37/hg19 6q16.1-21(chr6:98949950-114533905)x1 copy number loss Deletion 6q16 q21 [RCV001263224] Chr6:98949950..114533905 [GRCh37]
Chr6:6q16.1-21
pathogenic
GRCh37/hg19 6q21(chr6:106330947-106730123)x3 copy number gain not provided [RCV001259395] Chr6:106330947..106730123 [GRCh37]
Chr6:6q21
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:9346 AgrOrtholog
COSMIC PRDM1 COSMIC
Ensembl Genes ENSG00000057657 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000358085 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000358087 UniProtKB/Swiss-Prot
  ENSP00000358092 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000395566 UniProtKB/TrEMBL
  ENSP00000399772 UniProtKB/TrEMBL
  ENSP00000498029 ENTREZGENE, UniProtKB/TrEMBL
  ENSP00000498580 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000498716 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000369089 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000369091 UniProtKB/Swiss-Prot
  ENST00000369096 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000424894 UniProtKB/TrEMBL
  ENST00000450060 UniProtKB/TrEMBL
  ENST00000648754 ENTREZGENE, UniProtKB/TrEMBL
  ENST00000651185 UniProtKB/Swiss-Prot
  ENST00000652320 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000057657 GTEx
HGNC ID HGNC:9346 ENTREZGENE
Human Proteome Map PRDM1 Human Proteome Map
InterPro PRDM1 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 hsa:639 UniProtKB/Swiss-Prot
NCBI Gene 639 ENTREZGENE
OMIM 603423 OMIM
Pfam SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA33707 PharmGKB
PIRSF PRDM1 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 SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Hs.436023 ENTREZGENE
UniProt A0A3B3IU23_HUMAN UniProtKB/TrEMBL
  A1YZ20_HUMAN UniProtKB/TrEMBL
  B2REA4_HUMAN UniProtKB/TrEMBL
  B2REA5_HUMAN UniProtKB/TrEMBL
  B4DW27 ENTREZGENE, UniProtKB/TrEMBL
  O75626 ENTREZGENE, UniProtKB/Swiss-Prot
  Q3SYG0_HUMAN UniProtKB/TrEMBL
  Q5T4E8 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary B2REA6 UniProtKB/Swiss-Prot
  E1P5E0 UniProtKB/Swiss-Prot
  Q86WM7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-26 PRDM1  PR/SET domain 1  PRDM1  PR domain 1  Symbol and/or name change 5135510 APPROVED
2016-02-02 PRDM1  PR domain 1  PRDM1  PR domain containing 1, with ZNF domain  Symbol and/or name change 5135510 APPROVED