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Q60636 (PRDM1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 121. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
PR domain zinc finger protein 1

EC=2.1.1.-
Alternative name(s):
B lymphocyte-induced maturation protein 1
Short name=Blimp-1
Beta-interferon gene positive regulatory domain I-binding factor
PR domain-containing protein 1
Gene names
Name:Prdm1
Synonyms:Blimp1
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length856 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Transcriptional repressor that binds specifically to the PRDI element in the promoter of the beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells.

Subunit structure

Interacts with PRMT5. Ref.5

Subcellular location

Nucleus. Cytoplasm By similarity Ref.1.

Tissue specificity

Isoform 1 is detected in bone marrow, spleen and lymph node but not in brain, heart, kidney, liver, ovary or muscle. Weak expression detected in the lung. Isoform 3 is detected only in yolk sac. Isoform 4 is detected in embryo, yolk sac, placenta, splenocytes, and activated T-cells. Ref.1 Ref.2 Ref.6

Induction

By lymphokines, specifically IL-2 AND IL-5. Up-regulated during dendritic cell maturation.

Post-translational modification

Sumoylation at Lys-847 by PIAS1 augments transcriptional repressor activity, and is critical for plasma cell differentiation By similarity.

Disruption phenotype

Early embryonic lethality. Compound heterozygotes display germ cell defects and a rudimentary or missing fifth digit of the forelimb. Ref.6

Sequence similarities

Belongs to the class V-like SAM-binding methyltransferase superfamily.

Contains 4 C2H2-type zinc fingers.

Contains 1 SET domain.

Sequence caution

The sequence AAI29802.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative promoter usage
Alternative splicing
   DomainRepeat
Zinc-finger
   LigandDNA-binding
Metal-binding
S-adenosyl-L-methionine
Zinc
   Molecular functionDevelopmental protein
Methyltransferase
Repressor
Transferase
   PTMIsopeptide bond
Ubl conjugation
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcell fate commitment

Inferred from mutant phenotype PubMed 15750184PubMed 15937476. Source: MGI

embryonic placenta development

Inferred from mutant phenotype PubMed 15750184. Source: MGI

eye photoreceptor cell development

Inferred from mutant phenotype PubMed 20463215. Source: MGI

germ cell development

Inferred from genetic interaction PubMed 19578360. Source: MGI

in utero embryonic development

Inferred from mutant phenotype PubMed 15750184. Source: MGI

maternal placenta development

Inferred from mutant phenotype PubMed 15750184. Source: MGI

multicellular organismal development

Inferred from electronic annotation. Source: UniProtKB-KW

negative regulation of B cell proliferation

Inferred from direct assay PubMed 18845144. Source: MGI

negative regulation of lipopolysaccharide-mediated signaling pathway

Inferred from direct assay PubMed 18845144. Source: MGI

negative regulation of transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 18845144PubMed 20463215. Source: MGI

positive regulation of B cell differentiation

Inferred from direct assay PubMed 18845144. Source: MGI

positive regulation of gene expression

Inferred from direct assay PubMed 18622394. Source: MGI

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

trophoblast giant cell differentiation

Inferred from mutant phenotype PubMed 22987638. Source: MGI

   Cellular_componentcytoplasm

Inferred from direct assay PubMed 18845144. Source: MGI

nucleus

Inferred from direct assay PubMed 18845144. Source: MGI

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

histone deacetylase binding

Inferred from direct assay PubMed 18845144. Source: MGI

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

methyltransferase activity

Inferred from electronic annotation. Source: UniProtKB-KW

sequence-specific DNA binding

Inferred from direct assay PubMed 18845144. Source: MGI

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

SUMO1P631653EBI-7000804,EBI-80140From a different organism.

Alternative products

This entry describes 5 isoforms produced by alternative promoter usage and alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q60636-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Note: Produced by alternative splicing.
Isoform 2 (identifier: Q60636-2)

Also known as: 1A;

The sequence of this isoform differs from the canonical sequence as follows:
     1-47: MREAYLRCWIFSWKNVWVRPCQRLHFKTVLLQGSLLYTALDSYSTVQ → MLDLLLEKRVGTTL
Note: Produced by alternative splicing of isoform 1.
Isoform 3 (identifier: Q60636-3)

Also known as: 1B;

The sequence of this isoform differs from the canonical sequence as follows:
     1-67: Missing.
Note: Produced by alternative promoter usage of isoform 2.
Isoform 4 (identifier: Q60636-4)

Also known as: 1C;

The sequence of this isoform differs from the canonical sequence as follows:
     1-47: MREAYLRCWI...TALDSYSTVQ → MTPGVPGHRTQQRPQHISALSDKAKDCSK
Note: Produced by alternative promoter usage of isoform 2.
Isoform 5 (identifier: Q60636-5)

Also known as: delta exon 7;

The sequence of this isoform differs from the canonical sequence as follows:
     624-666: Missing.
Note: Produced by alternative splicing of isoform 1. Does not bind DNA.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 856856PR domain zinc finger protein 1
PRO_0000047758

Regions

Domain115 – 233119SET
Zinc finger606 – 62823C2H2-type 1
Zinc finger634 – 65623C2H2-type 2
Zinc finger662 – 68423C2H2-type 3
Zinc finger690 – 71223C2H2-type 4
Region558 – 60548Interaction with PIAS1 By similarity
Compositional bias351 – 39444Glu/Pro/Ser/Thr-rich

Amino acid modifications

Cross-link847Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1) By similarity

Natural variations

Alternative sequence1 – 6767Missing in isoform 3.
VSP_041570
Alternative sequence1 – 4747MREAY…YSTVQ → MLDLLLEKRVGTTL in isoform 2.
VSP_039189
Alternative sequence1 – 4747MREAY…YSTVQ → MTPGVPGHRTQQRPQHISAL SDKAKDCSK in isoform 4.
VSP_041571
Alternative sequence624 – 66643Missing in isoform 5.
VSP_041572

Experimental info

Sequence conflict1551N → K in AAI29802. Ref.4
Sequence conflict2051L → M in AK077622. Ref.3

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: B9AC6FC2E29ECF4A

FASTA85695,836
        10         20         30         40         50         60 
MREAYLRCWI FSWKNVWVRP CQRLHFKTVL LQGSLLYTAL DSYSTVQAAP KSSSGSVKFQ 

        70         80         90        100        110        120 
GLAETGIMKM DMEDADMTLW TEAEFEEKCT YIVNDHPWDS GADGGTSVQA EASLPRNLLF 

       130        140        150        160        170        180 
KYAANNSKEV IGVVSKEYIP KGTRFGPLIG EVYTNDTVPK NANRKYFWRI YSREEFHHFI 

       190        200        210        220        230        240 
DGFNEEKSNW MRYVNPAHSA REQNLAACQN GMNIYFYTIK PIPANQELLV WYCRDFAERL 

       250        260        270        280        290        300 
HYPYPGELTV INLTQTESNP KQYSSEKNEL YPKSVPKREY SVKEILKLDS NPSKRKDIYR 

       310        320        330        340        350        360 
SNISPFTLEK DMDGFRKNGS PDMPFYPRVV YPIRAPLPED FLKASLAYGM ERPTYITHSP 

       370        380        390        400        410        420 
LPSSTTPSPP ASSSPEQSLK SSSPHSSPGN TVSPLAPGLP EHRDSYSYLN VSYGSEGLGS 

       430        440        450        460        470        480 
YPGYAPAPHL PPAFIPSYNA HYPKFLLPPY GISSNGLSTM NNINGINNFS LFPRLYPVYS 

       490        500        510        520        530        540 
NLLSGSSLPH PMLNPASLPS SLPTDGARRL LPPEHPKEVL IPAPHSAFSL TGAAASMKDE 

       550        560        570        580        590        600 
SSPPSGSPTA GTAATSEHVV QPKATSSVMA APSTDGAMNL IKNKRNMTGY KTLPYPLKKQ 

       610        620        630        640        650        660 
NGKIKYECNV CAKTFGQLSN LKVHLRVHSG ERPFKCQTCN KGFTQLAHLQ KHYLVHTGEK 

       670        680        690        700        710        720 
PHECQVCHKR FSSTSNLKTH LRLHSGEKPY QCKVCPAKFT QFVHLKLHKR LHTRERPHKC 

       730        740        750        760        770        780 
AQCHKSYIHL CSLKVHLKGN CPAGPAAGLP LEDLTRINEE IERFDISDNA DRLEDMEDSV 

       790        800        810        820        830        840 
DVTSMVEKEI LAVVRKEKEE TSLKVSLQRN MGNGLLSSGC SLYESSDLSL MKLPHSNPLP 

       850 
LVPVKVKQET VEPMDP 

« Hide

Isoform 2 (1A) [UniParc].

Checksum: 8B5904D42DDB2193
Show »

FASTA82391,729
Isoform 3 (1B) [UniParc].

Checksum: D9C1AAA129A608C4
Show »

FASTA78988,228
Isoform 4 (1C) [UniParc].

Checksum: EF258AECEFFB6B1A
Show »

FASTA83893,302
Isoform 5 (delta exon 7) [UniParc].

Checksum: DDC40E049A8BE135
Show »

FASTA81390,830

References

« Hide 'large scale' references
[1]"Blimp-1, a novel zinc finger-containing protein that can drive the maturation of B lymphocytes into immunoglobulin-secreting cells."
Turner C.A., Mack D.H., Davis M.M.
Cell 77:297-306(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
Strain: BALB/c.
Tissue: B-cell.
[2]"Characterization of the B lymphocyte-induced maturation protein-1 (Blimp-1) gene, mRNA isoforms and basal promoter."
Tunyaplin C., Shapiro M.A., Calame K.L.
Nucleic Acids Res. 28:4846-4855(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING (ISOFORMS 1 AND 5), TISSUE SPECIFICITY.
Strain: 129.
[3]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [MRNA] OF 1-253 (ISOFORM 3).
Strain: C57BL/6J.
Tissue: Embryo and Retina.
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
[5]"Blimp1 associates with Prmt5 and directs histone arginine methylation in mouse germ cells."
Ancelin K., Lange U.C., Hajkova P., Schneider R., Bannister A.J., Kouzarides T., Surani M.A.
Nat. Cell Biol. 8:623-630(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH PRMT5.
[6]"Blimp-1/Prdm1 alternative promoter usage during mouse development and plasma cell differentiation."
Morgan M.A., Magnusdottir E., Kuo T.C., Tunyaplin C., Harper J., Arnold S.J., Calame K., Robertson E.J., Bikoff E.K.
Mol. Cell. Biol. 29:5813-5827(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ALTERNATIVE PROMOTER USAGE (ISOFORMS 3 AND 4), ALTERNATIVE SPLICING (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
Tissue: Embryo, Placenta and Yolk sac.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U08185 mRNA. Translation: AAA19252.1.
AF305539 expand/collapse EMBL AC list , AF305534, AF305535, AF305536, AF305537, AF305538 Genomic DNA. Translation: AAG42212.1.
AK077622 mRNA. No translation available.
AK149344 mRNA. Translation: BAE28822.1.
BC129801 mRNA. Translation: AAI29802.1. Different initiation.
PIRA53503.
RefSeqNP_031574.2. NM_007548.3.
XP_006512565.1. XM_006512502.1.
XP_006512566.1. XM_006512503.1.
XP_006512568.1. XM_006512505.1.
UniGeneMm.4800.

3D structure databases

ProteinModelPortalQ60636.
SMRQ60636. Positions 75-289, 556-770.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid198355. 1 interaction.
IntActQ60636. 1 interaction.
STRING10090.ENSMUSP00000101129.

PTM databases

PhosphoSiteQ60636.

Proteomic databases

PaxDbQ60636.
PRIDEQ60636.

Protocols and materials databases

DNASU12142.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000039174; ENSMUSP00000039248; ENSMUSG00000038151. [Q60636-1]
ENSMUST00000105490; ENSMUSP00000101129; ENSMUSG00000038151. [Q60636-2]
GeneID12142.
KEGGmmu:12142.
UCSCuc007ezu.2. mouse. [Q60636-1]
uc007ezv.2. mouse. [Q60636-2]

Organism-specific databases

CTD639.
MGIMGI:99655. Prdm1.

Phylogenomic databases

eggNOGCOG5048.
GeneTreeENSGT00740000115517.
HOGENOMHOG000059670.
HOVERGENHBG053670.
InParanoidQ3UET9.
OMATGYKTLP.
OrthoDBEOG7060Q3.
PhylomeDBQ60636.
TreeFamTF316545.

Gene expression databases

BgeeQ60636.
CleanExMM_PRDM1.
GenevestigatorQ60636.

Family and domain databases

Gene3D3.30.160.60. 5 hits.
InterProIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR016608. Znf_PRDM1.
[Graphical view]
PfamPF00856. SET. 1 hit.
[Graphical view]
PIRSFPIRSF013212. PRDM1. 1 hit.
SMARTSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]
ProtoNetSearch...

Other

NextBio280465.
PROQ60636.
SOURCESearch...

Entry information

Entry namePRDM1_MOUSE
AccessionPrimary (citable) accession number: Q60636
Secondary accession number(s): A2VDE8, Q3UET9
Entry history
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: November 1, 1996
Last modified: April 16, 2014
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot