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Q60636

- PRDM1_MOUSE

UniProt

Q60636 - PRDM1_MOUSE

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Protein

PR domain zinc finger protein 1

Gene
Prdm1, Blimp1
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri606 – 62823C2H2-type 1Add
BLAST
Zinc fingeri634 – 65623C2H2-type 2Add
BLAST
Zinc fingeri662 – 68423C2H2-type 3Add
BLAST
Zinc fingeri690 – 71223C2H2-type 4Add
BLAST

GO - Molecular functioni

  1. histone deacetylase binding Source: MGI
  2. metal ion binding Source: UniProtKB-KW
  3. methyltransferase activity Source: UniProtKB-KW
  4. protein binding Source: IntAct
  5. sequence-specific DNA binding Source: MGI

GO - Biological processi

  1. cell fate commitment Source: MGI
  2. embryonic placenta development Source: MGI
  3. eye photoreceptor cell development Source: MGI
  4. germ cell development Source: MGI
  5. intestinal epithelial cell development Source: MGI
  6. in utero embryonic development Source: MGI
  7. maternal placenta development Source: MGI
  8. negative regulation of B cell proliferation Source: MGI
  9. negative regulation of gene expression Source: MGI
  10. negative regulation of lipopolysaccharide-mediated signaling pathway Source: MGI
  11. negative regulation of transcription from RNA polymerase II promoter Source: MGI
  12. positive regulation of B cell differentiation Source: MGI
  13. positive regulation of gene expression Source: MGI
  14. post-embryonic development Source: MGI
  15. transcription, DNA-templated Source: UniProtKB-KW
  16. trophoblast giant cell differentiation Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Methyltransferase, Repressor, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, S-adenosyl-L-methionine, Zinc

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:Prdm1
Synonyms:Blimp1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 10

Organism-specific databases

MGIiMGI:99655. Prdm1.

Subcellular locationi

Nucleus. Cytoplasm By similarity 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: MGI
  2. nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Early embryonic lethality. Compound heterozygotes display germ cell defects and a rudimentary or missing fifth digit of the forelimb.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 856856PR domain zinc finger protein 1PRO_0000047758Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki847 – 847Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1) By similarity

Post-translational modificationi

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

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiQ60636.
PRIDEiQ60636.

PTM databases

PhosphoSiteiQ60636.

Expressioni

Tissue specificityi

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.3 Publications

Inductioni

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

Gene expression databases

BgeeiQ60636.
CleanExiMM_PRDM1.
GenevestigatoriQ60636.

Interactioni

Subunit structurei

Interacts with PRMT5.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
SUMO1P631653EBI-7000804,EBI-80140From a different organism.

Protein-protein interaction databases

BioGridi198355. 1 interaction.
IntActiQ60636. 1 interaction.
STRINGi10090.ENSMUSP00000101129.

Structurei

3D structure databases

ProteinModelPortaliQ60636.
SMRiQ60636. Positions 75-289, 556-768.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini115 – 233119SETAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni558 – 60548Interaction with PIAS1 By similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi351 – 39444Glu/Pro/Ser/Thr-richAdd
BLAST

Sequence similaritiesi

Contains 1 SET domain.

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri606 – 62823C2H2-type 1Add
BLAST
Zinc fingeri634 – 65623C2H2-type 2Add
BLAST
Zinc fingeri662 – 68423C2H2-type 3Add
BLAST
Zinc fingeri690 – 71223C2H2-type 4Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5048.
GeneTreeiENSGT00740000115517.
HOGENOMiHOG000059670.
HOVERGENiHBG053670.
InParanoidiQ3UET9.
OMAiTGYKTLP.
OrthoDBiEOG7060Q3.
PhylomeDBiQ60636.
TreeFamiTF316545.

Family and domain databases

Gene3Di3.30.160.60. 5 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR016608. Znf_PRDM1.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
PIRSFiPIRSF013212. PRDM1. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 5 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative promoter usage and alternative splicing. Align

Isoform 1 (identifier: Q60636-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MREAYLRCWI FSWKNVWVRP CQRLHFKTVL LQGSLLYTAL DSYSTVQAAP    50
KSSSGSVKFQ GLAETGIMKM DMEDADMTLW TEAEFEEKCT YIVNDHPWDS 100
GADGGTSVQA EASLPRNLLF KYAANNSKEV IGVVSKEYIP KGTRFGPLIG 150
EVYTNDTVPK NANRKYFWRI YSREEFHHFI DGFNEEKSNW MRYVNPAHSA 200
REQNLAACQN GMNIYFYTIK PIPANQELLV WYCRDFAERL HYPYPGELTV 250
INLTQTESNP KQYSSEKNEL YPKSVPKREY SVKEILKLDS NPSKRKDIYR 300
SNISPFTLEK DMDGFRKNGS PDMPFYPRVV YPIRAPLPED FLKASLAYGM 350
ERPTYITHSP LPSSTTPSPP ASSSPEQSLK SSSPHSSPGN TVSPLAPGLP 400
EHRDSYSYLN VSYGSEGLGS YPGYAPAPHL PPAFIPSYNA HYPKFLLPPY 450
GISSNGLSTM NNINGINNFS LFPRLYPVYS NLLSGSSLPH PMLNPASLPS 500
SLPTDGARRL LPPEHPKEVL IPAPHSAFSL TGAAASMKDE SSPPSGSPTA 550
GTAATSEHVV QPKATSSVMA APSTDGAMNL IKNKRNMTGY KTLPYPLKKQ 600
NGKIKYECNV CAKTFGQLSN LKVHLRVHSG ERPFKCQTCN KGFTQLAHLQ 650
KHYLVHTGEK PHECQVCHKR FSSTSNLKTH LRLHSGEKPY QCKVCPAKFT 700
QFVHLKLHKR LHTRERPHKC AQCHKSYIHL CSLKVHLKGN CPAGPAAGLP 750
LEDLTRINEE IERFDISDNA DRLEDMEDSV DVTSMVEKEI LAVVRKEKEE 800
TSLKVSLQRN MGNGLLSSGC SLYESSDLSL MKLPHSNPLP LVPVKVKQET 850
VEPMDP 856

Note: Produced by alternative splicing.

Length:856
Mass (Da):95,836
Last modified:November 1, 1996 - v1
Checksum:iB9AC6FC2E29ECF4A
GO
Isoform 2 (identifier: Q60636-2) [UniParc]FASTAAdd to Basket

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.

Show »
Length:823
Mass (Da):91,729
Checksum:i8B5904D42DDB2193
GO
Isoform 3 (identifier: Q60636-3) [UniParc]FASTAAdd to Basket

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.

Show »
Length:789
Mass (Da):88,228
Checksum:iD9C1AAA129A608C4
GO
Isoform 4 (identifier: Q60636-4) [UniParc]FASTAAdd to Basket

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.

Show »
Length:838
Mass (Da):93,302
Checksum:iEF258AECEFFB6B1A
GO
Isoform 5 (identifier: Q60636-5) [UniParc]FASTAAdd to Basket

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.

Show »
Length:813
Mass (Da):90,830
Checksum:iDDC40E049A8BE135
GO

Sequence cautioni

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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 6767Missing in isoform 3. VSP_041570Add
BLAST
Alternative sequencei1 – 4747MREAY…YSTVQ → MLDLLLEKRVGTTL in isoform 2. VSP_039189Add
BLAST
Alternative sequencei1 – 4747MREAY…YSTVQ → MTPGVPGHRTQQRPQHISAL SDKAKDCSK in isoform 4. VSP_041571Add
BLAST
Alternative sequencei624 – 66643Missing in isoform 5. VSP_041572Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti155 – 1551N → K in AAI29802. 1 Publication
Sequence conflicti205 – 2051L → M in AK077622. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U08185 mRNA. Translation: AAA19252.1.
AF305539
, 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.
CCDSiCCDS23825.2. [Q60636-2]
PIRiA53503.
RefSeqiNP_031574.2. NM_007548.3. [Q60636-2]
XP_006512565.1. XM_006512502.1. [Q60636-4]
XP_006512566.1. XM_006512503.1. [Q60636-3]
XP_006512568.1. XM_006512505.1. [Q60636-1]
UniGeneiMm.4800.

Genome annotation databases

EnsembliENSMUST00000039174; ENSMUSP00000039248; ENSMUSG00000038151. [Q60636-1]
ENSMUST00000105490; ENSMUSP00000101129; ENSMUSG00000038151. [Q60636-2]
GeneIDi12142.
KEGGimmu:12142.
UCSCiuc007ezu.2. mouse. [Q60636-1]
uc007ezv.2. mouse. [Q60636-2]

Keywords - Coding sequence diversityi

Alternative promoter usage, Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U08185 mRNA. Translation: AAA19252.1 .
AF305539
, 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.
CCDSi CCDS23825.2. [Q60636-2 ]
PIRi A53503.
RefSeqi NP_031574.2. NM_007548.3. [Q60636-2 ]
XP_006512565.1. XM_006512502.1. [Q60636-4 ]
XP_006512566.1. XM_006512503.1. [Q60636-3 ]
XP_006512568.1. XM_006512505.1. [Q60636-1 ]
UniGenei Mm.4800.

3D structure databases

ProteinModelPortali Q60636.
SMRi Q60636. Positions 75-289, 556-768.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 198355. 1 interaction.
IntActi Q60636. 1 interaction.
STRINGi 10090.ENSMUSP00000101129.

PTM databases

PhosphoSitei Q60636.

Proteomic databases

PaxDbi Q60636.
PRIDEi Q60636.

Protocols and materials databases

DNASUi 12142.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000039174 ; ENSMUSP00000039248 ; ENSMUSG00000038151 . [Q60636-1 ]
ENSMUST00000105490 ; ENSMUSP00000101129 ; ENSMUSG00000038151 . [Q60636-2 ]
GeneIDi 12142.
KEGGi mmu:12142.
UCSCi uc007ezu.2. mouse. [Q60636-1 ]
uc007ezv.2. mouse. [Q60636-2 ]

Organism-specific databases

CTDi 639.
MGIi MGI:99655. Prdm1.

Phylogenomic databases

eggNOGi COG5048.
GeneTreei ENSGT00740000115517.
HOGENOMi HOG000059670.
HOVERGENi HBG053670.
InParanoidi Q3UET9.
OMAi TGYKTLP.
OrthoDBi EOG7060Q3.
PhylomeDBi Q60636.
TreeFami TF316545.

Miscellaneous databases

NextBioi 280465.
PROi Q60636.
SOURCEi Search...

Gene expression databases

Bgeei Q60636.
CleanExi MM_PRDM1.
Genevestigatori Q60636.

Family and domain databases

Gene3Di 3.30.160.60. 5 hits.
InterProi IPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR016608. Znf_PRDM1.
[Graphical view ]
Pfami PF00856. SET. 1 hit.
[Graphical view ]
PIRSFi PIRSF013212. PRDM1. 1 hit.
SMARTi SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 5 hits.
[Graphical view ]
PROSITEi PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiPRDM1_MOUSE
AccessioniPrimary (citable) accession number: Q60636
Secondary accession number(s): A2VDE8, Q3UET9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: November 1, 1996
Last modified: September 3, 2014
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi