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PHF2_MOUSE
ID   PHF2_MOUSE              Reviewed;        1096 AA.
AC   Q9WTU0; Q6A023; Q80WA8;
DT   15-AUG-2003, integrated into UniProtKB/Swiss-Prot.
DT   15-AUG-2003, sequence version 2.
DT   03-AUG-2022, entry version 145.
DE   RecName: Full=Lysine-specific demethylase PHF2;
DE            EC=1.14.11.- {ECO:0000250|UniProtKB:O75151};
DE   AltName: Full=GRC5;
DE   AltName: Full=PHD finger protein 2;
GN   Name=Phf2; Synonyms=Kiaa0662;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RX   PubMed=10051327; DOI=10.1007/s003359900989;
RA   Hasenpusch-Theil K., Chadwick B.P., Theil T., Heath S.K., Wilkinson D.G.,
RA   Frischauf A.M.;
RT   "PHF2, a novel PHD finger gene located on human chromosome 9q22.";
RL   Mamm. Genome 10:294-298(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C57BL/6J;
RX   PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA   Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA   Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA   Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA   Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA   Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA   Eichler E.E., Ponting C.P.;
RT   "Lineage-specific biology revealed by a finished genome assembly of the
RT   mouse.";
RL   PLoS Biol. 7:E1000112-E1000112(2009).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Limb;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 59-1096.
RX   PubMed=15368895; DOI=10.1093/dnares/11.3.205;
RA   Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S.,
RA   Saga Y., Seino S., Nishimura M., Kaisho T., Hoshino K., Kitamura H.,
RA   Nagase T., Ohara O., Koga H.;
RT   "Prediction of the coding sequences of mouse homologues of KIAA gene: IV.
RT   The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs
RT   identified by screening of terminal sequences of cDNA clones randomly
RT   sampled from size-fractionated libraries.";
RL   DNA Res. 11:205-218(2004).
RN   [5]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-474; SER-651; SER-677;
RP   TYR-724; SER-726; SER-729; SER-730; SER-734; SER-873; SER-876 AND SER-893,
RP   AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas,
RC   Spleen, and Testis;
RX   PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA   Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA   Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT   "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL   Cell 143:1174-1189(2010).
RN   [6]
RP   CATALYTIC ACTIVITY.
RX   PubMed=20129925; DOI=10.1074/jbc.c109.097667;
RA   Wen H., Li J., Song T., Lu M., Kan P.Y., Lee M.G., Sha B., Shi X.;
RT   "Recognition of histone H3K4 trimethylation by the plant homeodomain of
RT   PHF2 modulates histone demethylation.";
RL   J. Biol. Chem. 285:9322-9326(2010).
RN   [7]
RP   FUNCTION, CATALYTIC ACTIVITY, AND INTERACTION WITH RELA.
RX   PubMed=22921934; DOI=10.1016/j.molcel.2012.07.020;
RA   Stender J.D., Pascual G., Liu W., Kaikkonen M.U., Do K., Spann N.J.,
RA   Boutros M., Perrimon N., Rosenfeld M.G., Glass C.K.;
RT   "Control of proinflammatory gene programs by regulated trimethylation and
RT   demethylation of histone H4K20.";
RL   Mol. Cell 48:28-38(2012).
RN   [8]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-716, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Embryonic fibroblast;
RX   PubMed=23806337; DOI=10.1016/j.molcel.2013.06.001;
RA   Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y.,
RA   Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.;
RT   "SIRT5-mediated lysine desuccinylation impacts diverse metabolic
RT   pathways.";
RL   Mol. Cell 50:919-930(2013).
CC   -!- FUNCTION: Lysine demethylase that demethylates both histones and non-
CC       histone proteins (PubMed:22921934). Enzymatically inactive by itself,
CC       and becomes active following phosphorylation by PKA: forms a complex
CC       with ARID5B and mediates demethylation of methylated ARID5B.
CC       Demethylation of ARID5B leads to target the PHF2-ARID5B complex to
CC       target promoters, where PHF2 mediates demethylation of dimethylated
CC       'Lys-9' of histone H3 (H3K9me2), followed by transcription activation
CC       of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A
CC       in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3
CC       (H3K4me3) at rDNA promoters and promotes expression of rDNA (By
CC       similarity). Involved in the activation of toll-like receptor 4 (TLR4)-
CC       target inflammatory genes in macrophages by catalyzing the
CC       demethylation of trimethylated histone H4 lysine 20 (H4K20me3) at the
CC       gene promoters (PubMed:22921934). {ECO:0000250|UniProtKB:O75151,
CC       ECO:0000269|PubMed:22921934}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] +
CC         O2 = CO2 + formaldehyde + N(6)-methyl-L-lysyl(9)-[histone H3] +
CC         succinate; Xref=Rhea:RHEA:60192, Rhea:RHEA-COMP:15541, Rhea:RHEA-
CC         COMP:15542, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC         ChEBI:CHEBI:16842, ChEBI:CHEBI:30031, ChEBI:CHEBI:61929,
CC         ChEBI:CHEBI:61976; Evidence={ECO:0000250|UniProtKB:O75151};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60193;
CC         Evidence={ECO:0000250|UniProtKB:O75151};
CC   -!- ACTIVITY REGULATION: Enzymatically inactive by itself, and become
CC       active following phosphorylation by PKA. {ECO:0000250}.
CC   -!- SUBUNIT: Component of the PHF2-ARID5B complex, at least composed of
CC       PHF2 and ARID5B. Interacts with HNF4A and NR1H4 (By similarity).
CC       Interacts with RELA (PubMed:22921934). {ECO:0000250|UniProtKB:O75151,
CC       ECO:0000269|PubMed:22921934}.
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC       {ECO:0000250|UniProtKB:O75151}. Chromosome, centromere, kinetochore
CC       {ECO:0000250|UniProtKB:O75151}.
CC   -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me2 and
CC       H3K4me3. {ECO:0000250}.
CC   -!- PTM: Phosphorylated by PKA on specific serine residues, leading to the
CC       formation of an active lysine demethylase complex. {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family. JHDM1D
CC       subfamily. {ECO:0000305}.
CC   -!- CAUTION: In contrast to the related histone demethylases JHDM1D and
CC       PHF8, the conserved active His in position 321 is replaced by a Tyr.
CC       However, the presence of a Tyr residue neither affects binding to the
CC       catalytic iron nor abolishes demethylase activity. {ECO:0000305}.
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DR   EMBL; AF043726; AAD21792.1; -; mRNA.
DR   EMBL; AC109249; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; BC051633; AAH51633.1; -; mRNA.
DR   EMBL; AK172995; BAD32273.1; -; mRNA.
DR   CCDS; CCDS26496.1; -.
DR   RefSeq; NP_035208.2; NM_011078.3.
DR   AlphaFoldDB; Q9WTU0; -.
DR   SMR; Q9WTU0; -.
DR   BioGRID; 202144; 6.
DR   IntAct; Q9WTU0; 4.
DR   STRING; 10090.ENSMUSP00000047308; -.
DR   iPTMnet; Q9WTU0; -.
DR   PhosphoSitePlus; Q9WTU0; -.
DR   EPD; Q9WTU0; -.
DR   jPOST; Q9WTU0; -.
DR   MaxQB; Q9WTU0; -.
DR   PaxDb; Q9WTU0; -.
DR   PeptideAtlas; Q9WTU0; -.
DR   PRIDE; Q9WTU0; -.
DR   ProteomicsDB; 287703; -.
DR   Antibodypedia; 2009; 99 antibodies from 23 providers.
DR   DNASU; 18676; -.
DR   Ensembl; ENSMUST00000035540; ENSMUSP00000047308; ENSMUSG00000038025.
DR   GeneID; 18676; -.
DR   KEGG; mmu:18676; -.
DR   UCSC; uc007qim.1; mouse.
DR   CTD; 5253; -.
DR   MGI; MGI:1338034; Phf2.
DR   VEuPathDB; HostDB:ENSMUSG00000038025; -.
DR   eggNOG; KOG1633; Eukaryota.
DR   GeneTree; ENSGT00940000158148; -.
DR   HOGENOM; CLU_003540_2_0_1; -.
DR   InParanoid; Q9WTU0; -.
DR   OMA; AKKTKFQ; -.
DR   OrthoDB; 1384737at2759; -.
DR   PhylomeDB; Q9WTU0; -.
DR   TreeFam; TF106480; -.
DR   Reactome; R-MMU-3214842; HDMs demethylate histones.
DR   BioGRID-ORCS; 18676; 0 hits in 77 CRISPR screens.
DR   ChiTaRS; Phf1; mouse.
DR   PRO; PR:Q9WTU0; -.
DR   Proteomes; UP000000589; Chromosome 13.
DR   RNAct; Q9WTU0; protein.
DR   Bgee; ENSMUSG00000038025; Expressed in ascending aorta and 248 other tissues.
DR   Genevisible; Q9WTU0; MM.
DR   GO; GO:0000776; C:kinetochore; ISS:UniProtKB.
DR   GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
DR   GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR   GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR   GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; ISS:UniProtKB.
DR   GO; GO:0035575; F:histone H4-methyl-lysine-20 demethylase activity; IMP:UniProtKB.
DR   GO; GO:0005506; F:iron ion binding; ISS:UniProtKB.
DR   GO; GO:0035064; F:methylated histone binding; ISS:UniProtKB.
DR   GO; GO:0003713; F:transcription coactivator activity; ISS:UniProtKB.
DR   GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR   GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR   GO; GO:0045815; P:epigenetic maintenance of chromatin in transcription-competent conformation; IMP:UniProtKB.
DR   GO; GO:0033169; P:histone H3-K9 demethylation; IDA:UniProtKB.
DR   GO; GO:0035574; P:histone H4-K20 demethylation; IMP:UniProtKB.
DR   GO; GO:0061188; P:negative regulation of ribosomal DNA heterochromatin assembly; ISS:UniProtKB.
DR   GO; GO:0006482; P:protein demethylation; ISS:UniProtKB.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR   Gene3D; 3.30.40.10; -; 1.
DR   InterPro; IPR041070; JHD.
DR   InterPro; IPR003347; JmjC_dom.
DR   InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR   InterPro; IPR011011; Znf_FYVE_PHD.
DR   InterPro; IPR001965; Znf_PHD.
DR   InterPro; IPR019787; Znf_PHD-finger.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   Pfam; PF17811; JHD; 1.
DR   Pfam; PF02373; JmjC; 1.
DR   Pfam; PF00628; PHD; 1.
DR   SMART; SM00558; JmjC; 1.
DR   SMART; SM00249; PHD; 1.
DR   SUPFAM; SSF57903; SSF57903; 1.
DR   PROSITE; PS51184; JMJC; 1.
DR   PROSITE; PS01359; ZF_PHD_1; 1.
DR   PROSITE; PS50016; ZF_PHD_2; 1.
PE   1: Evidence at protein level;
KW   Acetylation; Activator; Centromere; Chromatin regulator; Chromosome;
KW   Dioxygenase; Iron; Isopeptide bond; Kinetochore; Metal-binding; Nucleus;
KW   Oxidoreductase; Phosphoprotein; Reference proteome; Transcription;
KW   Transcription regulation; Ubl conjugation; Zinc; Zinc-finger.
FT   CHAIN           1..1096
FT                   /note="Lysine-specific demethylase PHF2"
FT                   /id="PRO_0000059291"
FT   DOMAIN          197..353
FT                   /note="JmjC"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   ZN_FING         5..56
FT                   /note="PHD-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   REGION          448..630
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          719..755
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          811..841
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          871..1080
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        461..475
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        515..533
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        548..562
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        578..625
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        721..749
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        879..896
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        953..1041
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1053..1067
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         193
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250"
FT   BINDING         246
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250"
FT   BINDING         249
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   BINDING         251
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   BINDING         259
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250"
FT   BINDING         266
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250"
FT   BINDING         321
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   BINDING         323
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         474
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         479
FT                   /note="Phosphothreonine"
FT                   /evidence="ECO:0000250|UniProtKB:O75151"
FT   MOD_RES         536
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:O75151"
FT   MOD_RES         651
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         677
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         701
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:O75151"
FT   MOD_RES         716
FT                   /note="N6-acetyllysine"
FT                   /evidence="ECO:0007744|PubMed:23806337"
FT   MOD_RES         724
FT                   /note="Phosphotyrosine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         726
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         729
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         730
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         734
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         873
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         876
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         893
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   MOD_RES         1057
FT                   /note="Phosphoserine; by PKA"
FT                   /evidence="ECO:0000250|UniProtKB:O75151"
FT   CROSSLNK        707
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:O75151"
FT   CONFLICT        938
FT                   /note="Q -> L (in Ref. 1; AAD21792)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        955
FT                   /note="P -> S (in Ref. 4; BAD32273)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1096 AA;  120814 MW;  778B822C007D8860 CRC64;
     MATVPVYCVC RLPYDVTRFM IECDACKDWF HGSCVGVEEE EAPDIDIYHC PNCEKTHGKS
     TLKKKRTWHK HGPGPTPDVK PVQNGSQLFI KELRSRTFPS AEDVVSRVPG SQLTVGYMEE
     HGFTEPILVP KKDGLGLAVP APTFYVSDVE NYVGPERSVD VTDVTKQKDC KMKLKEFVDY
     YYSTNRKRVL NVTNLEFSDT RMSSFVEPPD IVKKLSWVEN YWPDDALLAK PKVTKYCLIC
     VKDSYTDFHI DSGGASAWYH VLKGEKIFYL IRPASANISL YERWRSASNH SEMFFADQVD
     RCYKCTVKQG QTLFIPSGWI YATLTPVDCL AFAGHFLHSL SVEMQMRAYE VERRLKLGSL
     TQFPNFETAC WYMGKHLLEA FKGSHKSGKQ LPPHLVQGAK ILNGAFRSWT KKQALAEHED
     ELPEHFRPSQ LIKDLAKEIR LSENASKTVR PEVNAAASSD EVCDGDREKE EPPSPVETTP
     PRSLLEKVSK KKTSKTVKMP KPSKIPKPPK SPKPPKTLKL KDGSKKKGKK CKESASPTIP
     NLDLLEAHTK EALTKMEPPK KGKTPKSVLS VPNKDTVHTQ NDMERLEIRE QTKSKSEAKW
     KYKNSKPDSL LKMEEEQRLE KSPLAGNKDK FSFSFSNRKL LGSKALRPPS SPGVFGALQS
     FKEDKAKPVR DEYEYVSDDG ELKIDEFPIR RKKSAPKRDL SFLLDKKEAL LMPTSKPKLD
     SAVYKSDDSS DEGSLHIDTD TKPGRNAKVK KESGSSAAGI LDLLQASEEV GALEYNPNSQ
     PPASPSTQEA IQGMLSMANL QASDSCLQTT WGTGQAKGGS LAAHGARKIG GGNKGTGKRL
     LKRTAKNSVD LEDYEEQDHL DACFKDSDYV YPSLESDEDN PVFKSRSKKR KGSDDAPYSP
     TARVGPSVPR QDRPVREGTR VASIETGLAA AAAKLSQQEE QKNRKKKNTK RKPAPNTASP
     SISTSASAST GTTSASTTPA STTPASTTPA STTPASTSTA SSQASQEGSS PEPPPESHSS
     SLADHEYTAA GTFSGSQAGR ASQPMAPGVF LTQRRPSASS PNNTAAKGKR TKKGMATAKQ
     RLGKILKIHR NGKLLL
 
 
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