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CLF1_YEAST
ID   CLF1_YEAST              Reviewed;         687 AA.
AC   Q12309; D6VYB5;
DT   30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   03-AUG-2022, entry version 168.
DE   RecName: Full=Pre-mRNA-splicing factor CLF1;
DE   AltName: Full=Crooked neck-like factor 1;
DE   AltName: Full=PRP19-associated complex protein 77;
DE   AltName: Full=Synthetic lethal with CDC40 protein 3;
GN   Name=CLF1; Synonyms=NTC77, SYF3; OrderedLocusNames=YLR117C; ORFNames=L2952;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 90840 / EAY235 / FY23;
RX   PubMed=9090053;
RX   DOI=10.1002/(sici)1097-0061(19970315)13:3<241::aid-yea61>3.0.co;2-#;
RA   Verhasselt P., Volckaert G.;
RT   "Sequence analysis of a 37.6 kbp cosmid clone from the right arm of
RT   Saccharomyces cerevisiae chromosome XII, carrying YAP3, HOG1, SNR6, tRNA-
RT   Arg3 and 23 new open reading frames, among which several homologies to
RT   proteins involved in cell division control and to mammalian growth factors
RT   and other animal proteins are found.";
RL   Yeast 13:241-250(1997).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169871;
RA   Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA   Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA   Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA   Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA   Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA   Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA   Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA   Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA   Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA   Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA   Zollner A., Hani J., Hoheisel J.D.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL   Nature 387:87-90(1997).
RN   [4]
RP   PROTEIN SEQUENCE OF 15-25, AND IDENTIFICATION IN THE PRP19-ASSOCIATED
RP   COMPLEX.
RX   PubMed=11842115; DOI=10.1093/nar/30.4.1029;
RA   Chen C.-H., Yu W.-C., Tsao T.Y., Wang L.-Y., Chen H.-R., Lin J.-Y.,
RA   Tsai W.-Y., Cheng S.-C.;
RT   "Functional and physical interactions between components of the Prp19p-
RT   associated complex.";
RL   Nucleic Acids Res. 30:1029-1037(2002).
RN   [5]
RP   FUNCTION, AND INTERACTION WITH MUD2 AND PRP40.
RX   PubMed=10445879; DOI=10.1017/s1355838299990635;
RA   Chung S., McLean M.R., Rymond B.C.;
RT   "Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome
RT   assembly through stable U4/U6.U5 snRNP addition.";
RL   RNA 5:1042-1054(1999).
RN   [6]
RP   FUNCTION, AND INTERACTION WITH CEF1; ISY1; NTC20; PRP22 AND SYF2.
RX   PubMed=11102353; DOI=10.1093/genetics/156.4.1503;
RA   Ben-Yehuda S., Dix I., Russell C.S., McGarvey M., Beggs J.D., Kupiec M.;
RT   "Genetic and physical interactions between factors involved in both cell
RT   cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae.";
RL   Genetics 156:1503-1517(2000).
RN   [7]
RP   FUNCTION, AND IDENTIFICATION IN THE SPLICEOSOME.
RX   PubMed=11105756; DOI=10.1017/s1355838200000984;
RA   Russell C.S., Ben-Yehuda S., Dix I., Kupiec M., Beggs J.D.;
RT   "Functional analyses of interacting factors involved in both pre-mRNA
RT   splicing and cell cycle progression in Saccharomyces cerevisiae.";
RL   RNA 6:1565-1572(2000).
RN   [8]
RP   FUNCTION, AND INTERACTION WITH ORC2.
RX   PubMed=11973290; DOI=10.1093/genetics/160.4.1319;
RA   Zhu W., Rainville I.R., Ding M., Bolus M., Heintz N.H., Pederson D.S.;
RT   "Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA
RT   replication in Saccharomyces cerevisiae.";
RL   Genetics 160:1319-1333(2002).
RN   [9]
RP   IDENTIFICATION IN THE CWC COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX   PubMed=11884590; DOI=10.1128/mcb.22.7.2011-2024.2002;
RA   Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.;
RT   "Proteomics analysis reveals stable multiprotein complexes in both fission
RT   and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA
RT   splicing factors, and snRNAs.";
RL   Mol. Cell. Biol. 22:2011-2024(2002).
RN   [10]
RP   INTERACTION WITH ISY1; NTC20; PRP46 AND SYF1.
RX   PubMed=12088152; DOI=10.1017/s1355838202025050;
RA   Ohi M.D., Gould K.L.;
RT   "Characterization of interactions among the Cef1p-Prp19p-associated
RT   splicing complex.";
RL   RNA 8:798-815(2002).
RN   [11]
RP   FUNCTION, AND IDENTIFICATION IN THE SPLICEOSOME.
RX   PubMed=12509417; DOI=10.1074/jbc.m210839200;
RA   Wang Q., Hobbs K., Lynn B., Rymond B.C.;
RT   "The Clf1p splicing factor promotes spliceosome assembly through N-terminal
RT   tetratricopeptide repeat contacts.";
RL   J. Biol. Chem. 278:7875-7883(2003).
RN   [12]
RP   IDENTIFICATION BY MASS SPECTROMETRY.
RX   PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3;
RA   Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M.,
RA   Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E.,
RA   Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.;
RT   "Assigning function to yeast proteins by integration of technologies.";
RL   Mol. Cell 12:1353-1365(2003).
RN   [13]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [14]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
CC   -!- FUNCTION: Involved in pre-mRNA splicing and cell cycle progression.
CC       Required for the spliceosome assembly by promoting the functional
CC       integration of the U4/U6.U5 tri-snRNP particle into the U1-, U2-
CC       dependent pre-spliceosome. Also recruits PRP19 to the spliceosome, as a
CC       component of the NTC complex (or PRP19-associated complex). The
CC       association of the NTC complex to the spliceosome mediates
CC       conformational rearrangement or stabilizes the structure of the
CC       spliceosome after U4 snRNA dissociation, which leads to spliceosome
CC       maturation. Required for initiation of the DNA replication by binding
CC       the RNA replication origins, probably through its interaction with the
CC       origin recognition complex (ORC). {ECO:0000269|PubMed:10445879,
CC       ECO:0000269|PubMed:11102353, ECO:0000269|PubMed:11105756,
CC       ECO:0000269|PubMed:11973290, ECO:0000269|PubMed:12509417}.
CC   -!- SUBUNIT: Belongs to the NTC complex (or PRP19-associated complex),
CC       composed of at least CEF1, CLF1, ISY1, NTC20, SNT309, SYF1, SYF2, and
CC       PRP19. The NTC complex associates with the spliceosome after the
CC       release of the U1 and U4 snRNAs and forms the CWC spliceosome
CC       subcomplex (or CEF1-associated complex) reminiscent of a late-stage
CC       spliceosome composed also of the U2, U5 and U6 snRNAs and at least
CC       BUD13, BUD31, BRR2, CDC40, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23,
CC       CWC24, CWC25, CWC27, ECM2, HSH155, IST3, LEA1, MSL1, PRP8, PRP9, PRP11,
CC       PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3,
CC       SNU114, SPP2, RSE1 and YJU2. Interacts with CEF1, ISY1, MUD2, NTC20,
CC       PRP22, PRP40, PRP46, SYF1, SYF2, and the ORC2 subunit of the origin
CC       recognition complex. {ECO:0000269|PubMed:10445879,
CC       ECO:0000269|PubMed:11102353, ECO:0000269|PubMed:11105756,
CC       ECO:0000269|PubMed:11842115, ECO:0000269|PubMed:11884590,
CC       ECO:0000269|PubMed:11973290, ECO:0000269|PubMed:12088152,
CC       ECO:0000269|PubMed:12509417}.
CC   -!- INTERACTION:
CC       Q12309; Q03654: CEF1; NbExp=8; IntAct=EBI-484, EBI-476;
CC       Q12309; P21374: ISY1; NbExp=4; IntAct=EBI-484, EBI-9382;
CC       Q12309; P38302: NTC20; NbExp=6; IntAct=EBI-484, EBI-20921;
CC       Q12309; P32523: PRP19; NbExp=9; IntAct=EBI-484, EBI-493;
CC       Q12309; Q06091: SNT309; NbExp=4; IntAct=EBI-484, EBI-818;
CC       Q12309; Q04048: SYF1; NbExp=4; IntAct=EBI-484, EBI-540;
CC       Q12309; P53277: SYF2; NbExp=2; IntAct=EBI-484, EBI-23308;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
CC   -!- MISCELLANEOUS: Present with 2140 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the crooked-neck family. {ECO:0000305}.
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DR   EMBL; X89514; CAA61696.1; -; Genomic_DNA.
DR   EMBL; U53877; AAB82364.1; -; Genomic_DNA.
DR   EMBL; Z73289; CAA97685.1; -; Genomic_DNA.
DR   EMBL; BK006945; DAA09431.1; -; Genomic_DNA.
DR   PIR; S64954; S64954.
DR   RefSeq; NP_013218.1; NM_001182004.1.
DR   PDB; 5GM6; EM; 3.50 A; d=1-275.
DR   PDB; 5GMK; EM; 3.40 A; d=1-275.
DR   PDB; 5LJ3; EM; 3.80 A; S=1-687.
DR   PDB; 5LJ5; EM; 3.80 A; S=1-687.
DR   PDB; 5LQW; EM; 5.80 A; R=1-687.
DR   PDB; 5MPS; EM; 3.85 A; S=1-687.
DR   PDB; 5MQ0; EM; 4.17 A; S=1-687.
DR   PDB; 5WSG; EM; 4.00 A; d=36-275.
DR   PDB; 5Y88; EM; 3.70 A; I=1-687.
DR   PDB; 5YLZ; EM; 3.60 A; I=1-687.
DR   PDB; 6BK8; EM; 3.30 A; T=1-687.
DR   PDB; 6EXN; EM; 3.70 A; S=1-687.
DR   PDB; 6J6G; EM; 3.20 A; d=1-687.
DR   PDB; 6J6H; EM; 3.60 A; d=1-687.
DR   PDB; 6J6N; EM; 3.86 A; d=1-687.
DR   PDB; 6J6Q; EM; 3.70 A; d=1-687.
DR   PDBsum; 5GM6; -.
DR   PDBsum; 5GMK; -.
DR   PDBsum; 5LJ3; -.
DR   PDBsum; 5LJ5; -.
DR   PDBsum; 5LQW; -.
DR   PDBsum; 5MPS; -.
DR   PDBsum; 5MQ0; -.
DR   PDBsum; 5WSG; -.
DR   PDBsum; 5Y88; -.
DR   PDBsum; 5YLZ; -.
DR   PDBsum; 6BK8; -.
DR   PDBsum; 6EXN; -.
DR   PDBsum; 6J6G; -.
DR   PDBsum; 6J6H; -.
DR   PDBsum; 6J6N; -.
DR   PDBsum; 6J6Q; -.
DR   AlphaFoldDB; Q12309; -.
DR   SMR; Q12309; -.
DR   BioGRID; 31389; 285.
DR   ComplexPortal; CPX-1651; PRP19-associated complex.
DR   ComplexPortal; CPX-1885; NineTeen complex.
DR   DIP; DIP-1685N; -.
DR   IntAct; Q12309; 36.
DR   MINT; Q12309; -.
DR   STRING; 4932.YLR117C; -.
DR   MoonProt; Q12309; -.
DR   MaxQB; Q12309; -.
DR   PaxDb; Q12309; -.
DR   PRIDE; Q12309; -.
DR   EnsemblFungi; YLR117C_mRNA; YLR117C; YLR117C.
DR   GeneID; 850808; -.
DR   KEGG; sce:YLR117C; -.
DR   SGD; S000004107; CLF1.
DR   VEuPathDB; FungiDB:YLR117C; -.
DR   eggNOG; KOG1915; Eukaryota.
DR   GeneTree; ENSGT00550000074931; -.
DR   HOGENOM; CLU_011554_1_0_1; -.
DR   InParanoid; Q12309; -.
DR   OMA; HIKVWIS; -.
DR   BioCyc; YEAST:G3O-32262-MON; -.
DR   PRO; PR:Q12309; -.
DR   Proteomes; UP000002311; Chromosome XII.
DR   RNAct; Q12309; protein.
DR   GO; GO:0000785; C:chromatin; IDA:SGD.
DR   GO; GO:0071014; C:post-mRNA release spliceosomal complex; IBA:GO_Central.
DR   GO; GO:0000974; C:Prp19 complex; IDA:SGD.
DR   GO; GO:0071006; C:U2-type catalytic step 1 spliceosome; IDA:SGD.
DR   GO; GO:0071007; C:U2-type catalytic step 2 spliceosome; IDA:SGD.
DR   GO; GO:0071008; C:U2-type post-mRNA release spliceosomal complex; IDA:SGD.
DR   GO; GO:0071004; C:U2-type prespliceosome; IDA:SGD.
DR   GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR   GO; GO:0003688; F:DNA replication origin binding; IDA:SGD.
DR   GO; GO:0000354; P:cis assembly of pre-catalytic spliceosome; IMP:SGD.
DR   GO; GO:0006270; P:DNA replication initiation; IMP:SGD.
DR   GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR   GO; GO:0000245; P:spliceosomal complex assembly; IBA:GO_Central.
DR   Gene3D; 1.25.40.10; -; 2.
DR   InterPro; IPR003107; HAT.
DR   InterPro; IPR045075; Syf1-like.
DR   InterPro; IPR011990; TPR-like_helical_dom_sf.
DR   PANTHER; PTHR11246; PTHR11246; 1.
DR   Pfam; PF02184; HAT; 1.
DR   SMART; SM00386; HAT; 12.
DR   SUPFAM; SSF48452; SSF48452; 2.
PE   1: Evidence at protein level;
KW   3D-structure; Direct protein sequencing; mRNA processing; mRNA splicing;
KW   Nucleus; Reference proteome; Repeat; Spliceosome.
FT   CHAIN           1..687
FT                   /note="Pre-mRNA-splicing factor CLF1"
FT                   /id="PRO_0000205753"
FT   REPEAT          45..77
FT                   /note="HAT 1"
FT   REPEAT          79..111
FT                   /note="HAT 2"
FT   REPEAT          113..145
FT                   /note="HAT 3"
FT   REPEAT          147..178
FT                   /note="HAT 4"
FT   REPEAT          180..211
FT                   /note="HAT 5"
FT   REPEAT          213..247
FT                   /note="HAT 6"
FT   REPEAT          251..283
FT                   /note="HAT 7"
FT   REPEAT          300..332
FT                   /note="HAT 8"
FT   REPEAT          337..369
FT                   /note="HAT 9"
FT   REPEAT          383..416
FT                   /note="HAT 10"
FT   REPEAT          451..483
FT                   /note="HAT 11"
FT   REPEAT          525..557
FT                   /note="HAT 12"
FT   REPEAT          629..661
FT                   /note="HAT 13"
FT   HELIX           15..27
FT                   /evidence="ECO:0007829|PDB:6BK8"
FT   HELIX           40..60
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           65..77
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           81..94
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           99..111
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           115..128
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           133..145
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           149..159
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           166..179
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           182..195
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           199..212
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           215..231
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           232..234
FT                   /evidence="ECO:0007829|PDB:6BK8"
FT   HELIX           240..256
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           260..273
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           278..291
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           294..315
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           320..333
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           337..349
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           354..369
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           375..382
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           383..385
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           389..395
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   STRAND          398..400
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           406..417
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           425..438
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           447..459
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           463..474
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           481..493
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           498..511
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           515..522
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           532..547
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           557..570
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           576..589
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           597..614
FT                   /evidence="ECO:0007829|PDB:6J6G"
FT   HELIX           621..635
FT                   /evidence="ECO:0007829|PDB:6J6G"
SQ   SEQUENCE   687 AA;  82445 MW;  AE7D5EC5B3979E00 CRC64;
     MDTLEPTAVD THVSAEQILR DVYKKGQKAR GSTNIDILDL EELREYQRRK RTEYEGYLKR
     NRLDMGQWIR YAQFEIEQHD MRRARSIFER ALLVDSSFIP LWIRYIDAEL KVKCINHARN
     LMNRAISTLP RVDKLWYKYL IVEESLNNVE IVRSLYTKWC SLEPGVNAWN SFVDFEIRQK
     NWNGVREIYS KYVMAHPQMQ TWLKWVRFEN RHGNTEFTRS VYSLAIDTVA NLQNLQIWSD
     MEVAKLVNSF AHWEAAQQEY ERSSALYQIA IEKWPSNQLL KAGLLDFEKQ FGDINSIEET
     ISYKRKMEYE TILSNNAYDY DTWWLYLDLI SESFPKQIMQ TFEKAIVDSR PKELSKNVQW
     KRYIYLWMRY ICYVELELEN SLLEEELFQR LIDDIIPHKH FTFSKIWLMY AKFLIRHDDV
     PKARKILGKA IGLCPKAKTF KGYIELEVKL KEFDRVRKIY EKFIEFQPSD LQIWSQYGEL
     EENLGDWDRV RGIYTIALDE NSDFLTKEAK IVLLQKYITF ETESQEFEKA RKLYRRYLEL
     NQYSPQSWIE FAMYQTSTPT EQQLLDLAKL QSENVDEDIE FEITDENKLE ARKVFEEAIV
     FFKEKDDKQG RLSILEALKD YEETYGTELD QETVKKRFPK VIKKVRLQNG VEEEFVDYIF
     PDDIDDDKPK PSKFLELAKK WKQEQAL
 
 
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