DDX42_MOUSE
ID DDX42_MOUSE Reviewed; 929 AA.
AC Q810A7; Q3TAN3; Q3TE60; Q8BWZ7; Q9D8Q2;
DT 20-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 3.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=ATP-dependent RNA helicase DDX42;
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:Q86XP3};
DE AltName: Full=DEAD box protein 42;
GN Name=Ddx42;
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 [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=C57BL/6J, and NOD;
RC TISSUE=Embryonic stem cell, Pancreas, Spleen, and Thymus;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
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] (ISOFORM 1).
RC STRAIN=C57BL/6J; TISSUE=Brain;
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 PROTEIN SEQUENCE OF 616-626, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=OF1; TISSUE=Hippocampus;
RA Lubec G., Sunyer B., Chen W.-Q.;
RL Submitted (JAN-2009) to UniProtKB.
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic brain;
RX PubMed=15345747; DOI=10.1074/mcp.m400085-mcp200;
RA Ballif B.A., Villen J., Beausoleil S.A., Schwartz D., Gygi S.P.;
RT "Phosphoproteomic analysis of the developing mouse brain.";
RL Mol. Cell. Proteomics 3:1093-1101(2004).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-104, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Teratocarcinoma;
RX PubMed=17622165; DOI=10.1021/pr070122r;
RA Smith J.C., Duchesne M.A., Tozzi P., Ethier M., Figeys D.;
RT "A differential phosphoproteomic analysis of retinoic acid-treated P19
RT cells.";
RL J. Proteome Res. 6:3174-3186(2007).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-109, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT "Large-scale phosphorylation analysis of mouse liver.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-104 AND SER-109, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19144319; DOI=10.1016/j.immuni.2008.11.006;
RA Trost M., English L., Lemieux S., Courcelles M., Desjardins M.,
RA Thibault P.;
RT "The phagosomal proteome in interferon-gamma-activated macrophages.";
RL Immunity 30:143-154(2009).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic fibroblast;
RX PubMed=19131326; DOI=10.1074/mcp.m800451-mcp200;
RA Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.;
RT "Large scale localization of protein phosphorylation by use of electron
RT capture dissociation mass spectrometry.";
RL Mol. Cell. Proteomics 8:904-912(2009).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-104; SER-109; SER-111 AND
RP SER-185, 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 [11]
RP METHYLATION [LARGE SCALE ANALYSIS] AT ARG-12, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, and Embryo;
RX PubMed=24129315; DOI=10.1074/mcp.o113.027870;
RA Guo A., Gu H., Zhou J., Mulhern D., Wang Y., Lee K.A., Yang V., Aguiar M.,
RA Kornhauser J., Jia X., Ren J., Beausoleil S.A., Silva J.C., Vemulapalli V.,
RA Bedford M.T., Comb M.J.;
RT "Immunoaffinity enrichment and mass spectrometry analysis of protein
RT methylation.";
RL Mol. Cell. Proteomics 13:372-387(2014).
CC -!- FUNCTION: ATP-dependent RNA helicase. Binds to partially double-
CC stranded RNAs (dsRNAs) in order to unwind RNA secondary structures.
CC Unwinding is promoted in the presence of single-strand binding
CC proteins. Mediates also RNA duplex formation thereby displacing the
CC single-strand RNA binding protein. ATP and ADP modulate its activity:
CC ATP binding and hydrolysis by DDX42 triggers RNA strand separation,
CC whereas the ADP-bound form of the protein triggers annealing of
CC complementary RNA strands. Involved in the survival of cells by
CC interacting with TP53BP2 and thereby counteracting the apoptosis-
CC stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.
CC {ECO:0000250|UniProtKB:Q86XP3}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000250|UniProtKB:Q86XP3};
CC -!- SUBUNIT: Component of splicing factor SF3B complex which is composed of
CC at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6,
CC PHF5A/SF3B14B, and DDX42/SF3B125. Interacts (via the C-terminus) with
CC TP53BP2; the interaction is not inhibitied by TP53BP2 ubiquitination
CC and is independent of p53/TP53. {ECO:0000250|UniProtKB:Q86XP3}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q86XP3}. Nucleus
CC {ECO:0000250|UniProtKB:Q86XP3}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q810A7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q810A7-2; Sequence=VSP_023519;
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX42 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH43036.4; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AK007805; BAB25270.3; -; mRNA.
DR EMBL; AK049311; BAC33675.1; -; mRNA.
DR EMBL; AK169816; BAE41388.1; -; mRNA.
DR EMBL; AK171730; BAE42635.1; -; mRNA.
DR EMBL; AL604045; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC043036; AAH43036.4; ALT_INIT; mRNA.
DR CCDS; CCDS48956.1; -. [Q810A7-1]
DR RefSeq; NP_082350.3; NM_028074.4. [Q810A7-1]
DR AlphaFoldDB; Q810A7; -.
DR SMR; Q810A7; -.
DR BioGRID; 215115; 15.
DR IntAct; Q810A7; 1.
DR STRING; 10090.ENSMUSP00000021046; -.
DR iPTMnet; Q810A7; -.
DR PhosphoSitePlus; Q810A7; -.
DR EPD; Q810A7; -.
DR jPOST; Q810A7; -.
DR MaxQB; Q810A7; -.
DR PaxDb; Q810A7; -.
DR PeptideAtlas; Q810A7; -.
DR PRIDE; Q810A7; -.
DR ProteomicsDB; 279852; -. [Q810A7-1]
DR ProteomicsDB; 279853; -. [Q810A7-2]
DR Antibodypedia; 18710; 105 antibodies from 20 providers.
DR DNASU; 72047; -.
DR Ensembl; ENSMUST00000021046; ENSMUSP00000021046; ENSMUSG00000020705. [Q810A7-1]
DR GeneID; 72047; -.
DR KEGG; mmu:72047; -.
DR UCSC; uc007lyk.2; mouse. [Q810A7-1]
DR CTD; 11325; -.
DR MGI; MGI:1919297; Ddx42.
DR VEuPathDB; HostDB:ENSMUSG00000020705; -.
DR eggNOG; KOG0339; Eukaryota.
DR GeneTree; ENSGT00940000156559; -.
DR HOGENOM; CLU_003041_9_0_1; -.
DR InParanoid; Q810A7; -.
DR OMA; FRSQYNS; -.
DR OrthoDB; 245118at2759; -.
DR PhylomeDB; Q810A7; -.
DR TreeFam; TF300351; -.
DR Reactome; R-MMU-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-MMU-72165; mRNA Splicing - Minor Pathway.
DR BioGRID-ORCS; 72047; 17 hits in 76 CRISPR screens.
DR ChiTaRS; Ddx42; mouse.
DR PRO; PR:Q810A7; -.
DR Proteomes; UP000000589; Chromosome 11.
DR RNAct; Q810A7; protein.
DR Bgee; ENSMUSG00000020705; Expressed in retinal neural layer and 255 other tissues.
DR Genevisible; Q810A7; MM.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005829; C:cytosol; ISO:MGI.
DR GO; GO:0016607; C:nuclear speck; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003723; F:RNA binding; ISO:MGI.
DR GO; GO:0003724; F:RNA helicase activity; ISO:MGI.
DR GO; GO:0008104; P:protein localization; ISS:UniProtKB.
DR GO; GO:0042981; P:regulation of apoptotic process; ISS:UniProtKB.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; ATP-binding; Coiled coil; Cytoplasm;
KW Direct protein sequencing; Helicase; Hydrolase; Isopeptide bond;
KW Methylation; Nucleotide-binding; Nucleus; Phosphoprotein;
KW Reference proteome; RNA-binding; Ubl conjugation.
FT CHAIN 1..929
FT /note="ATP-dependent RNA helicase DDX42"
FT /id="PRO_0000280059"
FT DOMAIN 284..459
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 487..632
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 25..119
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 182..203
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 662..682
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 723..929
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 739..828
FT /note="Necessary for interaction with TP53BP2"
FT /evidence="ECO:0000250|UniProtKB:Q86XP3"
FT COILED 116..157
FT /evidence="ECO:0000255"
FT MOTIF 253..281
FT /note="Q motif"
FT MOTIF 407..410
FT /note="DEAD box"
FT COMPBIAS 36..52
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 89..104
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 723..800
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 803..929
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 297..304
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 5
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q86XP3"
FT MOD_RES 12
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0007744|PubMed:24129315"
FT MOD_RES 58
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q86XP3"
FT MOD_RES 96
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q86XP3"
FT MOD_RES 104
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17622165,
FT ECO:0007744|PubMed:19144319, ECO:0007744|PubMed:21183079"
FT MOD_RES 109
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17242355,
FT ECO:0007744|PubMed:19144319, ECO:0007744|PubMed:21183079"
FT MOD_RES 111
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 185
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT CROSSLNK 894
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q86XP3"
FT VAR_SEQ 1..119
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_023519"
FT CONFLICT 503
FT /note="L -> M (in Ref. 1; BAB25270)"
FT /evidence="ECO:0000305"
FT CONFLICT 537
FT /note="R -> G (in Ref. 1; BAE42635)"
FT /evidence="ECO:0000305"
FT CONFLICT 859
FT /note="H -> Y (in Ref. 1; BAC33675)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 929 AA; 101965 MW; 0E8F3D30D07BDFCF CRC64;
MNWNKGGPGT KRGFGFGGFA ISAGKKEEAK LPQQSHSAFG AASSSSGFGK SAPPQLPSFY
KIGSKRANFD EENAYFEDEE EDSSNVDLPY IPAENSPTRQ QFHSKPADSD SDDDPLEAFM
AEVEDQAARD MKRLEEKDKE RKNVKGIRDD IEEEDDQEAY FRYMAENPTA GVVQEEEEDN
LEYDSDGNPI APSKKIIDPL PPIDHSEIDY PPFEKNFYNE HEEITNLTPQ QLIDLRHKLN
LRVSGAAPPR PGSSFAHFGF DEQLMHQIRK SEYTQPTPIQ CQGVPVALSG RDMIGIAKTG
SGKTAAFIWP MLIHIMDQKE LEPGDGPIAV IVCPTRELCQ QIHAECKRFG KAYNLRSVAV
YGGGSMWEQA KALQEGAEIV VCTPGRLIDH VKKKATNLQR VSYLVFDEAD RMFDMGFEYQ
VRSIASHVRP DRQTLLFSAT FRKKIEKLAR DILIDPIRVV QGDIGEANED VTQIVEILHS
GPSKWNWLTR RLVEFTSSGS VLLFVTKKAN AEELASNLKQ EGHNLGLLHG DMDQSERNKV
ISDFKKKDIP VLVATDVAAR GLDIPSIKTV INYDVARDID THTHRIGRTG RAGEKGVAYT
LLTPKDSNFA GDLVRNLEGA NQHVSKELLD LAMQNAWFRK SRFKGGKGKK LNIGGGGLGY
RERPGLGSEN SDRGNNNNVM SNYEAYKPST GAMGDRLTAM KAAFQSQYKS HFVAASLSNQ
KAGTSSAGAS GWTSAGSLNS VPTNSAQQGH NSPDNPMTSS TKNIPGFNNS GNISSAPVTY
PSIGAQGVNN TASGNNSREG IGGGNGKRER YTENRGGSRH SHGDGGNRHG DGGRHGDGYR
YPESGSRHTD GHRHGETRHG GSAGRHGESR GANDGRNGES RKEGFNRENK MDPKVDSSRM
DKVDSKTDKT PDGFAVPEPP KRKKSRWDS
