HNRPD_RAT
ID HNRPD_RAT Reviewed; 353 AA.
AC Q9JJ54; G3V9G2; P17132; Q9JJ51; Q9JJ52; Q9JJ53;
DT 21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT 04-MAR-2015, sequence version 2.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Heterogeneous nuclear ribonucleoprotein D0;
DE Short=hnRNP D0;
DE AltName: Full=AU-rich element RNA-binding protein 1;
GN Name=Hnrnpd; Synonyms=Auf1, Hnrpd;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3 AND 4).
RC TISSUE=Kidney;
RA Arao Y., Kikuchi A.;
RT "Differential expression of AUF1 isoforms in rat tissues.";
RL Submitted (JUL-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 147-304 (ISOFORMS 3/4).
RC TISSUE=Pituitary;
RX PubMed=2088340; DOI=10.1016/0167-4781(90)90073-b;
RA Sharp Z.D., Smith K.P., Cao Z., Helsel S.;
RT "Cloning of the nucleic acid-binding domain of the rat HnRNP C-type
RT protein.";
RL Biochim. Biophys. Acta 1048:306-309(1990).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=16396499; DOI=10.1021/pr0503073;
RA Moser K., White F.M.;
RT "Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-
RT MS/MS.";
RL J. Proteome Res. 5:98-104(2006).
RN [6]
RP METHYLATION.
RX PubMed=18492485; DOI=10.1016/j.bbrc.2008.05.051;
RA Iwasaki H.;
RT "Involvement of PRMT1 in hnRNPQ activation and internalization of insulin
RT receptor.";
RL Biochem. Biophys. Res. Commun. 372:314-319(2008).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-78; SER-81 AND SER-188, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Binds with high affinity to RNA molecules that contain AU-
CC rich elements (AREs) found within the 3'-UTR of many proto-oncogenes
CC and cytokine mRNAs. Also binds to double- and single-stranded DNA
CC sequences in a specific manner and functions a transcription factor.
CC Each of the RNA-binding domains specifically can bind solely to a
CC single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to
CC the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA
CC oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the
CC telomeric single-stranded DNA 5'-TTAGGG-3' repeats. Binding of RRM1 to
CC DNA inhibits the formation of DNA quadruplex structure which may play a
CC role in telomere elongation. May be involved in translationally coupled
CC mRNA turnover. Implicated with other RNA-binding proteins in the
CC cytoplasmic deadenylation/translational and decay interplay of the FOS
CC mRNA mediated by the major coding-region determinant of instability
CC (mCRD) domain. May play a role in the regulation of the rhythmic
CC expression of circadian clock core genes. Directly binds to the 3'UTR
CC of CRY1 mRNA and induces CRY1 rhythmic translation. May also be
CC involved in the regulation of PER2 translation.
CC {ECO:0000250|UniProtKB:Q14103}.
CC -!- SUBUNIT: Identified in a IGF2BP1-dependent mRNP granule complex
CC containing untranslated mRNAs. Part of a complex associated with the
CC FOS mCRD domain and consisting of PABPC1, PAIP1, CSDE1/UNR and SYNCRIP.
CC Interacts with IGF2BP2. Interacts with GTPBP1. Interacts with EIF4G1;
CC the interaction requires RNA. Interacts with EIF3B and RPS3.
CC {ECO:0000250|UniProtKB:Q14103}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q14103}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q14103}. Note=Localized in cytoplasmic mRNP
CC granules containing untranslated mRNAs. Component of ribonucleosomes.
CC Cytoplasmic localization oscillates diurnally.
CC {ECO:0000250|UniProtKB:Q14103}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=1; Synonyms=p45;
CC IsoId=Q9JJ54-1; Sequence=Displayed;
CC Name=2; Synonyms=p42;
CC IsoId=Q9JJ54-2; Sequence=VSP_005836;
CC Name=3; Synonyms=p40;
CC IsoId=Q9JJ54-3; Sequence=VSP_005837;
CC Name=4; Synonyms=p37;
CC IsoId=Q9JJ54-4; Sequence=VSP_005836, VSP_005837;
CC -!- PTM: Methylated by PRMT1, in an insulin-dependent manner. The PRMT1-
CC mediated methylation regulates its phosphorylation.
CC {ECO:0000269|PubMed:18492485}.
CC -!- PTM: Arg-343 is dimethylated, probably to asymmetric dimethylarginine.
CC {ECO:0000250|UniProtKB:Q14103}.
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DR EMBL; AB046615; BAB03465.1; -; mRNA.
DR EMBL; AB046616; BAB03466.1; -; mRNA.
DR EMBL; AB046617; BAB03467.1; -; mRNA.
DR EMBL; AB046618; BAB03468.1; -; mRNA.
DR EMBL; AABR06077578; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH474022; EDL99590.1; -; Genomic_DNA.
DR EMBL; X16933; CAA34808.1; -; mRNA.
DR PIR; S09017; S09017.
DR RefSeq; NP_001076008.1; NM_001082539.1. [Q9JJ54-2]
DR RefSeq; NP_001076009.1; NM_001082540.1. [Q9JJ54-3]
DR RefSeq; NP_001076010.1; NM_001082541.1. [Q9JJ54-4]
DR RefSeq; NP_077380.2; NM_024404.2. [Q9JJ54-1]
DR AlphaFoldDB; Q9JJ54; -.
DR SMR; Q9JJ54; -.
DR BioGRID; 249454; 3.
DR IntAct; Q9JJ54; 4.
DR MINT; Q9JJ54; -.
DR STRING; 10116.ENSRNOP00000046491; -.
DR iPTMnet; Q9JJ54; -.
DR PhosphoSitePlus; Q9JJ54; -.
DR jPOST; Q9JJ54; -.
DR PaxDb; Q9JJ54; -.
DR PRIDE; Q9JJ54; -.
DR Ensembl; ENSRNOT00000003158; ENSRNOP00000003158; ENSRNOG00000002292. [Q9JJ54-3]
DR Ensembl; ENSRNOT00000003173; ENSRNOP00000003173; ENSRNOG00000002292. [Q9JJ54-2]
DR Ensembl; ENSRNOT00000047840; ENSRNOP00000046491; ENSRNOG00000002292. [Q9JJ54-1]
DR GeneID; 79256; -.
DR KEGG; rno:79256; -.
DR UCSC; RGD:620365; rat. [Q9JJ54-1]
DR CTD; 3184; -.
DR RGD; 620365; Hnrnpd.
DR eggNOG; KOG0118; Eukaryota.
DR GeneTree; ENSGT00940000158010; -.
DR InParanoid; Q9JJ54; -.
DR OMA; GPNQSWN; -.
DR OrthoDB; 1055256at2759; -.
DR TreeFam; TF314808; -.
DR Reactome; R-RNO-450408; AUF1 (hnRNP D0) binds and destabilizes mRNA.
DR Reactome; R-RNO-72163; mRNA Splicing - Major Pathway.
DR PRO; PR:Q9JJ54; -.
DR Proteomes; UP000002494; Chromosome 14.
DR Proteomes; UP000234681; Chromosome 14.
DR Bgee; ENSRNOG00000002292; Expressed in thymus and 20 other tissues.
DR Genevisible; Q9JJ54; RN.
DR GO; GO:0005829; C:cytosol; IDA:RGD.
DR GO; GO:0106002; C:mCRD-mediated mRNA stability complex; ISO:RGD.
DR GO; GO:0005654; C:nucleoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:RGD.
DR GO; GO:1990904; C:ribonucleoprotein complex; ISS:UniProtKB.
DR GO; GO:0045202; C:synapse; ISO:RGD.
DR GO; GO:0003682; F:chromatin binding; IDA:RGD.
DR GO; GO:0042826; F:histone deacetylase binding; IPI:RGD.
DR GO; GO:0003680; F:minor groove of adenine-thymine-rich DNA binding; IDA:RGD.
DR GO; GO:0035925; F:mRNA 3'-UTR AU-rich region binding; IDA:RGD.
DR GO; GO:0003729; F:mRNA binding; IDA:RGD.
DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB.
DR GO; GO:0042162; F:telomeric DNA binding; ISS:UniProtKB.
DR GO; GO:0061158; P:3'-UTR-mediated mRNA destabilization; IMP:RGD.
DR GO; GO:0007420; P:brain development; IEP:RGD.
DR GO; GO:0071230; P:cellular response to amino acid stimulus; IEP:RGD.
DR GO; GO:0071392; P:cellular response to estradiol stimulus; IEP:RGD.
DR GO; GO:0071732; P:cellular response to nitric oxide; IDA:RGD.
DR GO; GO:1904586; P:cellular response to putrescine; IDA:RGD.
DR GO; GO:0021549; P:cerebellum development; IEP:RGD.
DR GO; GO:0097167; P:circadian regulation of translation; ISS:UniProtKB.
DR GO; GO:0070934; P:CRD-mediated mRNA stabilization; ISO:RGD.
DR GO; GO:1990828; P:hepatocyte dedifferentiation; IEP:RGD.
DR GO; GO:0001889; P:liver development; IEP:RGD.
DR GO; GO:0048255; P:mRNA stabilization; IDA:RGD.
DR GO; GO:0042789; P:mRNA transcription by RNA polymerase II; ISO:RGD.
DR GO; GO:0010629; P:negative regulation of gene expression; IMP:RGD.
DR GO; GO:1900152; P:negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; ISO:RGD.
DR GO; GO:0000291; P:nuclear-transcribed mRNA catabolic process, exonucleolytic; TAS:RGD.
DR GO; GO:0006913; P:nucleocytoplasmic transport; TAS:RGD.
DR GO; GO:2000767; P:positive regulation of cytoplasmic translation; ISO:RGD.
DR GO; GO:0010628; P:positive regulation of gene expression; IMP:RGD.
DR GO; GO:1905663; P:positive regulation of telomerase RNA reverse transcriptase activity; ISO:RGD.
DR GO; GO:1904355; P:positive regulation of telomere capping; ISO:RGD.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISO:RGD.
DR GO; GO:0045727; P:positive regulation of translation; ISS:UniProtKB.
DR GO; GO:0042752; P:regulation of circadian rhythm; ISS:UniProtKB.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0043488; P:regulation of mRNA stability; ISO:RGD.
DR GO; GO:0032204; P:regulation of telomere maintenance; ISO:RGD.
DR GO; GO:0051592; P:response to calcium ion; IDA:RGD.
DR GO; GO:0051602; P:response to electrical stimulus; IEP:RGD.
DR GO; GO:0032355; P:response to estradiol; IEP:RGD.
DR GO; GO:1901355; P:response to rapamycin; IDA:RGD.
DR GO; GO:1904383; P:response to sodium phosphate; IDA:RGD.
DR Gene3D; 3.30.70.330; -; 2.
DR InterPro; IPR012956; CARG-binding_factor_N.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR Pfam; PF08143; CBFNT; 1.
DR Pfam; PF00076; RRM_1; 2.
DR SMART; SM00360; RRM; 2.
DR SUPFAM; SSF54928; SSF54928; 2.
DR PROSITE; PS50102; RRM; 2.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Biological rhythms; Cytoplasm;
KW Isopeptide bond; Methylation; Nucleus; Phosphoprotein; Reference proteome;
KW Repeat; Ribonucleoprotein; RNA-binding; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT CHAIN 2..353
FT /note="Heterogeneous nuclear ribonucleoprotein D0"
FT /id="PRO_0000081851"
FT DOMAIN 95..177
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 180..259
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 1..89
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 65..89
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 69
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 78
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 80
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 81
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 89
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 117
FT /note="N6-methyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 125
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 163
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 188
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 191
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 241
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q60668"
FT MOD_RES 249
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 269
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 270
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 276
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 278
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 280
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000250|UniProtKB:Q60668"
FT MOD_RES 343
FT /note="Asymmetric dimethylarginine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q60668"
FT MOD_RES 343
FT /note="Dimethylated arginine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT MOD_RES 343
FT /note="Omega-N-methylarginine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT CROSSLNK 70
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT CROSSLNK 127
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT CROSSLNK 195
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q14103"
FT VAR_SEQ 77..95
FT /note="Missing (in isoform 2 and isoform 4)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_005836"
FT VAR_SEQ 283..332
FT /note="GPSQNWNQGYSNYWNQGYGSYGYNSQGYGGYGGYDYTGYNSYYGYGDYSN
FT -> D (in isoform 3 and isoform 4)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_005837"
FT CONFLICT 51
FT /note="P -> A (in Ref. 1; BAB03465/BAB03466/BAB03467/
FT BAB03468)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 353 AA; 38218 MW; 7C21381A6B4A199F CRC64;
MSEEQFGGDG AAAAATAAVG GSAGEQEGAM VAAAQGAAAA AGSGSGGGSA PGGTEGGSTE
AEGAKIDASK NEEDEGHSNS SPRHTEAATA QREEWKMFIG GLSWDTTKKD LKDYFSKFGD
VVDCTLKLDP ITGRSRGFGF VLFKESESVD KVMDQKEHKL NGKVIDPKRA KAMKTKEPVK
KIFVGGLSPD TPEEKIREYF GGFGEVESIE LPMDNKTNKR RGFCFITFKE EEPVKKIMEK
KYHNVGLSKC EIKVAMSKEQ YQQQQQWGSR GGFAGRARGR GGGPSQNWNQ GYSNYWNQGY
GSYGYNSQGY GGYGGYDYTG YNSYYGYGDY SNQQSGYGKV SRRGGHQNSY KPY
