GDPD2_HUMAN
ID GDPD2_HUMAN Reviewed; 539 AA.
AC Q9HCC8; B4DRH4; B4DVC9; Q9NXJ6;
DT 03-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Glycerophosphoinositol inositolphosphodiesterase GDPD2;
DE EC=3.1.4.43;
DE AltName: Full=Glycerophosphodiester phosphodiesterase 3;
DE AltName: Full=Glycerophosphodiester phosphodiesterase domain-containing protein 2;
DE AltName: Full=Osteoblast differentiation promoting factor;
GN Name=GDPD2; Synonyms=GDE3, OBDPF; ORFNames=UNQ1935/PRO4418;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC TISSUE=Spleen;
RX PubMed=12933806; DOI=10.1074/jbc.m302867200;
RA Yanaka N., Imai Y., Kawai E., Akatsuka H., Wakimoto K., Nogusa Y., Kato N.,
RA Chiba H., Kotani E., Omori K., Sakurai N.;
RT "Novel membrane protein containing glycerophosphodiester phosphodiesterase
RT motif is transiently expressed during osteoblast differentiation.";
RL J. Biol. Chem. 278:43595-43602(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RX PubMed=12975309; DOI=10.1101/gr.1293003;
RA Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J.,
RA Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P.,
RA Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E., Heldens S., Huang A.,
RA Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D.,
RA Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L.,
RA Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C.,
RA Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J.,
RA Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.;
RT "The secreted protein discovery initiative (SPDI), a large-scale effort to
RT identify novel human secreted and transmembrane proteins: a bioinformatics
RT assessment.";
RL Genome Res. 13:2265-2270(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3).
RC TISSUE=Caudate nucleus, Colon mucosa, and Spleen;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15772651; DOI=10.1038/nature03440;
RA Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D.,
RA Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L.,
RA Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.,
RA Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A.,
RA Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P.,
RA Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D.,
RA Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D.,
RA Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L.,
RA Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P.,
RA Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G.,
RA Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J.,
RA Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D.,
RA Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L.,
RA Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z.,
RA Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S.,
RA Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S.,
RA Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O.,
RA Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H.,
RA Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T.,
RA Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L.,
RA Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R.,
RA Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y.,
RA Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K.,
RA Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J.,
RA Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L.,
RA Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S.,
RA Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A.,
RA Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L.,
RA Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D.,
RA Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H.,
RA McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S.,
RA Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C.,
RA Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S.,
RA Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V.,
RA Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K.,
RA Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K.,
RA Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D.,
RA Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R.,
RA Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B.,
RA Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C.,
RA d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q.,
RA Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N.,
RA Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A.,
RA Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J.,
RA Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A.,
RA Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F.,
RA Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L.,
RA Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S.,
RA Rogers J., Bentley D.R.;
RT "The DNA sequence of the human X chromosome.";
RL Nature 434:325-337(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Skin;
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).
CC -!- FUNCTION: Has glycerophosphoinositol inositolphosphodiesterase activity
CC and specifically hydrolyzes glycerophosphoinositol, with no activity
CC for other substrates such as glycerophosphoinositol 4-phosphate,
CC glycerophosphocholine, glycerophosphoethanolamine, and
CC glycerophosphoserine. Accelerates the program of osteoblast
CC differentiation and growth. May play a role in remodeling of the actin
CC cytoskeleton (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + sn-glycero-3-phospho-1D-myo-inositol = 1D-myo-inositol
CC 1-phosphate + glycerol + H(+); Xref=Rhea:RHEA:14033,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17754,
CC ChEBI:CHEBI:58433, ChEBI:CHEBI:58444; EC=3.1.4.43;
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC -!- SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
CC Cytoplasm. Cytoplasm, cytoskeleton {ECO:0000250}. Note=Colocalizes with
CC the actin cytoskeleton. {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9HCC8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9HCC8-2; Sequence=VSP_042622;
CC Name=3;
CC IsoId=Q9HCC8-3; Sequence=VSP_042623;
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
CC -!- CAUTION: The catalytic domain of GDPD2 is oriented extracellularly;
CC Glycerophosphoinositol is hydrolyzed in the medium of cells
CC overexpressing Gdpd2, whereas intracellular levels of
CC glycerophosphoinositol is not affected. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA91014.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AB048363; BAB13350.1; -; mRNA.
DR EMBL; AY358986; AAQ89345.1; -; mRNA.
DR EMBL; AK000214; BAA91014.1; ALT_FRAME; mRNA.
DR EMBL; AK299255; BAG61286.1; -; mRNA.
DR EMBL; AK301025; BAG62641.1; -; mRNA.
DR EMBL; AK316035; BAH14406.1; -; mRNA.
DR EMBL; AL139398; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC032009; AAH32009.1; -; mRNA.
DR CCDS; CCDS14402.1; -. [Q9HCC8-1]
DR CCDS; CCDS55437.1; -. [Q9HCC8-3]
DR CCDS; CCDS55438.1; -. [Q9HCC8-2]
DR RefSeq; NP_001164662.1; NM_001171191.1. [Q9HCC8-2]
DR RefSeq; NP_001164663.1; NM_001171192.1. [Q9HCC8-3]
DR RefSeq; NP_001164664.1; NM_001171193.1. [Q9HCC8-2]
DR RefSeq; NP_060181.2; NM_017711.3. [Q9HCC8-1]
DR AlphaFoldDB; Q9HCC8; -.
DR SMR; Q9HCC8; -.
DR BioGRID; 120207; 5.
DR IntAct; Q9HCC8; 43.
DR MINT; Q9HCC8; -.
DR STRING; 9606.ENSP00000414019; -.
DR GlyGen; Q9HCC8; 1 site.
DR iPTMnet; Q9HCC8; -.
DR PhosphoSitePlus; Q9HCC8; -.
DR BioMuta; GDPD2; -.
DR DMDM; 74752794; -.
DR EPD; Q9HCC8; -.
DR jPOST; Q9HCC8; -.
DR MassIVE; Q9HCC8; -.
DR PeptideAtlas; Q9HCC8; -.
DR PRIDE; Q9HCC8; -.
DR ProteomicsDB; 81668; -. [Q9HCC8-1]
DR ProteomicsDB; 81669; -. [Q9HCC8-2]
DR ProteomicsDB; 81670; -. [Q9HCC8-3]
DR Antibodypedia; 27419; 139 antibodies from 21 providers.
DR DNASU; 54857; -.
DR Ensembl; ENST00000374382.4; ENSP00000363503.3; ENSG00000130055.14. [Q9HCC8-1]
DR Ensembl; ENST00000453994.6; ENSP00000414019.2; ENSG00000130055.14. [Q9HCC8-3]
DR Ensembl; ENST00000536730.5; ENSP00000445982.1; ENSG00000130055.14. [Q9HCC8-2]
DR Ensembl; ENST00000538649.5; ENSP00000444601.1; ENSG00000130055.14. [Q9HCC8-2]
DR GeneID; 54857; -.
DR KEGG; hsa:54857; -.
DR MANE-Select; ENST00000374382.4; ENSP00000363503.3; NM_017711.4; NP_060181.2.
DR UCSC; uc004dyh.4; human. [Q9HCC8-1]
DR CTD; 54857; -.
DR DisGeNET; 54857; -.
DR GeneCards; GDPD2; -.
DR HGNC; HGNC:25974; GDPD2.
DR HPA; ENSG00000130055; Tissue enhanced (intestine, lymphoid tissue, skin).
DR MIM; 300940; gene.
DR neXtProt; NX_Q9HCC8; -.
DR OpenTargets; ENSG00000130055; -.
DR PharmGKB; PA134907263; -.
DR VEuPathDB; HostDB:ENSG00000130055; -.
DR eggNOG; KOG2258; Eukaryota.
DR GeneTree; ENSGT00940000159625; -.
DR HOGENOM; CLU_024259_1_0_1; -.
DR InParanoid; Q9HCC8; -.
DR OMA; PPNHTYH; -.
DR OrthoDB; 404866at2759; -.
DR PhylomeDB; Q9HCC8; -.
DR TreeFam; TF313692; -.
DR BRENDA; 3.1.4.46; 2681.
DR BRENDA; 4.6.1.14; 2681.
DR PathwayCommons; Q9HCC8; -.
DR SignaLink; Q9HCC8; -.
DR BioGRID-ORCS; 54857; 19 hits in 698 CRISPR screens.
DR ChiTaRS; GDPD2; human.
DR GenomeRNAi; 54857; -.
DR Pharos; Q9HCC8; Tbio.
DR PRO; PR:Q9HCC8; -.
DR Proteomes; UP000005640; Chromosome X.
DR RNAct; Q9HCC8; protein.
DR Bgee; ENSG00000130055; Expressed in spleen and 127 other tissues.
DR Genevisible; Q9HCC8; HS.
DR GO; GO:0005884; C:actin filament; IEA:Ensembl.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0030027; C:lamellipodium; IEA:Ensembl.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0047394; F:glycerophosphoinositol inositolphosphodiesterase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0090527; P:actin filament reorganization; IEA:Ensembl.
DR GO; GO:0006629; P:lipid metabolic process; IEA:InterPro.
DR GO; GO:0045669; P:positive regulation of osteoblast differentiation; IEA:Ensembl.
DR Gene3D; 3.20.20.190; -; 1.
DR InterPro; IPR030395; GP_PDE_dom.
DR InterPro; IPR017946; PLC-like_Pdiesterase_TIM-brl.
DR Pfam; PF03009; GDPD; 1.
DR SUPFAM; SSF51695; SSF51695; 1.
DR PROSITE; PS51704; GP_PDE; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Cell membrane; Cytoplasm; Cytoskeleton; Glycoprotein;
KW Hydrolase; Membrane; Metal-binding; Reference proteome; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..539
FT /note="Glycerophosphoinositol inositolphosphodiesterase
FT GDPD2"
FT /id="PRO_0000251934"
FT TOPO_DOM 1..38
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 39..59
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 60..85
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 86..106
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 107..121
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 122..142
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 143..154
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 155..175
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 176..188
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 189..209
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 210..490
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 491..511
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 512..539
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 224..479
FT /note="GP-PDE"
FT BINDING 256
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 258
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 271
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT CARBOHYD 442
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT VAR_SEQ 1..79
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_042622"
FT VAR_SEQ 436
FT /note="K -> KDRFLLPAQAGLKLLASSNLPASASQSAGITGLSHCPPQPPGYKHEL
FT SHLAM (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_042623"
FT CONFLICT 418
FT /note="E -> G (in Ref. 3; BAA91014)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 539 AA; 61729 MW; 8271C3A74766D540 CRC64;
MAESPGCCSV WARCLHCLYS CHWRKCPRER MQTSKCDCIW FGLLFLTFLL SLSWLYIGLV
LLNDLHNFNE FLFRRWGHWM DWSLAFLLVI SLLVTYASLL LVLALLLRLC RQPLHLHSLH
KVLLLLIMLL VAAGLVGLDI QWQQEWHSLR VSLQATAPFL HIGAAAGIAL LAWPVADTFY
RIHRRGPKIL LLLLFFGVVL VIYLAPLCIS SPCIMEPRDL PPKPGLVGHR GAPMLAPENT
LMSLRKTAEC GATVFETDVM VSSDGVPFLM HDEHLSRTTN VASVFPTRIT AHSSDFSWTE
LKRLNAGSWF LERRPFWGAK PLAGPDQKEA ESQTVPALEE LLEEAAALNL SIMFDLRRPP
QNHTYYDTFV IQTLETVLNA RVPQAMVFWL PDEDRANVQR RAPGMRQIYG RQGGNRTERP
QFLNLPYQDL PLLDIKALHK DNVSVNLFVV NKPWLFSLLW CAGVDSVTTN DCQLLQQMRY
PIWLITPQTY LIIWVITNCV STMLLLWTFL LQRRFVKKRG KTGLETAVLL TRINNFMME
