GDPD5_HUMAN
ID GDPD5_HUMAN Reviewed; 605 AA.
AC Q8WTR4; Q49AQ5; Q6UX76; Q7Z4S0; Q8N781; Q8NCB7; Q8TB77;
DT 03-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 2.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=Glycerophosphodiester phosphodiesterase domain-containing protein 5 {ECO:0000305};
DE AltName: Full=Glycerophosphocholine phosphodiesterase GDPD5 {ECO:0000250|UniProtKB:Q640M6};
DE EC=3.1.4.2 {ECO:0000250|UniProtKB:Q640M6};
DE AltName: Full=Glycerophosphodiester phosphodiesterase 2;
DE AltName: Full=Phosphoinositide phospholipase C GDPD5 {ECO:0000305};
DE EC=3.1.4.11 {ECO:0000250|UniProtKB:Q3KTM2};
GN Name=GDPD5 {ECO:0000312|HGNC:HGNC:28804};
GN Synonyms=GDE2 {ECO:0000250|UniProtKB:Q3KTM2};
GN ORFNames=PP6037, PP9363, UNQ1850/PRO3580 {ECO:0000303|PubMed:12975309};
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 [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT THR-480.
RX PubMed=15498874; DOI=10.1073/pnas.0404089101;
RA Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X.,
RA Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X.,
RA Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J.;
RT "Large-scale cDNA transfection screening for genes related to cancer
RT development and progression.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), AND VARIANT THR-480.
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] (ISOFORM 5), AND VARIANT THR-480.
RC TISSUE=Thyroid;
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 MRNA] (ISOFORMS 3 AND 4), AND VARIANT
RP THR-480.
RC TISSUE=Eye, and Testis;
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 142-605.
RC TISSUE=Teratocarcinoma;
RX PubMed=16303743; DOI=10.1093/dnares/12.2.117;
RA Otsuki T., Ota T., Nishikawa T., Hayashi K., Suzuki Y., Yamamoto J.,
RA Wakamatsu A., Kimura K., Sakamoto K., Hatano N., Kawai Y., Ishii S.,
RA Saito K., Kojima S., Sugiyama T., Ono T., Okano K., Yoshikawa Y.,
RA Aotsuka S., Sasaki N., Hattori A., Okumura K., Nagai K., Sugano S.,
RA Isogai T.;
RT "Signal sequence and keyword trap in silico for selection of full-length
RT human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA
RT libraries.";
RL DNA Res. 12:117-126(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 166-605.
RC TISSUE=Brain;
RA Guo J.H., Zan Q., Yu L.;
RL Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Glycerophosphodiester phosphodiesterase that promotes neurite
CC formation and drives spinal motor neuron differentiation (By
CC similarity). Mediates the cleavage of glycosylphosphatidylinositol
CC (GPI) anchor of target proteins: removes the GPI-anchor of RECK,
CC leading to release RECK from the plasma membrane (By similarity). May
CC contribute to the osmotic regulation of cellular glycerophosphocholine
CC (By similarity). {ECO:0000250|UniProtKB:Q3KTM2,
CC ECO:0000250|UniProtKB:Q640M6}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-
CC bisphosphate) + H2O = 1D-myo-inositol 1,4,5-trisphosphate + a 1,2-
CC diacyl-sn-glycerol + H(+); Xref=Rhea:RHEA:33179, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:17815, ChEBI:CHEBI:58456,
CC ChEBI:CHEBI:203600; EC=3.1.4.11;
CC Evidence={ECO:0000250|UniProtKB:Q3KTM2};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + sn-glycerol 3-phosphocholine = choline + H(+) + sn-
CC glycerol 3-phosphate; Xref=Rhea:RHEA:16061, ChEBI:CHEBI:15354,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16870,
CC ChEBI:CHEBI:57597; EC=3.1.4.2;
CC Evidence={ECO:0000250|UniProtKB:Q640M6};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16062;
CC Evidence={ECO:0000250|UniProtKB:Q640M6};
CC -!- SUBUNIT: Interacts with PRDX1; forms a mixed-disulfide with PRDX1,
CC leading to disrupt intramolecular disulfide bond between Cys-25 and
CC Cys-571. {ECO:0000250|UniProtKB:Q3KTM2}.
CC -!- INTERACTION:
CC Q8WTR4; P50542: PEX5; NbExp=3; IntAct=EBI-2833203, EBI-597835;
CC Q8WTR4; Q8IUQ4: SIAH1; NbExp=3; IntAct=EBI-2833203, EBI-747107;
CC Q8WTR4-3; Q14677: CLINT1; NbExp=3; IntAct=EBI-16430931, EBI-1171113;
CC -!- SUBCELLULAR LOCATION: Endomembrane system
CC {ECO:0000250|UniProtKB:Q640M6}; Multi-pass membrane protein
CC {ECO:0000255}. Cytoplasm, perinuclear region
CC {ECO:0000250|UniProtKB:Q640M6}. Cell projection, growth cone
CC {ECO:0000250|UniProtKB:Q640M6}. Note=In a punctate perinuclear pattern.
CC {ECO:0000250|UniProtKB:Q640M6}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=1;
CC IsoId=Q8WTR4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8WTR4-2; Sequence=VSP_020816;
CC Name=3;
CC IsoId=Q8WTR4-3; Sequence=VSP_020815;
CC Name=4;
CC IsoId=Q8WTR4-4; Sequence=VSP_020814;
CC Name=5;
CC IsoId=Q8WTR4-5; Sequence=VSP_020813;
CC -!- PTM: Intramolecular disulfide bond between Cys-25 and Cys-571 is
CC reduced by PRDX1. {ECO:0000250|UniProtKB:Q3KTM2}.
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAP97686.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=BAC11242.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AF318351; AAL55858.1; -; mRNA.
DR EMBL; AF318377; AAL55884.1; -; mRNA.
DR EMBL; AY358477; AAQ88841.1; -; mRNA.
DR EMBL; AK098808; BAC05418.1; -; mRNA.
DR EMBL; BC018771; AAH18771.1; -; mRNA.
DR EMBL; BC033391; AAH33391.1; -; mRNA.
DR EMBL; AK074848; BAC11242.1; ALT_INIT; mRNA.
DR EMBL; AF451987; AAP97686.1; ALT_INIT; mRNA.
DR CCDS; CCDS8238.1; -. [Q8WTR4-1]
DR CCDS; CCDS86229.1; -. [Q8WTR4-5]
DR CCDS; CCDS86230.1; -. [Q8WTR4-3]
DR RefSeq; NP_110419.5; NM_030792.6. [Q8WTR4-1]
DR RefSeq; XP_006718760.1; XM_006718697.3. [Q8WTR4-1]
DR RefSeq; XP_011543587.1; XM_011545285.2.
DR RefSeq; XP_011543589.1; XM_011545287.1.
DR AlphaFoldDB; Q8WTR4; -.
DR SMR; Q8WTR4; -.
DR BioGRID; 123512; 75.
DR IntAct; Q8WTR4; 39.
DR STRING; 9606.ENSP00000337972; -.
DR GlyGen; Q8WTR4; 5 sites.
DR iPTMnet; Q8WTR4; -.
DR PhosphoSitePlus; Q8WTR4; -.
DR BioMuta; GDPD5; -.
DR DMDM; 115502213; -.
DR MassIVE; Q8WTR4; -.
DR PaxDb; Q8WTR4; -.
DR PeptideAtlas; Q8WTR4; -.
DR PRIDE; Q8WTR4; -.
DR ProteomicsDB; 74586; -. [Q8WTR4-1]
DR ProteomicsDB; 74587; -. [Q8WTR4-2]
DR ProteomicsDB; 74588; -. [Q8WTR4-3]
DR ProteomicsDB; 74589; -. [Q8WTR4-4]
DR ProteomicsDB; 74590; -. [Q8WTR4-5]
DR Antibodypedia; 45087; 152 antibodies from 27 providers.
DR DNASU; 81544; -.
DR Ensembl; ENST00000336898.8; ENSP00000337972.3; ENSG00000158555.15. [Q8WTR4-1]
DR Ensembl; ENST00000526177.5; ENSP00000434050.1; ENSG00000158555.15. [Q8WTR4-3]
DR Ensembl; ENST00000529721.5; ENSP00000433214.1; ENSG00000158555.15. [Q8WTR4-1]
DR Ensembl; ENST00000533784.5; ENSP00000437049.1; ENSG00000158555.15. [Q8WTR4-2]
DR Ensembl; ENST00000533805.5; ENSP00000435196.1; ENSG00000158555.15. [Q8WTR4-5]
DR GeneID; 81544; -.
DR KEGG; hsa:81544; -.
DR MANE-Select; ENST00000336898.8; ENSP00000337972.3; NM_030792.8; NP_110419.5.
DR UCSC; uc001own.5; human. [Q8WTR4-1]
DR CTD; 81544; -.
DR DisGeNET; 81544; -.
DR GeneCards; GDPD5; -.
DR HGNC; HGNC:28804; GDPD5.
DR HPA; ENSG00000158555; Tissue enhanced (lymphoid tissue, retina).
DR MIM; 609632; gene.
DR neXtProt; NX_Q8WTR4; -.
DR OpenTargets; ENSG00000158555; -.
DR PharmGKB; PA142671743; -.
DR VEuPathDB; HostDB:ENSG00000158555; -.
DR eggNOG; KOG2258; Eukaryota.
DR GeneTree; ENSGT00940000159690; -.
DR HOGENOM; CLU_024259_1_0_1; -.
DR InParanoid; Q8WTR4; -.
DR OMA; REPPREH; -.
DR OrthoDB; 404866at2759; -.
DR PhylomeDB; Q8WTR4; -.
DR TreeFam; TF313692; -.
DR BRENDA; 3.1.4.11; 2681.
DR BRENDA; 3.1.4.2; 2681.
DR BRENDA; 3.1.4.46; 2681.
DR PathwayCommons; Q8WTR4; -.
DR Reactome; R-HSA-6814848; Glycerophospholipid catabolism.
DR SignaLink; Q8WTR4; -.
DR BioGRID-ORCS; 81544; 13 hits in 1082 CRISPR screens.
DR ChiTaRS; GDPD5; human.
DR GenomeRNAi; 81544; -.
DR Pharos; Q8WTR4; Tbio.
DR PRO; PR:Q8WTR4; -.
DR Proteomes; UP000005640; Chromosome 11.
DR RNAct; Q8WTR4; protein.
DR Bgee; ENSG00000158555; Expressed in spleen and 185 other tissues.
DR ExpressionAtlas; Q8WTR4; baseline and differential.
DR Genevisible; Q8WTR4; HS.
DR GO; GO:0012505; C:endomembrane system; IEA:UniProtKB-SubCell.
DR GO; GO:0030426; C:growth cone; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0047389; F:glycerophosphocholine phosphodiesterase activity; IEA:UniProtKB-EC.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0004435; F:phosphatidylinositol phospholipase C activity; IEA:UniProtKB-EC.
DR GO; GO:0006629; P:lipid metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0007399; P:nervous system development; IEA:UniProtKB-KW.
DR GO; GO:0045666; P:positive regulation of neuron differentiation; IBA:GO_Central.
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 1: Evidence at protein level;
KW Alternative splicing; Cell projection; Cytoplasm; Disulfide bond;
KW Glycoprotein; Hydrolase; Lipid metabolism; Membrane; Neurogenesis;
KW Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..605
FT /note="Glycerophosphodiester phosphodiesterase domain-
FT containing protein 5"
FT /id="PRO_0000251941"
FT TOPO_DOM 1..42
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 43..63
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 64..89
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 90..110
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 111..125
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 126..146
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 147..160
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 161..181
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 182..192
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 193..213
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 214..496
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 497..517
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 518..605
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 228..485
FT /note="GP-PDE"
FT REGION 582..605
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CARBOHYD 301
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 336
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 352
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 374
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 448
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 15..18
FT /evidence="ECO:0000250|UniProtKB:Q3KTM2"
FT DISULFID 25..571
FT /evidence="ECO:0000250|UniProtKB:Q3KTM2"
FT VAR_SEQ 1..245
FT /note="Missing (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_020813"
FT VAR_SEQ 1..218
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_020814"
FT VAR_SEQ 1..138
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_020815"
FT VAR_SEQ 40..158
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12975309"
FT /id="VSP_020816"
FT VARIANT 480
FT /note="A -> T (in dbSNP:rs571353)"
FT /evidence="ECO:0000269|PubMed:12975309,
FT ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334,
FT ECO:0000269|PubMed:15498874"
FT /id="VAR_027733"
FT CONFLICT 233
FT /note="H -> N (in Ref. 4; AAH33391)"
FT /evidence="ECO:0000305"
FT CONFLICT 397..399
FT /note="QRP -> GS (in Ref. 6; AAP97686)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 605 AA; 68586 MW; A4AC52A6773FB7EF CRC64;
MVRHQPLQYY EPQLCLSCLT GIYGCRWKRY QRSHDDTTPW ERLWFLLLTF TFGLTLTWLY
FWWEVHNDYD EFNWYLYNRM GYWSDWPVPI LVTTAAAFAY IAGLLVLALC HIAVGQQMNL
HWLHKIGLVV ILASTVVAMS AVAQLWEDEW EVLLISLQGT APFLHVGAVA AVTMLSWIVA
GQFARAERTS SQVTILCTFF TVVFALYLAP LTISSPCIME KKDLGPKPAL IGHRGAPMLA
PEHTLMSFRK ALEQKLYGLQ ADITISLDGV PFLMHDTTLR RTTNVEEEFP ELARRPASML
NWTTLQRLNA GQWFLKTDPF WTASSLSPSD HREAQNQSIC SLAELLELAK GNATLLLNLR
DPPREHPYRS SFINVTLEAV LHSGFPQHQV MWLPSRQRPL VRKVAPGFQQ TSGSKEAVAS
LRRGHIQRLN LRYTQVSRQE LRDYASWNLS VNLYTVNAPW LFSLLWCAGV PSVTSDNSHA
LSQVPSPLWI MPPDEYCLMW VTADLVSFTL IVGIFVLQKW RLGGIRSYNP EQIMLSAAVR
RTSRDVSIMK EKLIFSEISD GVEVSDVLSV CSDNSYDTYA NSTATPVGPR GGGSHTKTLI
ERSGR
