TRDMT_HUMAN
ID TRDMT_HUMAN Reviewed; 391 AA.
AC O14717; B0YJ02; B0YJ03; B0YJ07; B0YJ08; O43669; Q86WW6;
DT 26-SEP-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 181.
DE RecName: Full=tRNA (cytosine(38)-C(5))-methyltransferase;
DE EC=2.1.1.204 {ECO:0000269|PubMed:16424344};
DE AltName: Full=DNA (cytosine-5)-methyltransferase-like protein 2 {ECO:0000303|PubMed:16424344};
DE Short=Dnmt2 {ECO:0000303|PubMed:16424344};
DE AltName: Full=DNA methyltransferase homolog HsaIIP;
DE Short=DNA MTase homolog HsaIIP;
DE Short=M.HsaIIP;
DE AltName: Full=PuMet;
GN Name=TRDMT1; Synonyms=DNMT2 {ECO:0000303|PubMed:16424344};
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 A).
RX PubMed=9425235; DOI=10.1093/hmg/7.2.279;
RA Yoder J.A., Bestor T.H.;
RT "A candidate mammalian DNA methyltransferase related to pmt1p of fission
RT yeast.";
RL Hum. Mol. Genet. 7:279-284(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A).
RX PubMed=9599025; DOI=10.1016/s0014-5793(98)00362-7;
RA Van den Wyngaert I., Sprengel J., Kass S.U., Luyten W.H.M.L.;
RT "Cloning and analysis of a novel human putative DNA methyltransferase.";
RL FEBS Lett. 426:283-289(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A).
RC TISSUE=Heart;
RX PubMed=9592134; DOI=10.1093/nar/26.11.2536;
RA Okano M., Xie S., Li E.;
RT "Dnmt2 is not required for de novo and maintenance methylation of viral DNA
RT in embryonic stem cells.";
RL Nucleic Acids Res. 26:2536-2540(1998).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RG NHLBI resequencing and genotyping service (RS&G);
RL Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15164054; DOI=10.1038/nature02462;
RA Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L.,
RA Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K.,
RA Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L.,
RA Taylor A., Battles J., Bird C.P., Ainscough R., Almeida J.P.,
RA Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J.,
RA Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y.,
RA Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P.,
RA Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N.,
RA Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A.,
RA Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C.,
RA Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D.,
RA Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C.,
RA Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K.,
RA Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A.,
RA Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S.,
RA McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S.,
RA Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V.,
RA Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A.,
RA Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M.,
RA Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A.,
RA Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P.,
RA Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y.,
RA Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D.,
RA Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.;
RT "The DNA sequence and comparative analysis of human chromosome 10.";
RL Nature 429:375-381(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A), AND VARIANT TYR-101.
RC TISSUE=Uterus;
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 [8]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 19-179 (ISOFORMS A; B; C; D; E AND F).
RC TISSUE=Peripheral blood leukocyte;
RX PubMed=11551826; DOI=10.1016/s1357-2725(01)00074-7;
RA Franchina M., Hooper J., Kay P.H.;
RT "Five novel alternatively spliced transcripts of DNA (cytosine-5)
RT methyltransferase 2 in human peripheral blood leukocytes.";
RL Int. J. Biochem. Cell Biol. 33:1104-1115(2001).
RN [9]
RP FUNCTION, SUBCELLULAR LOCATION, AND CATALYTIC ACTIVITY.
RX PubMed=16424344; DOI=10.1126/science.1120976;
RA Goll M.G., Kirpekar F., Maggert K.A., Yoder J.A., Hsieh C.L., Zhang X.,
RA Golic K.G., Jacobsen S.E., Bestor T.H.;
RT "Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2.";
RL Science 311:395-398(2006).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE.
RX PubMed=11139614; DOI=10.1093/nar/29.2.439;
RA Dong A., Yoder J.A., Zhang X., Zhou L., Bestor T.H., Cheng X.;
RT "Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that
RT displays denaturant-resistant binding to DNA.";
RL Nucleic Acids Res. 29:439-448(2001).
CC -!- FUNCTION: Specifically methylates cytosine 38 in the anticodon loop of
CC tRNA(Asp). {ECO:0000269|PubMed:16424344}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(38) in tRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(38) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42956, Rhea:RHEA-COMP:10299, Rhea:RHEA-COMP:10300,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.204;
CC Evidence={ECO:0000269|PubMed:16424344};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:42957;
CC Evidence={ECO:0000269|PubMed:16424344};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16424344}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=6;
CC Comment=Additional isoforms seem to exist.;
CC Name=A;
CC IsoId=O14717-1; Sequence=Displayed;
CC Name=B;
CC IsoId=O14717-2; Sequence=VSP_005628;
CC Name=C;
CC IsoId=O14717-3; Sequence=VSP_005629;
CC Name=D;
CC IsoId=O14717-4; Sequence=VSP_005630, VSP_005631;
CC Name=E;
CC IsoId=O14717-5; Sequence=VSP_005632, VSP_005633;
CC Name=F;
CC IsoId=O14717-6; Sequence=VSP_005634, VSP_005635;
CC -!- TISSUE SPECIFICITY: Ubiquitous. Higher expression in testis, ovary and
CC thymus and at much lower levels in spleen, prostate, colon, small
CC intestine, and peripheral blood leukocytes.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. C5-methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01016}.
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DR EMBL; AF012128; AAC51939.1; -; mRNA.
DR EMBL; AJ223333; CAA11272.1; -; mRNA.
DR EMBL; AF045888; AAC39764.1; -; mRNA.
DR EMBL; EF444974; ACA05980.1; -; Genomic_DNA.
DR EMBL; EF444974; ACA05984.1; -; Genomic_DNA.
DR EMBL; EF444974; ACA05985.1; -; Genomic_DNA.
DR EMBL; EF444974; ACA05986.1; -; Genomic_DNA.
DR EMBL; AC067747; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AL133415; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471072; EAW86218.1; -; Genomic_DNA.
DR EMBL; CH471072; EAW86219.1; -; Genomic_DNA.
DR EMBL; BC047733; AAH47733.1; -; mRNA.
DR EMBL; AF329940; AAK68034.1; -; mRNA.
DR EMBL; AF329941; AAK68035.1; -; mRNA.
DR EMBL; AF329942; AAK68036.1; -; mRNA.
DR EMBL; AF329943; AAK68037.1; -; mRNA.
DR EMBL; AF329944; AAK68033.1; -; mRNA.
DR CCDS; CCDS7114.1; -. [O14717-1]
DR RefSeq; NP_001307935.1; NM_001321006.1.
DR RefSeq; NP_001307936.1; NM_001321007.1.
DR RefSeq; NP_004403.1; NM_004412.6. [O14717-1]
DR RefSeq; XP_005252432.1; XM_005252375.4. [O14717-3]
DR PDB; 1G55; X-ray; 1.80 A; A=2-391.
DR PDBsum; 1G55; -.
DR AlphaFoldDB; O14717; -.
DR SMR; O14717; -.
DR BioGRID; 108124; 20.
DR IntAct; O14717; 15.
DR STRING; 9606.ENSP00000367030; -.
DR ChEMBL; CHEMBL4523124; -.
DR DrugBank; DB09462; Glycerin.
DR DrugBank; DB00738; Pentamidine.
DR DrugBank; DB01752; S-adenosyl-L-homocysteine.
DR iPTMnet; O14717; -.
DR PhosphoSitePlus; O14717; -.
DR BioMuta; TRDMT1; -.
DR EPD; O14717; -.
DR MassIVE; O14717; -.
DR MaxQB; O14717; -.
DR PaxDb; O14717; -.
DR PeptideAtlas; O14717; -.
DR PRIDE; O14717; -.
DR ProteomicsDB; 48175; -. [O14717-1]
DR ProteomicsDB; 48176; -. [O14717-2]
DR ProteomicsDB; 48177; -. [O14717-3]
DR ProteomicsDB; 48178; -. [O14717-4]
DR ProteomicsDB; 48179; -. [O14717-5]
DR ProteomicsDB; 48180; -. [O14717-6]
DR Antibodypedia; 4005; 470 antibodies from 36 providers.
DR DNASU; 1787; -.
DR Ensembl; ENST00000377799.8; ENSP00000367030.3; ENSG00000107614.22. [O14717-1]
DR Ensembl; ENST00000495022.5; ENSP00000417594.1; ENSG00000107614.22. [O14717-4]
DR GeneID; 1787; -.
DR KEGG; hsa:1787; -.
DR MANE-Select; ENST00000377799.8; ENSP00000367030.3; NM_004412.7; NP_004403.1.
DR UCSC; uc057sar.1; human. [O14717-1]
DR CTD; 1787; -.
DR DisGeNET; 1787; -.
DR GeneCards; TRDMT1; -.
DR HGNC; HGNC:2977; TRDMT1.
DR HPA; ENSG00000107614; Low tissue specificity.
DR MIM; 602478; gene.
DR neXtProt; NX_O14717; -.
DR OpenTargets; ENSG00000107614; -.
DR PharmGKB; PA162406922; -.
DR VEuPathDB; HostDB:ENSG00000107614; -.
DR eggNOG; KOG0919; Eukaryota.
DR GeneTree; ENSGT00390000016416; -.
DR HOGENOM; CLU_049101_0_0_1; -.
DR InParanoid; O14717; -.
DR OMA; VMDIIHP; -.
DR PhylomeDB; O14717; -.
DR TreeFam; TF300024; -.
DR BioCyc; MetaCyc:HS03011-MON; -.
DR BRENDA; 2.1.1.202; 2681.
DR BRENDA; 2.1.1.204; 2681.
DR PathwayCommons; O14717; -.
DR Reactome; R-HSA-6782315; tRNA modification in the nucleus and cytosol.
DR SignaLink; O14717; -.
DR BioGRID-ORCS; 1787; 11 hits in 1082 CRISPR screens.
DR ChiTaRS; TRDMT1; human.
DR EvolutionaryTrace; O14717; -.
DR GeneWiki; TRDMT1; -.
DR GenomeRNAi; 1787; -.
DR Pharos; O14717; Tbio.
DR PRO; PR:O14717; -.
DR Proteomes; UP000005640; Chromosome 10.
DR RNAct; O14717; protein.
DR Bgee; ENSG00000107614; Expressed in ventricular zone and 129 other tissues.
DR ExpressionAtlas; O14717; baseline and differential.
DR Genevisible; O14717; HS.
DR GO; GO:0005737; C:cytoplasm; IDA:MGI.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; EXP:Reactome.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IDA:MGI.
DR GO; GO:0001975; P:response to amphetamine; IEA:Ensembl.
DR GO; GO:0002946; P:tRNA C5-cytosine methylation; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IDA:MGI.
DR GO; GO:0006400; P:tRNA modification; TAS:Reactome.
DR GO; GO:0036416; P:tRNA stabilization; ISS:UniProtKB.
DR Gene3D; 3.40.50.150; -; 1.
DR IDEAL; IID00004; -.
DR InterPro; IPR001525; C5_MeTfrase.
DR InterPro; IPR031303; C5_meth_CS.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF00145; DNA_methylase; 1.
DR PRINTS; PR00105; C5METTRFRASE.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00675; dcm; 1.
DR PROSITE; PS00095; C5_MTASE_2; 1.
DR PROSITE; PS51679; SAM_MT_C5; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cytoplasm; Methyltransferase;
KW Reference proteome; RNA-binding; S-adenosyl-L-methionine; Transferase;
KW tRNA processing.
FT CHAIN 1..391
FT /note="tRNA (cytosine(38)-C(5))-methyltransferase"
FT /id="PRO_0000088040"
FT DOMAIN 4..391
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT ACT_SITE 79
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT BINDING 13..15
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:11139614,
FT ECO:0007744|PDB:1G55"
FT BINDING 34
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:11139614,
FT ECO:0007744|PDB:1G55"
FT BINDING 57..58
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:11139614,
FT ECO:0007744|PDB:1G55"
FT BINDING 76
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:11139614,
FT ECO:0007744|PDB:1G55"
FT BINDING 376
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:11139614,
FT ECO:0007744|PDB:1G55"
FT VAR_SEQ 59..107
FT /note="GITLEEFDRLSFDMILMSPPCQPFTRIGRQGDMTDSRTNSFLHILDILP ->
FT RPLDTNNRKLWLSVPRVYIISNLSWHSKFKATIFSYCKASVRAITLSSP (in
FT isoform F)"
FT /evidence="ECO:0000303|PubMed:11551826"
FT /id="VSP_005634"
FT VAR_SEQ 59..71
FT /note="GITLEEFDRLSFD -> ITKITKVYSFGKC (in isoform E)"
FT /evidence="ECO:0000303|PubMed:11551826"
FT /id="VSP_005632"
FT VAR_SEQ 59..63
FT /note="GITLE -> DWPAG (in isoform D)"
FT /evidence="ECO:0000303|PubMed:11551826"
FT /id="VSP_005630"
FT VAR_SEQ 64..391
FT /note="Missing (in isoform D)"
FT /evidence="ECO:0000303|PubMed:11551826"
FT /id="VSP_005631"
FT VAR_SEQ 72..391
FT /note="Missing (in isoform E)"
FT /evidence="ECO:0000303|PubMed:11551826"
FT /id="VSP_005633"
FT VAR_SEQ 84..129
FT /note="Missing (in isoform C)"
FT /evidence="ECO:0000303|PubMed:11551826"
FT /id="VSP_005629"
FT VAR_SEQ 84..107
FT /note="Missing (in isoform B)"
FT /evidence="ECO:0000303|PubMed:11551826"
FT /id="VSP_005628"
FT VAR_SEQ 108..391
FT /note="Missing (in isoform F)"
FT /evidence="ECO:0000303|PubMed:11551826"
FT /id="VSP_005635"
FT VARIANT 101
FT /note="H -> Y (in dbSNP:rs11254413)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_051961"
FT CONFLICT 148
FT /note="L -> I (in Ref. 3; AAC39764)"
FT /evidence="ECO:0000305"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 15..23
FT /evidence="ECO:0007829|PDB:1G55"
FT STRAND 26..33
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 37..46
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 57..59
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 62..68
FT /evidence="ECO:0007829|PDB:1G55"
FT STRAND 71..75
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 98..105
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 106..108
FT /evidence="ECO:0007829|PDB:1G55"
FT STRAND 114..121
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 128..139
FT /evidence="ECO:0007829|PDB:1G55"
FT STRAND 142..149
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 151..154
FT /evidence="ECO:0007829|PDB:1G55"
FT STRAND 162..172
FT /evidence="ECO:0007829|PDB:1G55"
FT STRAND 182..185
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 253..256
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 263..266
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 270..276
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 277..279
FT /evidence="ECO:0007829|PDB:1G55"
FT TURN 295..299
FT /evidence="ECO:0007829|PDB:1G55"
FT STRAND 307..309
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 316..321
FT /evidence="ECO:0007829|PDB:1G55"
FT TURN 322..325
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 328..336
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 345..351
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 366..375
FT /evidence="ECO:0007829|PDB:1G55"
FT HELIX 379..390
FT /evidence="ECO:0007829|PDB:1G55"
SQ SEQUENCE 391 AA; 44597 MW; BCA549E4EB2E6950 CRC64;
MEPLRVLELY SGVGGMHHAL RESCIPAQVV AAIDVNTVAN EVYKYNFPHT QLLAKTIEGI
TLEEFDRLSF DMILMSPPCQ PFTRIGRQGD MTDSRTNSFL HILDILPRLQ KLPKYILLEN
VKGFEVSSTR DLLIQTIENC GFQYQEFLLS PTSLGIPNSR LRYFLIAKLQ SEPLPFQAPG
QVLMEFPKIE SVHPQKYAMD VENKIQEKNV EPNISFDGSI QCSGKDAILF KLETAEEIHR
KNQQDSDLSV KMLKDFLEDD TDVNQYLLPP KSLLRYALLL DIVQPTCRRS VCFTKGYGSY
IEGTGSVLQT AEDVQVENIY KSLTNLSQEE QITKLLILKL RYFTPKEIAN LLGFPPEFGF
PEKITVKQRY RLLGNSLNVH VVAKLIKILY E
