LYSM4_HUMAN
ID LYSM4_HUMAN Reviewed; 296 AA.
AC Q5XG99; A6NII6; A8K2N1; Q96LY7;
DT 05-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 13-NOV-2007, sequence version 2.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=LysM and putative peptidoglycan-binding domain-containing protein 4;
GN Name=LYSMD4;
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 GLY-180.
RC TISSUE=Thymus, and Tongue;
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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16572171; DOI=10.1038/nature04601;
RA Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K.,
RA Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K.,
RA FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N.,
RA Abouelleil A., Arachchi H.M., Baradarani L., Birditt B., Bloom S.,
RA Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K.,
RA DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J.,
RA Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E.,
RA Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B.,
RA Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R.,
RA O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B.,
RA Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S.,
RA Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.;
RT "Analysis of the DNA sequence and duplication history of human chromosome
RT 15.";
RL Nature 440:671-675(2006).
RN [3]
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 (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), AND VARIANTS
RP VAL-157; VAL-161 AND GLY-180.
RC TISSUE=Renal cell carcinoma;
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 -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q5XG99-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q5XG99-2; Sequence=VSP_039883;
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB71528.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AK057570; BAB71528.1; ALT_INIT; mRNA.
DR EMBL; AK290296; BAF82985.1; -; mRNA.
DR EMBL; AC022692; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471101; EAX02254.1; -; Genomic_DNA.
DR EMBL; CH471101; EAX02255.1; -; Genomic_DNA.
DR EMBL; BC084545; AAH84545.1; -; mRNA.
DR EMBL; BC041097; AAH41097.2; -; mRNA.
DR CCDS; CCDS10381.1; -. [Q5XG99-2]
DR CCDS; CCDS66877.1; -. [Q5XG99-1]
DR RefSeq; NP_001271346.1; NM_001284417.1. [Q5XG99-1]
DR RefSeq; NP_001271347.1; NM_001284418.1. [Q5XG99-1]
DR RefSeq; NP_001271351.1; NM_001284422.1.
DR RefSeq; NP_689662.2; NM_152449.3. [Q5XG99-2]
DR RefSeq; XP_016877415.1; XM_017021926.1. [Q5XG99-1]
DR RefSeq; XP_016877419.1; XM_017021930.1. [Q5XG99-2]
DR AlphaFoldDB; Q5XG99; -.
DR BioGRID; 126931; 5.
DR STRING; 9606.ENSP00000342840; -.
DR GlyGen; Q5XG99; 1 site.
DR iPTMnet; Q5XG99; -.
DR PhosphoSitePlus; Q5XG99; -.
DR BioMuta; LYSMD4; -.
DR DMDM; 160332305; -.
DR MassIVE; Q5XG99; -.
DR MaxQB; Q5XG99; -.
DR PaxDb; Q5XG99; -.
DR PeptideAtlas; Q5XG99; -.
DR PRIDE; Q5XG99; -.
DR ProteomicsDB; 65824; -. [Q5XG99-1]
DR ProteomicsDB; 65825; -. [Q5XG99-2]
DR Antibodypedia; 29207; 99 antibodies from 16 providers.
DR DNASU; 145748; -.
DR Ensembl; ENST00000344791.6; ENSP00000342840.2; ENSG00000183060.16. [Q5XG99-2]
DR Ensembl; ENST00000409796.5; ENSP00000386283.1; ENSG00000183060.16. [Q5XG99-1]
DR Ensembl; ENST00000684762.1; ENSP00000506747.1; ENSG00000183060.16. [Q5XG99-1]
DR GeneID; 145748; -.
DR KEGG; hsa:145748; -.
DR MANE-Select; ENST00000684762.1; ENSP00000506747.1; NM_001284417.2; NP_001271346.1.
DR UCSC; uc002bvk.5; human. [Q5XG99-1]
DR CTD; 145748; -.
DR DisGeNET; 145748; -.
DR GeneCards; LYSMD4; -.
DR HGNC; HGNC:26571; LYSMD4.
DR HPA; ENSG00000183060; Low tissue specificity.
DR neXtProt; NX_Q5XG99; -.
DR OpenTargets; ENSG00000183060; -.
DR PharmGKB; PA142671496; -.
DR VEuPathDB; HostDB:ENSG00000183060; -.
DR eggNOG; KOG2850; Eukaryota.
DR GeneTree; ENSGT00940000160583; -.
DR HOGENOM; CLU_070676_1_0_1; -.
DR InParanoid; Q5XG99; -.
DR OMA; MWRGENG; -.
DR OrthoDB; 1180847at2759; -.
DR PhylomeDB; Q5XG99; -.
DR TreeFam; TF326271; -.
DR PathwayCommons; Q5XG99; -.
DR BioGRID-ORCS; 145748; 6 hits in 1077 CRISPR screens.
DR ChiTaRS; LYSMD4; human.
DR GenomeRNAi; 145748; -.
DR Pharos; Q5XG99; Tdark.
DR PRO; PR:Q5XG99; -.
DR Proteomes; UP000005640; Chromosome 15.
DR RNAct; Q5XG99; protein.
DR Bgee; ENSG00000183060; Expressed in apex of heart and 129 other tissues.
DR ExpressionAtlas; Q5XG99; baseline and differential.
DR Genevisible; Q5XG99; HS.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR CDD; cd00118; LysM; 1.
DR Gene3D; 3.10.350.10; -; 1.
DR InterPro; IPR045030; LYSM1-4.
DR InterPro; IPR018392; LysM_dom.
DR InterPro; IPR036779; LysM_dom_sf.
DR PANTHER; PTHR20932; PTHR20932; 1.
DR SMART; SM00257; LysM; 1.
DR PROSITE; PS51782; LYSM; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Glycoprotein; Membrane; Reference proteome;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1..296
FT /note="LysM and putative peptidoglycan-binding domain-
FT containing protein 4"
FT /id="PRO_0000248013"
FT TOPO_DOM 1..217
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 218..238
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 239..296
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 74..118
FT /note="LysM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT REGION 29..67
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 35..49
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CARBOHYD 30
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT VAR_SEQ 1..93
FT /note="MRHEELLTKTFQGPAVVCGTPTSHVYMFKNGSGDSGDSSEEESHRVVLRPRG
FT KERHKSGVHQPPQAGAGDVVLLQRELAQEDSLNKLALQYGC -> MAVGTRGTLLKKSL
FT TVWFCGPGARSATRAVSTSLPRREQVTWCCCSGSWPRRTASTSWRCSMAANTFYFRPNG
FT AGDTRQNLIPDFYAFRVINNG (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_039883"
FT VARIANT 157
FT /note="A -> V (in dbSNP:rs8041089)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_027200"
FT VARIANT 161
FT /note="A -> V (in dbSNP:rs8041078)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_027201"
FT VARIANT 180
FT /note="A -> G (in dbSNP:rs2061007)"
FT /evidence="ECO:0000269|PubMed:14702039,
FT ECO:0000269|PubMed:15489334"
FT /id="VAR_027202"
FT CONFLICT 195
FT /note="T -> S (in Ref. 4; AAH41097)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 296 AA; 32066 MW; 9D7A1625A6445F18 CRC64;
MRHEELLTKT FQGPAVVCGT PTSHVYMFKN GSGDSGDSSE EESHRVVLRP RGKERHKSGV
HQPPQAGAGD VVLLQRELAQ EDSLNKLALQ YGCKVADIKK VNNFIREQDL YALKSVKIPV
RNHGILMETH KELKPLLSPS SETTVTVELP EADRAGAGTG AQAGQLMGFF KGIDQDIERA
VQSEIFLHES YCMDTSHQPL LPAPPKTPMD GADCGIQWWN AVFIMLLIGI VLPVFYLVYF
KIQASGETPN SLNTTVIPNG SMAMGTVPGQ APRLAVAVPA VTSADSQFSQ TTQAGS
