OMD_HUMAN
ID OMD_HUMAN Reviewed; 421 AA.
AC Q99983; Q5TBF4;
DT 11-FEB-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 182.
DE RecName: Full=Osteomodulin;
DE AltName: Full=Keratan sulfate proteoglycan osteomodulin;
DE Short=KSPG osteomodulin;
DE AltName: Full=Osteoadherin;
DE Short=OSAD;
DE Flags: Precursor;
GN Name=OMD; Synonyms=SLRR2C; ORFNames=UNQ190/PRO216;
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].
RC TISSUE=Osteoblast;
RA Ohno I., Hashimoto J., Takaoka K., Ochi T., Okubo K., Matsubara K.;
RT "The cloning of a cDNA for novel genes expressed in human osteoblast.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Ohno I., Matsubara K., Okubo K.;
RT "Human osteomodulin gene: intron-exon junctions and chromosomal
RT localization.";
RL Submitted (DEC-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15164053; DOI=10.1038/nature02465;
RA Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L.,
RA Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R.,
RA Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S.,
RA Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K.,
RA Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y.,
RA Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C.,
RA Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E.,
RA Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M.,
RA Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J.,
RA Frankish A., Frankland J.A., French L., Fricker D.G., Garner P.,
RA Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S.,
RA Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E.,
RA Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D.,
RA Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E.,
RA Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K.,
RA Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S.,
RA Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J.,
RA Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E.,
RA McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V.,
RA Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S.,
RA Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K.,
RA Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J.,
RA Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M.,
RA West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L.,
RA Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M.,
RA Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J.,
RA Dunham I.;
RT "DNA sequence and analysis of human chromosome 9.";
RL Nature 429:369-374(2004).
RN [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
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 [7]
RP SULFATION AT TYR-22; TYR-25; TYR-31; TYR-39; TYR-51; TYR-58; TYR-77;
RP TYR-416 AND TYR-417, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=14551184; DOI=10.1074/jbc.m308689200;
RA Onnerfjord P., Heathfield T.F., Heinegaard D.;
RT "Identification of tyrosine sulfation in extracellular leucine-rich repeat
RT proteins using mass spectrometry.";
RL J. Biol. Chem. 279:26-33(2004).
CC -!- FUNCTION: May be implicated in biomineralization processes. Has a
CC function in binding of osteoblasts via the alpha(V)beta(3)-integrin (By
CC similarity). {ECO:0000250}.
CC -!- SUBUNIT: Binds the alpha(V)beta(3)-integrin. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular
CC matrix {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Bone specific.
CC -!- PTM: Binds keratan sulfate chains. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the small leucine-rich proteoglycan (SLRP)
CC family. SLRP class II subfamily. {ECO:0000305}.
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DR EMBL; AB000114; BAA19055.1; -; mRNA.
DR EMBL; AB009589; BAA23982.1; -; Genomic_DNA.
DR EMBL; AY358872; AAQ89231.1; -; mRNA.
DR EMBL; AL137848; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471089; EAW62821.1; -; Genomic_DNA.
DR EMBL; BC046356; AAH46356.1; -; mRNA.
DR CCDS; CCDS6696.1; -.
DR RefSeq; NP_005005.1; NM_005014.2.
DR PDB; 5YQ5; X-ray; 2.17 A; A/B/C/D=21-421.
DR PDBsum; 5YQ5; -.
DR AlphaFoldDB; Q99983; -.
DR SMR; Q99983; -.
DR BioGRID; 111011; 5.
DR IntAct; Q99983; 5.
DR STRING; 9606.ENSP00000364700; -.
DR GlyConnect; 1588; 2 N-Linked glycans (1 site).
DR GlyGen; Q99983; 5 sites, 2 N-linked glycans (1 site).
DR iPTMnet; Q99983; -.
DR PhosphoSitePlus; Q99983; -.
DR BioMuta; OMD; -.
DR DMDM; 20138850; -.
DR jPOST; Q99983; -.
DR MassIVE; Q99983; -.
DR PaxDb; Q99983; -.
DR PeptideAtlas; Q99983; -.
DR PRIDE; Q99983; -.
DR ProteomicsDB; 78561; -.
DR Antibodypedia; 28259; 206 antibodies from 27 providers.
DR DNASU; 4958; -.
DR Ensembl; ENST00000375550.5; ENSP00000364700.4; ENSG00000127083.8.
DR GeneID; 4958; -.
DR KEGG; hsa:4958; -.
DR MANE-Select; ENST00000375550.5; ENSP00000364700.4; NM_005014.3; NP_005005.1.
DR UCSC; uc004asd.5; human.
DR CTD; 4958; -.
DR DisGeNET; 4958; -.
DR GeneCards; OMD; -.
DR HGNC; HGNC:8134; OMD.
DR HPA; ENSG00000127083; Low tissue specificity.
DR MIM; 618926; gene.
DR neXtProt; NX_Q99983; -.
DR OpenTargets; ENSG00000127083; -.
DR PharmGKB; PA31921; -.
DR VEuPathDB; HostDB:ENSG00000127083; -.
DR eggNOG; KOG0619; Eukaryota.
DR GeneTree; ENSGT00940000160986; -.
DR HOGENOM; CLU_000288_186_4_1; -.
DR InParanoid; Q99983; -.
DR OMA; YNIFNLS; -.
DR OrthoDB; 826997at2759; -.
DR PhylomeDB; Q99983; -.
DR TreeFam; TF334562; -.
DR PathwayCommons; Q99983; -.
DR Reactome; R-HSA-2022854; Keratan sulfate biosynthesis.
DR Reactome; R-HSA-2022857; Keratan sulfate degradation.
DR Reactome; R-HSA-3656225; Defective CHST6 causes MCDC1.
DR Reactome; R-HSA-3656243; Defective ST3GAL3 causes MCT12 and EIEE15.
DR Reactome; R-HSA-3656244; Defective B4GALT1 causes B4GALT1-CDG (CDG-2d).
DR SignaLink; Q99983; -.
DR SIGNOR; Q99983; -.
DR BioGRID-ORCS; 4958; 15 hits in 1034 CRISPR screens.
DR ChiTaRS; OMD; human.
DR GeneWiki; OMD_(gene); -.
DR GenomeRNAi; 4958; -.
DR Pharos; Q99983; Tbio.
DR PRO; PR:Q99983; -.
DR Proteomes; UP000005640; Chromosome 9.
DR RNAct; Q99983; protein.
DR Bgee; ENSG00000127083; Expressed in periodontal ligament and 144 other tissues.
DR Genevisible; Q99983; HS.
DR GO; GO:0062023; C:collagen-containing extracellular matrix; IEA:InterPro.
DR GO; GO:0070062; C:extracellular exosome; HDA:UniProtKB.
DR GO; GO:0005576; C:extracellular region; TAS:Reactome.
DR GO; GO:0005615; C:extracellular space; IBA:GO_Central.
DR GO; GO:0005796; C:Golgi lumen; TAS:Reactome.
DR GO; GO:0043202; C:lysosomal lumen; TAS:Reactome.
DR GO; GO:0007155; P:cell adhesion; IEA:UniProtKB-KW.
DR GO; GO:0030500; P:regulation of bone mineralization; IEA:InterPro.
DR Gene3D; 3.80.10.10; -; 3.
DR InterPro; IPR001611; Leu-rich_rpt.
DR InterPro; IPR003591; Leu-rich_rpt_typical-subtyp.
DR InterPro; IPR032675; LRR_dom_sf.
DR InterPro; IPR000372; LRRNT.
DR InterPro; IPR030705; Osteomodulin.
DR PANTHER; PTHR45712:SF3; PTHR45712:SF3; 1.
DR Pfam; PF13855; LRR_8; 3.
DR SMART; SM00369; LRR_TYP; 7.
DR SMART; SM00013; LRRNT; 1.
DR PROSITE; PS51450; LRR; 8.
PE 1: Evidence at protein level;
KW 3D-structure; Cell adhesion; Disulfide bond; Extracellular matrix;
KW Glycoprotein; Leucine-rich repeat; Proteoglycan; Reference proteome;
KW Repeat; Secreted; Signal; Sulfation.
FT SIGNAL 1..20
FT /evidence="ECO:0000255"
FT CHAIN 21..421
FT /note="Osteomodulin"
FT /id="PRO_0000032754"
FT DOMAIN 53..91
FT /note="LRRNT"
FT REPEAT 92..113
FT /note="LRR 1"
FT REPEAT 116..129
FT /note="LRR 2"
FT REPEAT 142..164
FT /note="LRR 3"
FT REPEAT 165..184
FT /note="LRR 4"
FT REPEAT 187..210
FT /note="LRR 5"
FT REPEAT 213..233
FT /note="LRR 6"
FT REPEAT 234..255
FT /note="LRR 7"
FT REPEAT 258..280
FT /note="LRR 8"
FT REPEAT 281..294
FT /note="LRR 9"
FT REPEAT 301..321
FT /note="LRR 10"
FT REPEAT 331..353
FT /note="LRR 11"
FT REGION 382..421
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 396..421
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 22
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000305|PubMed:14551184"
FT MOD_RES 25
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000305|PubMed:14551184"
FT MOD_RES 31
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000305|PubMed:14551184"
FT MOD_RES 39
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000269|PubMed:14551184"
FT MOD_RES 51
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000305|PubMed:14551184"
FT MOD_RES 58
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000305|PubMed:14551184"
FT MOD_RES 77
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000305|PubMed:14551184"
FT MOD_RES 416
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000269|PubMed:14551184"
FT MOD_RES 417
FT /note="Sulfotyrosine"
FT /evidence="ECO:0000269|PubMed:14551184"
FT CARBOHYD 113
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 121
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 187
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 242
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 316
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 321..353
FT /evidence="ECO:0000250"
FT VARIANT 200
FT /note="D -> G (in dbSNP:rs34069871)"
FT /id="VAR_052014"
FT VARIANT 212
FT /note="E -> G (in dbSNP:rs34413259)"
FT /id="VAR_052015"
FT VARIANT 221
FT /note="S -> N (in dbSNP:rs34860658)"
FT /id="VAR_052016"
FT VARIANT 282
FT /note="I -> T (in dbSNP:rs35779901)"
FT /id="VAR_052017"
FT VARIANT 353
FT /note="C -> W (in dbSNP:rs34059114)"
FT /id="VAR_052018"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:5YQ5"
FT HELIX 108..111
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 119..121
FT /evidence="ECO:0007829|PDB:5YQ5"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:5YQ5"
FT TURN 134..139
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:5YQ5"
FT TURN 179..184
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 190..192
FT /evidence="ECO:0007829|PDB:5YQ5"
FT HELIX 200..203
FT /evidence="ECO:0007829|PDB:5YQ5"
FT TURN 204..210
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 216..218
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:5YQ5"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 261..263
FT /evidence="ECO:0007829|PDB:5YQ5"
FT TURN 274..277
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 284..286
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 304..306
FT /evidence="ECO:0007829|PDB:5YQ5"
FT HELIX 317..320
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 334..336
FT /evidence="ECO:0007829|PDB:5YQ5"
FT HELIX 350..353
FT /evidence="ECO:0007829|PDB:5YQ5"
FT STRAND 359..361
FT /evidence="ECO:0007829|PDB:5YQ5"
SQ SEQUENCE 421 AA; 49492 MW; CED47B2BC33BB872 CRC64;
MGFLSPIYVI FFFFGVKVHC QYETYQWDED YDQEPDDDYQ TGFPFRQNVD YGVPFHQYTL
GCVSECFCPT NFPSSMYCDN RKLKTIPNIP MHIQQLYLQF NEIEAVTANS FINATHLKEI
NLSHNKIKSQ KIDYGVFAKL PNLLQLHLEH NNLEEFPFPL PKSLERLLLG YNEISKLQTN
AMDGLVNLTM LDLCYNYLHD SLLKDKIFAK MEKLMQLNLC SNRLESMPPG LPSSLMYLSL
ENNSISSIPE KYFDKLPKLH TLRMSHNKLQ DIPYNIFNLP NIVELSVGHN KLKQAFYIPR
NLEHLYLQNN EIEKMNLTVM CPSIDPLHYH HLTYIRVDQN KLKEPISSYI FFCFPHIHTI
YYGEQRSTNG QTIQLKTQVF RRFPDDDDES EDHDDPDNAH ESPEQEGAEG HFDLHYYENQ
E
