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LYSMD1 Gene

protein-coding   GIFtS: 42
GCID: GC01M151132

LysM, Putative Peptidoglycan-Binding, Domain Containing...

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
LysM, Putative Peptidoglycan-Binding, Domain Containing 11 2
RP11-68I18.52
SB1452
LysM And Putative Peptidoglycan-Binding Domain-Containing Protein 12

External Ids:    HGNC: 320701   Entrez Gene: 3886952   Ensembl: ENSG000001631557   UniProtKB: Q96S903   

Export aliases for LYSMD1 gene to outside databases

Previous GC identifers: GC01M147946 GC01M149398 GC01M122510


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for LYSMD1 Gene:
LYSMD1 (LysM, putative peptidoglycan-binding, domain containing 1) is a protein-coding gene. An important paralog of this gene is LYSMD2.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NC_018912.2  NT_004487.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the LYSMD1 gene promoter:
         MZF-1   Sox5   NRSF form 1   Sox9   NRSF form 2   GATA-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): LYSMD1 promoter sequence
   Search Chromatin IP Primers for LYSMD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LYSMD1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q21.3   Ensembl cytogenetic band:  1q21.3   HGNC cytogenetic band: 1q21.2

LYSMD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LYSMD1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M151132:  view genomic region     (about GC identifiers)

Start:
151,132,224 bp from pter      End:
151,138,424 bp from pter
Size:
6,201 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: LYSM1_HUMAN, Q96S90 (See protein sequence)
Recommended Name: LysM and putative peptidoglycan-binding domain-containing protein 1  
Size: 227 amino acids; 25003 Da
Sequence caution: Sequence=CAH10716.1; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for LYSMD1:
2DJP (3D)    
Secondary accessions: B4DQA1 Q69YX9
Alternative splicing: 2 isoforms:  Q96S90-1   Q96S90-2   

Explore the universe of human proteins at neXtProt for LYSMD1: NX_Q96S90

Explore proteomics data for LYSMD1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See LYSMD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001130015.1  NP_997716.1  

    ENSEMBL proteins: 
     ENSP00000357904   ENSP00000404059  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR018392 LysM_dom

    Graphical View of Domain Structure for InterPro Entry Q96S90

    ProtoNet protein and cluster: Q96S90

    1 Blocks protein domain: IPB002482 Peptidoglycan-binding LysM

    UniProtKB/Swiss-Prot: LYSM1_HUMAN, Q96S90
    Similarity: Contains 1 LysM repeat


    LYSMD1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LYSMD1
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    miRNA
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    hsa-mir-148a-3p (MIRT025999), hsa-mir-221-3p (MIRT024173), hsa-mir-148b-3p (MIRT019386)

    Block miRNA regulation of human, mouse, rat LYSMD1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LYSMD1 (see all 26):
    hsa-miR-148b* hsa-miR-148b hsa-miR-548v hsa-miR-29c hsa-miR-29a hsa-miR-221 hsa-miR-4267 hsa-miR-877*
    SwitchGear 3'UTR luciferase reporter plasmidLYSMD1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat LYSMD1

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol1
    mitochondrion1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LYSMD1
    Interactions:

        Search GeneGlobe Interaction Network for LYSMD1

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for LYSMD1 (ENSP000003579044) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PTGES3ENSP000002620334STRING: ENSP00000262033
    FLAD1ENSP000002921804STRING: ENSP00000292180
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016998cell wall macromolecule catabolic process IEA--

    LYSMD1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for LYSMD1 (LYSM1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for LYSMD1 gene (2 alternative transcripts): 
    NM_001136543.1  NM_212551.4  

    Unigene Cluster for LYSMD1:

    LysM, putative peptidoglycan-binding, domain containing 1
    Hs.591482  [show with all ESTs]
    Unigene Representative Sequence: NM_212551
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000368908(uc001ewy.3 uc010pcr.2) ENST00000440902
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate LYSMD1 (see all 26):
    hsa-miR-148b* hsa-miR-148b hsa-miR-548v hsa-miR-29c hsa-miR-29a hsa-miR-221 hsa-miR-4267 hsa-miR-877*
    SwitchGear 3'UTR luciferase reporter plasmidLYSMD1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat LYSMD1
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LYSMD1
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat LYSMD1
      QuantiFast Probe-based Assays in human, mouse, rat LYSMD1

    Additional mRNA sequence: 

    AK298706.1 AK298814.1 AL122088.1 AY037156.1 BC031649.1 BX647911.1 

    4 DOTS entries:

    DT.121409566  DT.70105220  DT.313060  DT.100759523 

    23 AceView cDNA sequences:

    BM464339 CD359960 AI658980 BC031649 BE348302 BU188407 AY037156 BI829491 
    BX355366 AL122088 NM_212551 BX647911 CN478585 AW615206 BQ879551 AI474548 
    BX361994 BF888368 BI058760 AI217830 AW015147 AI344968 BE139437 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    LYSMD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTATTGAGGA
    LYSMD1 Expression
    About this image

    LYSMD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LYSMD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.591482
        Custom PCR Arrays for LYSMD1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LYSMD1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for LYSMD1 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lysmd11 , 5 LysM, putative peptidoglycan-binding, domain containing more1, 5 85.4(n)1
    84.51(a)1
      3 (40.74 cM)5
    2177791  NM_153121.21  NP_694761.11 
     951340885 
    lizard
    (Anolis carolinensis)
    Reptilia LYSMD16
    LysM, putative peptidoglycan-binding, domain conta...
    53(a)
    1 ↔ 1
    GL343668.1(201606-213165)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia lysmd11 LysM, putative peptidoglycan-binding, domain containing more 57.44(n)
    56.41(a)
      100124927  NM_001102871.1  NP_001096341.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.143882 Transcribed sequence with weak similarity to protein more 71.37(n)    BI673103.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG122076
    --
    14(a)
    1 → many
    3R(10114794-10127998)


    ENSEMBL Gene Tree for LYSMD1 (if available)
    TreeFam Gene Tree for LYSMD1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LYSMD1 gene
    LYSMD22  
    1 SIMAP similar gene for LYSMD1 using alignment to 1 protein entry:     LYSM1_HUMAN:
    LYSMD2

    LYSMD1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for LYSMD1:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv2n68CNV Loss17160897
    nsv522840CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LYSMD1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for LYSMD1 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with LYSMD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    4. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    5. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (Sci. Signal. 2011)
    6. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    7. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    8. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 388695 HGNC: 32070 AceView: SB145 Ensembl:ENSG00000163155 euGenes: HUgn388695
    ECgene: LYSMD1 H-InvDB: LYSMD1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for LYSMD1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LYSMD1 gene:
    Search GeneIP for patents involving LYSMD1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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