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    LYSMD4 LysM domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 145748, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LYSMD4provided by HGNC
    Official Full Name
    LysM domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:26571
    See related
    Ensembl:ENSG00000183060 AllianceGenome:HGNC:26571
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to be located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in skin (RPKM 10.8), endometrium (RPKM 9.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LYSMD4 in Genome Data Viewer
    Location:
    15q26.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (99715697..99733444, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (97479959..97497213, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (100267606..100273649, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10160 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:100105511-100106486 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:100106487-100107460 Neighboring gene ribosomal protein L7 pseudogene 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:100119332-100119832 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:100119833-100120333 Neighboring gene myocyte enhancer factor 2A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10161 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:100169236-100169886 Neighboring gene MPRA-validated peak2449 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100266134-100266634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:100266635-100267135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6874 Neighboring gene MPRA-validated peak2450 silencer Neighboring gene uncharacterized LOC105371020 Neighboring gene RNA, 7SL, cytoplasmic 484, pseudogene Neighboring gene dynamin 1 pseudogene 46

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies. GENDEP Investigators, et al. Am J Psychiatry, 2013 Feb. PMID 23377640, Free PMC Article
    2. Genetics of coronary artery calcification among African Americans, a meta-analysis. Wojczynski MK, et al. BMC Med Genet, 2013 Jul 19. PMID 23870195, Free PMC Article
    3. Defining the proximal interaction networks of Arf GTPases reveals a mechanism for the regulation of PLD1 and PI4KB. Li FL, et al. EMBO J, 2022 Sep 1. PMID 35844135, Free PMC Article
    4. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512
    5. ER-export and ARFRP1/AP-1-dependent delivery of SARS-CoV-2 Envelope to lysosomes controls late stages of viral replication. Pearson GJ, et al. Sci Adv, 2024 Apr 5. PMID 38569033, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
    EBI GWAS Catalog
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ33008, MGC99501

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysM and putative peptidoglycan-binding domain-containing protein 4
    Names
    LysM, putative peptidoglycan-binding, domain containing 4

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001284417.2 → NP_001271346.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform b

      See identical proteins and their annotated locations for NP_001271346.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks two alternate exons in the coding region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (b) is shorter and has a distinct N-terminus, compared to isoform a. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AC022692, AK056718, AK290296, BC084545, KF459559
      Consensus CDS
      CCDS66877.1
      UniProtKB/Swiss-Prot
      A6NII6, A8K2N1, Q5XG99, Q96LY7
      Related
      ENSP00000506747.1, ENST00000684762.1
      Conserved Domains (1) summary
      smart00257
      Location:80 → 118
      LysM; Lysin motif

    2. NM_001284418.2 → NP_001271347.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform b

      See identical proteins and their annotated locations for NP_001271347.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks two alternate exons in the coding region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (b) is shorter and has a distinct N-terminus, compared to isoform a. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AC022692, BC084545, HY131530, KF459559
      Consensus CDS
      CCDS66877.1
      UniProtKB/Swiss-Prot
      A6NII6, A8K2N1, Q5XG99, Q96LY7
      Related
      ENSP00000386283.1, ENST00000409796.5
      Conserved Domains (1) summary
      smart00257
      Location:80 → 118
      LysM; Lysin motif

    3. NM_001284419.2 → NP_001271348.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC022692, AK056718, DA405564, DA594971
      Conserved Domains (1) summary
      COG1622
      Location:204 → 290
      CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]

    4. NM_001284420.1 → NP_001271349.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks three alternate exons in the coding region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (d) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC022692, AK056718, DA594971
      Consensus CDS
      CCDS73788.1
      UniProtKB/TrEMBL
      F6SJM1
      Related
      ENSP00000445357.2, ENST00000545021.2
      Conserved Domains (1) summary
      COG1622
      Location:147 → 233
      CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]

    5. NM_001284421.2 → NP_001271350.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform e

      See identical proteins and their annotated locations for NP_001271350.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, lacks an alternate exon in the coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (e) has a shorter N-terminus than isoform a. Variants 6 and 7 encoded the same isoform (e).
      Source sequence(s)
      AC022692, AK056718, CB989579
      Consensus CDS
      CCDS66876.1
      UniProtKB/TrEMBL
      A0A0A0MR78, B3KWE4
      Conserved Domains (1) summary
      COG1622
      Location:82 → 168
      CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]

    6. NM_001284422.2 → NP_001271351.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform e

      See identical proteins and their annotated locations for NP_001271351.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks an alternate exon in the coding region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (e) has a shorter N-terminus than isoform a. Variants 6 and 7 encoded the same isoform (e).
      Source sequence(s)
      AC022692, AK056718, BC041097, DA594971, DB044672
      Consensus CDS
      CCDS66876.1
      UniProtKB/TrEMBL
      A0A0A0MR78, B3KWE4
      Related
      ENSP00000333008.5, ENST00000332728.8
      Conserved Domains (1) summary
      COG1622
      Location:82 → 168
      CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]

    7. NM_152449.4 → NP_689662.2  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform a

      See identical proteins and their annotated locations for NP_689662.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC022692, AK056718, BC041097, KF459559
      Consensus CDS
      CCDS10381.1
      UniProtKB/Swiss-Prot
      Q5XG99
      Related
      ENSP00000342840.2, ENST00000344791.6
      Conserved Domains (1) summary
      COG1622
      Location:209 → 295
      CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      99715697..99733444 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521245.4 → XP_011519547.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X7

    2. XM_011521242.4 → XP_011519544.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X3

      Conserved Domains (1) summary
      smart00257
      Location:80 → 118
      LysM; Lysin motif

    3. XM_047432167.1 → XP_047288123.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X9

    4. XM_011521243.4 → XP_011519545.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X4

      Conserved Domains (1) summary
      smart00257
      Location:80 → 118
      LysM; Lysin motif

    5. XM_011521241.2 → XP_011519543.2  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X2

    6. XM_047432163.1 → XP_047288119.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A6NII6, A8K2N1, Q5XG99, Q96LY7

    7. XM_047432166.1 → XP_047288122.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X8

      UniProtKB/TrEMBL
      A0A0A0MR78, B3KWE4

    8. XM_047432164.1 → XP_047288120.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X5

    9. XM_017021930.3 → XP_016877419.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X10

      UniProtKB/Swiss-Prot
      Q5XG99
      Conserved Domains (1) summary
      COG1622
      Location:209 → 295
      CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]

    10. XM_047432165.1 → XP_047288121.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X6

    RNA

    1. XR_007064431.1 RNA Sequence

    2. XR_007064428.1 RNA Sequence

    3. XR_007064430.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      97479959..97497213 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377315.1 → XP_054233290.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X7

    2. XM_054377311.1 → XP_054233286.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X3

    3. XM_054377317.1 → XP_054233292.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X9

    4. XM_054377312.1 → XP_054233287.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X4

    5. XM_054377310.1 → XP_054233285.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X2

    6. XM_054377316.1 → XP_054233291.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X8

      UniProtKB/TrEMBL
      A0A0A0MR78, B3KWE4

    7. XM_054377313.1 → XP_054233288.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X5

    8. XM_054377318.1 → XP_054233293.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X10

    9. XM_054377314.1 → XP_054233289.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X6

    RNA

    1. XR_008488922.1 RNA Sequence

    2. XR_008488920.1 RNA Sequence

    3. XR_008488921.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5XG99.2 GenPept UniProtKB/Swiss-Prot:Q5XG99

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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