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

Gene ID: 145748, updated on 5-Mar-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 integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in skin (RPKM 10.8), endometrium (RPKM 9.0) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (99715697..99733444, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (97479959..97497213, complement)
105.20220307 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. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Aregger M, et al. Nat Metab, 2020 Jun. PMID 32694731, Free PMC Article

See all (10) 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)

Genotypes

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_2023_10

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

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