U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 145748, updated on 22-Sep-2022

Summary

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See LYSMD4 in Genome Data Viewer
Location:
15q26.3
Exon count:
7
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (99715697..99733444, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (97491166..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 ribosomal protein L7 pseudogene 5 Neighboring gene myocyte enhancer factor 2A Neighboring gene uncharacterized LOC105371020 Neighboring gene RNA, 7SL, cytoplasmic 484, pseudogene Neighboring gene dynamin 1 pseudogene 46

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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

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

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001284417.2NP_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
    Q5XG99, Q96LY7
    Related
    ENSP00000506747.1, ENST00000684762.1
    Conserved Domains (1) summary
    smart00257
    Location:80118
    LysM; Lysin motif
  2. NM_001284418.2NP_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
    Q5XG99, Q96LY7
    Related
    ENSP00000386283.1, ENST00000409796.5
    Conserved Domains (1) summary
    smart00257
    Location:80118
    LysM; Lysin motif
  3. NM_001284419.2NP_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:204290
    CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]
  4. NM_001284420.1NP_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:147233
    CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]
  5. NM_001284421.2NP_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
    B3KWE4
    Conserved Domains (1) summary
    COG1622
    Location:82168
    CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]
  6. NM_001284422.2NP_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/Swiss-Prot
    Q5XG99
    UniProtKB/TrEMBL
    B3KWE4
    Related
    ENSP00000333008.5, ENST00000332728.8
    Conserved Domains (1) summary
    COG1622
    Location:82168
    CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]
  7. NM_152449.4NP_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:209295
    CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_011521245.4XP_011519547.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X7

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

    Conserved Domains (1) summary
    smart00257
    Location:80118
    LysM; Lysin motif
  3. XM_047432167.1XP_047288123.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X9

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

    Conserved Domains (1) summary
    smart00257
    Location:80118
    LysM; Lysin motif
  5. XM_011521241.2XP_011519543.2  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X2

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

    UniProtKB/Swiss-Prot
    Q96LY7
  7. XM_047432166.1XP_047288122.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X8

    UniProtKB/TrEMBL
    B3KWE4
  8. XM_047432164.1XP_047288120.1  lysM and putative peptidoglycan-binding domain-containing protein 4 isoform X5

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

    UniProtKB/Swiss-Prot
    Q5XG99
    Conserved Domains (1) summary
    COG1622
    Location:209295
    CyoA; Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]
  10. XM_047432165.1XP_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
    97491166..97497213 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)