Lysmd3 Gene Detail

Summary

• Symbol
  Lysmd3
• Name
  LysM, putative peptidoglycan-binding, domain containing 3
• Synonyms
  1110030H10Rik, MGC:7041

• Feature Type
  protein coding gene
• IDs
  MGI:1915906
  NCBI Gene: 80289
• Alliance
  gene page
• Transcription Start Sites
  1 TSS

Location &
Maps

• Sequence Map
  Chr13:81805782-81820990 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 13, 43.64 cM, cytoband C3
• Mapping Data
  3 experiments

Strain
Comparison

• SNPs within 2kb
  503 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1915906	protein coding gene	Chr13:81805782-81820990 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0020787	protein coding gene	Chr13:82425204-82439153 (+)
A/J	MGP_AJ_G0020743	protein coding gene	Chr13:79550545-79567039 (+)
AKR/J	MGP_AKRJ_G0020716	protein coding gene	Chr13:81906443-81921053 (+)
BALB/cJ	MGP_BALBcJ_G0020739	protein coding gene	Chr13:80098437-80110433 (+)
C3H/HeJ	MGP_C3HHeJ_G0020533	protein coding gene	Chr13:81655645-81667642 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0021176	protein coding gene	Chr13:85106209-85120322 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018744	protein coding gene	Chr13:76018580-76033534 (+)
CAST/EiJ	MGP_CASTEiJ_G0020051	protein coding gene	Chr13:80747608-80761503 (+)
CBA/J	MGP_CBAJ_G0020492	protein coding gene	Chr13:88336743-88349486 (+)
DBA/2J	MGP_DBA2J_G0020617	protein coding gene	Chr13:79206044-79219583 (+)
FVB/NJ	MGP_FVBNJ_G0020597	protein coding gene	Chr13:78292143-78305268 (+)
LP/J	MGP_LPJ_G0020690	protein coding gene	Chr13:82647243-82661317 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0020626	protein coding gene	Chr13:87242205-87259385 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0021216	protein coding gene	Chr13:81323777-81338688 (+)
PWK/PhJ	MGP_PWKPhJ_G0019804	protein coding gene	Chr13:78122732-78136978 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0019627	protein coding gene	Chr13:77563560-77580755 (+)
WSB/EiJ	MGP_WSBEiJ_G0020108	protein coding gene	Chr13:81756482-81770043 (+)

Homology

• Human Ortholog
  LYSMD3, LysM domain containing 3

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  LYSMD3, LysM domain containing 3
  
• Links
  HGNC:26969

  NCBI Gene ID: 116068

  neXtProt AC: NX_Q7Z3D4

  UniProt: Q7Z3D4

  
  
• Chr Location
  5q14.3; chr5:90515611-90529584 (-)  GRCh38

---

• MGI Vertebrate Homology
  Lysmd3 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: LYSMD3
• Gene Tree
  Lysmd3
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  1 phenotype from 2 alleles in 2 genetic backgrounds
  6 phenotype references
  

• All Mutations and Alleles
  6
• Chemically induced (other)
  1
• Endonuclease-mediated
  1
• Gene trapped
  4
• Genomic Mutations
  1 involving Lysmd3
• Incidental Mutations
  APF , CvDC
• Find Mice (IMSR)
  12 strains or lines available

Mice homozygous for a knock-out allele are viable and fertile with normal response to a range of pathogens.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  12
• GO References
  4

Expression

• Assay Results
  706
• cDNA Data
  9

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase lysmd3
  ZFIN lysmd3

Sequences &
Gene Models

• All Sequences
  46
• RefSeq
  4
• UniProt
  4
• CCDS
  CCDS26660.1

• Ensembl
  ENSMUSG00000035840 (Evidence)
• NCBI Gene
  80289

Representative Sequences			Length	Strain/Species
genomic	80289	NCBI Gene Model | MGI Sequence Detail	15209	C57BL/6J
transcript	NM_030257	RefSeq | MGI Sequence Detail	3139	FVB/N
polypeptide	Q99LE3	UniProt | EBI | MGI Sequence Detail	305	Not Applicable

Protein
Information

• UniProt
  4 Sequences
• Protein Ontology
  PR:000029617 LysM and putative peptidoglycan-binding domain-containing protein 3
  (term hierarchy)
• InterPro Domains
  IPR045030 LysM and putative peptidoglycan-binding domain-containing protein 1-4
  IPR018392 LysM domain
  IPR036779 LysM domain superfamily
• GlyGen
  Q99LE3 3 sites

Molecular
Reagents

• All nucleic 9

  cDNA 9

  
  

  Microarray probesets 5

Other
Accession IDs

MGI:1933110

References

• Summaries
  All 32

  Gene Ontology 4

  Phenotypes 6
• Earliest
  J:182573 Roderick TH, Producing and detecting paracentric chromosomal inversions in mice. Mutat Res. 1971 Jan;11(1):59-69
• Latest
  J:263704 Yokoyama CC, et al., LysMD3 is a type II membrane protein without an in vivo role in the response to a range of pathogens. J Biol Chem. 2018 Apr 20;293(16):6022-6038

TSS for Lysmd3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr120480	Chr13:81805851-81805965 (+)	126 bp