LYSMD3 LysM domain containing 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LYSMD3provided by HGNC
Official Full Name: LysM domain containing 3provided by HGNC
Primary source: HGNC:HGNC:26969
See related: Ensembl:ENSG00000176018 AllianceGenome:HGNC:26969
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: Involved in Golgi organization. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thyroid (RPKM 11.6), adrenal (RPKM 8.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q14.3

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (90515626..90529584, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (91002230..91016199, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (89811443..89825401, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LYSMD3: A mammalian pattern recognition receptor for chitin.
Title: LYSMD3: A mammalian pattern recognition receptor for chitin.

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

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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables peptidoglycan binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in Golgi organization	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: lysM and putative peptidoglycan-binding domain-containing protein 3

Names: LysM, putative peptidoglycan-binding, domain containing 3

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)

NM_001286812.1 → NP_001273741.1 lysM and putative peptidoglycan-binding domain-containing protein 3 isoform 2

See identical proteins and their annotated locations for NP_001273741.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC027323, BC058027, BP873090

Consensus CDS

CCDS68911.1

UniProtKB/Swiss-Prot

Q7Z3D4

Related

ENSP00000427683.1, ENST00000509384.5
NM_198273.2 → NP_938014.1 lysM and putative peptidoglycan-binding domain-containing protein 3 isoform 1

See identical proteins and their annotated locations for NP_938014.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AL832721, BC136741, CR933624, DN994993

Consensus CDS

CCDS43338.1

UniProtKB/Swiss-Prot

Q5H9U0, Q6PEK0, Q7Z3D4, Q9NTE9

UniProtKB/TrEMBL

A8K613

Related

ENSP00000314518.6, ENST00000315948.11

Conserved Domains (1) summary

cd00118
Location:69 → 109

LysM; Lysine Motif is a small domain involved in binding peptidoglycan

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

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

90515626..90529584 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416694.1 → XP_047272650.1 lysM and putative peptidoglycan-binding domain-containing protein 3 isoform X1

UniProtKB/TrEMBL

G5E9N8

Related

ENSP00000405507.2, ENST00000453259.2