Lysmd3 (LysM domain containing 3) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Lysmd3 (LysM domain containing 3) Rattus norvegicus
Analyze
Symbol: Lysmd3
Name: LysM domain containing 3
RGD ID: 1308805
Description: Predicted to enable peptidoglycan binding activity. Predicted to be involved in Golgi organization. Predicted to be located in Golgi membrane and plasma membrane. Predicted to be active in Golgi apparatus. Orthologous to human LYSMD3 (LysM domain containing 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; chlorpyrifos.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC315923; lysM and putative peptidoglycan-binding domain-containing protein 3; LysM, putative peptidoglycan-binding, domain containing 3; MGC109090; RGD1308805; similar to cDNA sequence BC003322
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8213,669,465 - 13,675,622 (+)NCBIGRCr8
mRatBN7.2211,933,787 - 11,939,944 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl211,933,768 - 11,942,961 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx219,047,553 - 19,053,709 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0217,147,073 - 17,153,229 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0211,801,598 - 11,807,755 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.029,526,213 - 9,532,370 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl29,526,209 - 9,534,362 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.029,406,235 - 9,412,392 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.429,751,947 - 9,758,104 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.129,675,798 - 9,681,951 (+)NCBI
Celera28,293,736 - 8,299,893 (+)NCBICelera
Cytogenetic Map2q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
Golgi organization  (IBA,ISO,ISS)

Cellular Component
Golgi apparatus  (IBA,ISO,ISS)
Golgi membrane  (ISO)
plasma membrane  (ISO,ISS)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:29851555  


Genomics

Comparative Map Data
Lysmd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8213,669,465 - 13,675,622 (+)NCBIGRCr8
mRatBN7.2211,933,787 - 11,939,944 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl211,933,768 - 11,942,961 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx219,047,553 - 19,053,709 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0217,147,073 - 17,153,229 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0211,801,598 - 11,807,755 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.029,526,213 - 9,532,370 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl29,526,209 - 9,534,362 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.029,406,235 - 9,412,392 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.429,751,947 - 9,758,104 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.129,675,798 - 9,681,951 (+)NCBI
Celera28,293,736 - 8,299,893 (+)NCBICelera
Cytogenetic Map2q11NCBI
LYSMD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38590,515,626 - 90,529,584 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl590,515,611 - 90,529,584 (-)EnsemblGRCh38hg38GRCh38
GRCh37589,811,443 - 89,825,401 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36589,847,200 - 89,861,157 (-)NCBINCBI36Build 36hg18NCBI36
Celera585,713,583 - 85,727,549 (-)NCBICelera
Cytogenetic Map5q14.3NCBI
HuRef585,022,118 - 85,036,084 (-)NCBIHuRef
CHM1_1589,244,124 - 89,258,073 (-)NCBICHM1_1
T2T-CHM13v2.0591,002,230 - 91,016,199 (-)NCBIT2T-CHM13v2.0
Lysmd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391381,805,782 - 81,820,990 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1381,805,782 - 81,820,990 (+)EnsemblGRCm39 Ensembl
GRCm381381,657,658 - 81,672,871 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1381,657,663 - 81,672,871 (+)EnsemblGRCm38mm10GRCm38
MGSCv371381,796,805 - 81,810,891 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361382,135,143 - 82,149,229 (+)NCBIMGSCv36mm8
Celera1383,918,533 - 83,932,619 (+)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1343.64NCBI
Lysmd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541821,103,679 - 21,116,005 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541821,103,679 - 21,116,005 (+)NCBIChiLan1.0ChiLan1.0
LYSMD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2424,861,662 - 24,876,737 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1523,013,382 - 23,032,126 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0524,839,015 - 24,854,449 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1524,974,666 - 24,988,674 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl524,974,684 - 24,988,674 (+)Ensemblpanpan1.1panPan2
LYSMD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1318,412,824 - 18,425,832 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl318,412,829 - 18,422,454 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha319,780,296 - 19,793,017 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0318,319,106 - 18,331,831 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl318,319,221 - 18,332,542 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1318,292,758 - 18,305,479 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0318,258,057 - 18,270,773 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0318,546,862 - 18,559,580 (+)NCBIUU_Cfam_GSD_1.0
Lysmd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213174,000,095 - 174,012,343 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364698,612,690 - 8,625,652 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364698,612,758 - 8,625,566 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LYSMD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl297,689,376 - 97,703,745 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1297,688,763 - 97,703,918 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22100,768,843 - 100,781,843 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LYSMD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1484,460,745 - 84,475,669 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl484,460,821 - 84,475,196 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604933,520,700 - 33,534,643 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lysmd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247439,766,160 - 9,778,628 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247439,766,680 - 9,778,696 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lysmd3
35 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:61
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000021818
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731166Mamtr2Mammary tumor resistance QTL 20.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777212654247Rat
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
61368Mcs1Mammary carcinoma susceptibility QTL 14.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777223319447Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 20 36 21 17 21 31 23 34 11
Low 23 21 20 2 20 8 11 43 12 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021818   ⟹   ENSRNOP00000021818
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl211,933,768 - 11,942,961 (+)Ensembl
Rnor_6.0 Ensembl29,526,209 - 9,534,362 (+)Ensembl
RefSeq Acc Id: NM_001009698   ⟹   NP_001009698
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8213,669,465 - 13,675,622 (+)NCBI
mRatBN7.2211,933,787 - 11,939,944 (+)NCBI
Rnor_6.029,526,213 - 9,532,370 (+)NCBI
Rnor_5.029,406,235 - 9,412,392 (+)NCBI
RGSC_v3.429,751,947 - 9,758,104 (+)RGD
Celera28,293,736 - 8,299,893 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001009698 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88262 (Get FASTA)   NCBI Sequence Viewer  
  EDM09947 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021818
  ENSRNOP00000021818.4
  ENSRNOP00055032445
  ENSRNOP00060003131
  ENSRNOP00065005694
GenBank Protein Q5M836 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001009698   ⟸   NM_001009698
- UniProtKB: Q5M836 (UniProtKB/Swiss-Prot),   A6I4I9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021818   ⟸   ENSRNOT00000021818
Protein Domains
LysM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5M836-F1-model_v2 AlphaFold Q5M836 1-300 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13691044
Promoter ID:EPDNEW_R1569
Type:initiation region
Name:Lysmd3_1
Description:LysM domain containing 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.029,526,250 - 9,526,310EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308805 AgrOrtholog
BioCyc Gene G2FUF-55015 BioCyc
Ensembl Genes ENSRNOG00000016298 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055023274 UniProtKB/Swiss-Prot
  ENSRNOG00060002775 UniProtKB/Swiss-Prot
  ENSRNOG00065005499 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000021818 ENTREZGENE
  ENSRNOT00000021818.8 UniProtKB/Swiss-Prot
  ENSRNOT00055039984 UniProtKB/Swiss-Prot
  ENSRNOT00060004436 UniProtKB/Swiss-Prot
  ENSRNOT00065008139 UniProtKB/Swiss-Prot
Gene3D-CATH 3.10.350.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7376577 IMAGE-MGC_LOAD
InterPro LYSM1-4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LysM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LysM_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:315923 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:109090 IMAGE-MGC_LOAD
NCBI Gene 315923 ENTREZGENE
PANTHER AND PUTATIVE PEPTIDOGLYCAN-BINDING DOMAIN-CONTAINING PROTEIN 3-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYSM AND PUTATIVE PEPTIDOGLYCAN-BINDING DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
Pfam LysM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lysmd3 PhenoGen
PROSITE LYSM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016298 RatGTEx
  ENSRNOG00055023274 RatGTEx
  ENSRNOG00060002775 RatGTEx
  ENSRNOG00065005499 RatGTEx
SMART LysM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6I4I9 ENTREZGENE, UniProtKB/TrEMBL
  LYSM3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-10 Lysmd3  LysM domain containing 3  Lysmd3  LysM, putative peptidoglycan-binding, domain containing 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Lysmd3  LysM, putative peptidoglycan-binding, domain containing 3  RGD1308805  similar to cDNA sequence BC003322  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1308805  similar to cDNA sequence BC003322  RGD1308805_predicted  similar to cDNA sequence BC003322 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1308805_predicted  similar to cDNA sequence BC003322 (predicted)  LOC315923_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC315923_predicted  similar to cDNA sequence BC003322 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL