LYSMD4 (LysM domain containing 4) - 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 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
Advanced Search (OLGA)
Gene: LYSMD4 (LysM domain containing 4) Chlorocebus sabaeus
Analyze
Symbol: LYSMD4
Name: LysM domain containing 4
RGD ID: 18597760
Description: ASSOCIATED WITH chromosome 15q26-qter deletion syndrome (ortholog); FOUND IN membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: lysM and putative peptidoglycan-binding domain-containing protein 4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12918,325,403 - 18,329,678 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2918,323,749 - 18,329,648 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605928,238,096 - 28,242,551 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
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

Cellular Component
membrane  (IEA)

References

Genomics

Comparative Map Data
LYSMD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12918,325,403 - 18,329,678 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2918,323,749 - 18,329,648 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605928,238,096 - 28,242,551 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LYSMD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381599,715,697 - 99,733,444 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1599,715,697 - 99,733,561 (-)EnsemblGRCh38hg38GRCh38
GRCh3715100,267,606 - 100,273,649 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361598,085,133 - 98,091,149 (-)NCBINCBI36Build 36hg18NCBI36
Celera1576,686,562 - 76,692,579 (-)NCBICelera
Cytogenetic Map15q26.3NCBI
HuRef1576,397,456 - 76,403,473 (-)NCBIHuRef
CHM1_115100,108,944 - 100,114,962 (-)NCBICHM1_1
T2T-CHM13v2.01597,479,959 - 97,497,213 (-)NCBIT2T-CHM13v2.0
Lysmd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39766,872,292 - 66,878,216 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl766,872,292 - 66,957,078 (+)EnsemblGRCm39 Ensembl
GRCm38767,222,544 - 67,228,468 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl767,222,544 - 67,307,330 (+)EnsemblGRCm38mm10GRCm38
MGSCv37774,367,494 - 74,373,342 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36767,101,558 - 67,107,406 (+)NCBIMGSCv36mm8
Celera764,681,429 - 64,687,277 (+)NCBICelera
Cytogenetic Map7CNCBI
cM Map736.71NCBI
Lysmd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81130,249,340 - 130,255,357 (+)NCBIGRCr8
mRatBN7.21120,839,180 - 120,845,148 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1120,839,282 - 120,845,135 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1128,836,073 - 128,841,949 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01136,006,175 - 136,012,051 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01128,810,482 - 128,816,360 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01128,199,100 - 128,204,989 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1128,199,322 - 128,203,268 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01129,265,273 - 129,271,167 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1113,042,015 - 113,047,904 (+)NCBICelera
Cytogenetic Map1q22NCBI
Lysmd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541627,059,941 - 27,063,459 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541627,057,845 - 27,063,459 (-)NCBIChiLan1.0ChiLan1.0
LYSMD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21689,269,913 - 89,275,973 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11592,954,175 - 92,972,832 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01578,396,860 - 78,413,774 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11597,590,076 - 97,596,035 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1597,590,076 - 97,596,035 (-)Ensemblpanpan1.1panPan2
LYSMD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1340,983,350 - 40,989,611 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl340,982,907 - 40,988,434 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha343,681,096 - 43,687,371 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0341,384,613 - 41,390,889 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl341,384,677 - 41,390,879 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1340,917,065 - 40,923,341 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0341,148,236 - 41,154,527 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0341,367,887 - 41,374,163 (+)NCBIUU_Cfam_GSD_1.0
Lysmd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640142,508,527 - 142,515,130 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364833,819,381 - 3,824,128 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364833,819,427 - 3,824,449 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LYSMD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1138,560,995 - 138,567,562 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11138,560,985 - 138,567,570 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21154,770,996 - 154,777,327 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Lysmd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247684,689,264 - 4,692,902 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247684,689,536 - 4,694,577 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression

ectoderm
endocrine system
hemolymphoid system
mesenchyme
mesoderm
nervous system
reproductive system
76 36 20 36 36 60 20

Sequence


Ensembl Acc Id: ENSCSAT00000015011   ⟹   ENSCSAP00000012965
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl2918,323,749 - 18,329,648 (-)Ensembl
RefSeq Acc Id: XM_037987636   ⟹   XP_037843564
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366605928,238,096 - 28,242,551 (+)NCBI
Protein Sequences
Protein RefSeqs XP_037843564 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000012965.1
Ensembl Acc Id: ENSCSAP00000012965   ⟸   ENSCSAT00000015011
RefSeq Acc Id: XP_037843564   ⟸   XM_037987636


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000016917 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000015011.1 UniProtKB/TrEMBL
Gene3D-CATH 3.10.350.10 UniProtKB/TrEMBL
InterPro LYSM1-4 UniProtKB/TrEMBL
  LysM_dom UniProtKB/TrEMBL
  LysM_dom_sf UniProtKB/TrEMBL
KEGG Report csab:103231272 UniProtKB/TrEMBL
NCBI Gene LYSMD4 ENTREZGENE
PANTHER AND PUTATIVE PEPTIDOGLYCAN-BINDING DOMAIN-CONTAINING PROTEIN 4-RELATED UniProtKB/TrEMBL
  PTHR20932 UniProtKB/TrEMBL
Pfam LysM UniProtKB/TrEMBL
PROSITE LYSM UniProtKB/TrEMBL
SMART LysM UniProtKB/TrEMBL
UniProt A0A0D9RWH6_CHLSB UniProtKB/TrEMBL