Advanced Search (OLGA)

Gene: Lysmd2 (LysM domain containing 2) Ictidomys tridecemlineatus

Analyze

Symbol:

Lysmd2

Name:

LysM domain containing 2

RGD ID:

12484491

Description:

ASSOCIATED WITH Bloom syndrome (ortholog); colorectal cancer (ortholog); COVID-19 (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

lysM and putative peptidoglycan-binding domain-containing protein 2; LysM domain containing 2, transcript variant X1; LysM domain containing 2, transcript variant X2

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	95,707,101 - 95,722,257 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936471	13,555,157 - 13,562,256 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936471	13,555,166 - 13,570,268 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Bloom syndrome (ISO)

colorectal cancer (ISO)

COVID-19 (ISO)

developmental and epileptic encephalopathy 13 (ISO)

paraplegia (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Molecular Function

protein binding (ISO)

References

Genomics

Comparative Map Data

Lysmd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	95,707,101 - 95,722,257 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936471	13,555,157 - 13,562,256 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936471	13,555,166 - 13,570,268 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LYSMD2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	15	51,723,011 - 51,751,451 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	15	51,723,011 - 51,751,585 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	15	52,015,208 - 52,043,648 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	49,802,553 - 49,817,608 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	15	28,908,680 - 28,937,069 (-)	NCBI		Celera
Cytogenetic Map	15	q21.2	NCBI
HuRef	15	28,845,769 - 28,874,158 (-)	NCBI		HuRef
CHM1_1	15	52,133,295 - 52,161,686 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	15	49,530,506 - 49,558,957 (-)	NCBI		T2T-CHM13v2.0

Lysmd2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	9	75,532,403 - 75,545,055 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	9	75,533,023 - 75,545,053 (+)	Ensembl		GRCm39 Ensembl
GRCm38	9	75,625,121 - 75,637,773 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	9	75,625,741 - 75,637,771 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	9	75,473,539 - 75,485,580 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	9	75,411,650 - 75,423,680 (+)	NCBI		MGSCv36	mm8
Celera	9	72,789,273 - 72,801,670 (+)	NCBI		Celera
Cytogenetic Map	9	D	NCBI
cM Map	9	42.32	NCBI

Lysmd2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	8	85,259,443 - 85,274,876 (+)	NCBI		GRCr8
mRatBN7.2	8	76,378,984 - 76,394,396 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	8	76,379,219 - 76,394,654 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	8	81,886,735 - 81,901,921 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	8	80,151,634 - 80,166,707 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	8	77,986,076 - 78,001,262 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	8	82,560,363 - 82,576,662 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	8	82,560,761 - 82,577,019 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	8	82,160,974 - 82,178,174 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	8	80,446,544 - 80,462,607 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	8	80,465,376 - 80,482,027 (+)	NCBI
Celera	8	76,169,272 - 76,184,220 (+)	NCBI		Celera
Cytogenetic Map	8	q24	NCBI

Lysmd2
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955409	2,862,478 - 2,874,017 (+)	NCBI	ChiLan1.0	ChiLan1.0

LYSMD2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	16	40,957,284 - 40,985,782 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	15	45,137,692 - 45,166,309 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	15	30,661,922 - 30,690,653 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	15	48,992,788 - 49,021,152 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

LYSMD2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	30	17,409,338 - 17,424,092 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	30	17,409,326 - 17,419,698 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	30	17,335,717 - 17,350,954 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	30	17,555,537 - 17,570,863 (-)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	30	17,476,950 - 17,492,170 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	30	17,595,219 - 17,610,542 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	30	17,701,849 - 17,717,075 (-)	NCBI		UU_Cfam_GSD_1.0

LYSMD2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	120,026,532 - 120,043,127 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	120,009,417 - 120,043,146 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	133,183,213 - 133,216,939 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LYSMD2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	26	31,624,953 - 31,652,483 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	26	31,637,208 - 31,652,547 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666048	109,562,210 - 109,589,937 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lysmd2
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624731	8,630,532 - 8,644,577 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624731	8,630,551 - 8,644,510 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005316575	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_013358713	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040276266	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010003700	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000015370 ⟹ ENSSTOP00000013766

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936471	13,555,157 - 13,562,256 (-)	Ensembl

RefSeq Acc Id:

XM_005316575 ⟹ XP_005316632

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024408640	95,707,101 - 95,714,425 (-)	NCBI
SpeTri2.0	NW_004936471	13,555,166 - 13,562,396 (-)	NCBI

Sequence:

show sequence

TCTATGTCATTTGCAAAAGGTTGTACTTTCTATTTTCAGGCTTAAGTGGCTCTTAGGAAATGTT
GTGAGGTGGGCAGGTGGGAAGGCTGTGGAGTTTTCCAGCCCTTCCTTGGATTGGATAATGGCTT
TTCTTAGTTTCATGTGGGTCCAATTTCCAGAACAGGAAACCTAACCTATGTTCCAACAGAAGAA
TAAAACATTCCAAACAAAACGTCTTTCACTGTTTTAGATTACCCACGGTTCTCATATGAGCCTC
AGTGCTTACTTCCATAGCTGGACTTCCTGTTTCCACCAGTGCTTCTTTCTTGCCCACCCATTTT
CTGCACAGCTGCAAAGTGATCTTTAACTGTAATCAGATCATGTCATTCTCTTCCTTCATCTTCC
AGTGGCTTCTCATCACATTCAAAATGAATTCCAAATTCTTTACCTGGGCCTGAAGTTGGCTTAT
TACTCCCTACATTTCACCACACAGTTTGGGGTGTTGCTGCTGCTCTTTCTGGATGGAATCCTGG
ATGGAACAGATTAAAAGGGCCAATAAACTGTTTACCAATGATTGTATATTTCTGAAGAAAACTT
TGAACATCCCAGTTATATCAGAGAAGCCTTTGTTGTTTAATGGACTTAACTCCGTTGATTCTCC
AGAAAATGAAACTGTTGATAGCAGCTTTTCACATGAAGAGGAGCCTGTGGTGGGTGGGGAAGAC
CTCCCTCCTCCCAGTCCTCAGGAATCTGAGATTCAGCCTGTGCAGCCTGAAGAAGTGTCAGCCA
GAGATTTCCTTCAAAGACTTGATTTGCAGATTAAATTATCAACACAGGCAGCCAAGAAACTAAA
AGAAGAAAGCAGAGATGAAGAAAGTCCCTATGCAACGTCCCTCTATCACAGTTAGGTGATTAGT
GGCATGATTCTAACCTGGATTAAGTGGTGGTTGGGCCATAAAGAACCTGGTGACTGAAGATCCA
GAAGCATCCCTTTTGGATTCCCATAGCACTCATCTTAAAATCACGATTAAGTCTACCTACTGCA
GTTGCACTGAAGTGGTTATTTCCCTCTGGCTTTTTAAAATGTTCAGTTTTTATTATGGCATGAT
AGCAAAATTATATTCTGAAGCTTATTACTTTTGTAGGTGGTAATAGTTTTTAGACTAGCTTTTG
TAAATACTGGTGGAGATAAGCATCAAAGACTTTATATATTTAAGCTGAAAACAGTGTTTAGCTC
CTAATGAAATTCTAATTATGTGAAAAACATGGTGGCTGTTTAAGTGATGCTGAATTTGCTGTGT
GTTTATAACTTAAGTGCTATATACATATATATATTTCAATATGTATTACATATTCCGTATTAAT
ACAAAGAACCAAATTTTGTCTGCTATTTTGTAAAAATAAACTACAAAAGTCTGAGAAAATAAAC
TATGTTTTCACA

hide sequence

RefSeq Acc Id:

XM_013358713 ⟹ XP_013214167

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024408640	95,707,101 - 95,722,257 (-)	NCBI
SpeTri2.0	NW_004936471	13,555,166 - 13,570,268 (-)	NCBI

Sequence:

show sequence

CGCCCTGCCCAGACTCTGAACAGATCTGTTGGGTGAGGAAGATCAAGGAGGACCAGGACTTTGG
TATCACCGGCAGCCACCTTCACCCGATTTGCTCTCGCCATCTCACTACTATATATTTACTCAAA
GCCCCACTGAGGTGGATTCTGTTCTCCTTGTAAACAAGCTCTATGATGAGTCAGGAAGGGTACA
GTTGTGCCCGTTGTATGGTACTGGTTCTGTCGATTATGCTTCTTTATTTAGAAGTGAAATTACA
GCCCTGGGCTCACTGGCAACCGTGAATGTGACACCTGTGGAGAGGGCTGTGTTTATTACAAATT
TATGTGTGTGCGTCTTGGGTATATTGCATTACACCTCTGGGAAGAACATGGAAACCTGAGGGAA
CAAATTGTTTCATTAAAATTACTTATAATTAACTCTGAGCTATGTGATGGCCTTTTAACATTTG
AGTTGACTATCAGTTTCAGTATTCTTTCCTGAAGCACCATAGACAGCAGTGAGAAGAAATGTGA
TCATATCTTTCTCTTGAAGTGAAACTCCGACTCATTGCCAAGGATGGAAGTAATCTATTTTGCA
TATTTAAGCAGATGGAACAGATTAAAAGGGCCAATAAACTGTTTACCAATGATTGTATATTTCT
GAAGAAAACTTTGAACATCCCAGTTATATCAGAGAAGCCTTTGTTGTTTAATGGACTTAACTCC
GTTGATTCTCCAGAAAATGAAACTGTTGATAGCAGCTTTTCACATGAAGAGGAGCCTGTGGTGG
GTGGGGAAGACCTCCCTCCTCCCAGTCCTCAGGAATCTGAGATTCAGCCTGTGCAGCCTGAAGA
AGTGTCAGCCAGAGATTTCCTTCAAAGACTTGATTTGCAGATTAAATTATCAACACAGGCAGCC
AAGAAACTAAAAGAAGAAAGCAGAGATGAAGAAAGTCCCTATGCAACGTCCCTCTATCACAGTT
AGGTGATTAGTGGCATGATTCTAACCTGGATTAAGTGGTGGTTGGGCCATAAAGAACCTGGTGA
CTGAAGATCCAGAAGCATCCCTTTTGGATTCCCATAGCACTCATCTTAAAATCACGATTAAGTC
TACCTACTGCAGTTGCACTGAAGTGGTTATTTCCCTCTGGCTTTTTAAAATGTTCAGTTTTTAT
TATGGCATGATAGCAAAATTATATTCTGAAGCTTATTACTTTTGTAGGTGGTAATAGTTTTTAG
ACTAGCTTTTGTAAATACTGGTGGAGATAAGCATCAAAGACTTTATATATTTAAGCTGAAAACA
GTGTTTAGCTCCTAATGAAATTCTAATTATGTGAAAAACATGGTGGCTGTTTAAGTGATGCTGA
ATTTGCTGTGTGTTTATAACTTAAGTGCTATATACATATATATATTTCAATATGTATTACATAT
TCCGTATTAATACAAAGAACCAAATTTTGTCTGCTATTTTGTAAAAATAAACTACAAAAGTCTG
AGAAAATAAACTATGTTTTCACA

hide sequence

RefSeq Acc Id:

XM_040276266 ⟹ XP_040132200

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024408640	95,707,101 - 95,713,138 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_005316632	(Get FASTA)	NCBI Sequence Viewer
	XP_013214167	(Get FASTA)	NCBI Sequence Viewer
	XP_040132200	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000013766.3
GenBank Protein	KAG3261872	(Get FASTA)	NCBI Sequence Viewer
	KAG3261873	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	XP_013214167 ⟸ XM_013358713
- Peptide Label:	isoform X3
- Sequence:	show sequence MEQIKRANKLFTNDCIFLKKTLNIPVISEKPLLFNGLNSVDSPENETVDSSFSHEEEPVVGGED LPPPSPQESEIQPVQPEEVSARDFLQRLDLQIKLSTQAAKKLKEESRDEESPYATSLYHS hide sequence

RefSeq Acc Id:	XP_005316632 ⟸ XM_005316575
- Peptide Label:	isoform X1
- UniProtKB:	I3MPM0 (UniProtKB/TrEMBL)
- Sequence:	show sequence MESWMEQIKRANKLFTNDCIFLKKTLNIPVISEKPLLFNGLNSVDSPENETVDSSFSHEEEPVV GGEDLPPPSPQESEIQPVQPEEVSARDFLQRLDLQIKLSTQAAKKLKEESRDEESPYATSLYHS hide sequence

RefSeq Acc Id:	XP_040132200 ⟸ XM_040276266
- Peptide Label:	isoform X2

Ensembl Acc Id:

ENSSTOP00000013766 ⟸ ENSSTOT00000015370

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000015371	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000015370.3	UniProtKB/TrEMBL
InterPro	LYSM1-4	UniProtKB/TrEMBL
NCBI Gene	Lysmd2	ENTREZGENE
PANTHER	AND PUTATIVE PEPTIDOGLYCAN-BINDING DOMAIN-CONTAINING PROTEIN 2-RELATED	UniProtKB/TrEMBL
	PTHR20932	UniProtKB/TrEMBL
UniProt	I3MPM0	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Send us a Message

Imported Disease Annotations - ClinVar