Lrtm1 (leucine rich repeats and transmembrane domains 1)

Gene: Lrtm1 (leucine rich repeats and transmembrane domains 1) Chinchilla lanigera

Analyze

Symbol:

Lrtm1

Name:

leucine rich repeats and transmembrane domains 1

RGD ID:

8859943

Description:

INVOLVED IN positive regulation of synapse assembly (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

leucine-rich repeat and transmembrane domain-containing protein 1; leucine-rich repeats and transmembrane domains 1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955430	4,784,367 - 4,794,372 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955430	4,784,643 - 4,794,318 (-)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

positive regulation of synapse assembly (ISO)

Molecular Function

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Lrtm1
(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 Ensembl	NW_004955430	4,784,367 - 4,794,372 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955430	4,784,643 - 4,794,318 (-)	NCBI	ChiLan1.0	ChiLan1.0

LRTM1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	54,918,231 - 54,967,102 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	54,918,231 - 54,967,088 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	3	54,952,258 - 55,001,129 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	54,927,400 - 54,937,112 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	3	54,918,491 - 54,928,203 (-)	NCBI		Celera
Cytogenetic Map	3	p14.3	NCBI
HuRef	3	55,001,810 - 55,011,526 (-)	NCBI		HuRef
CHM1_1	3	54,903,712 - 54,913,435 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	3	54,952,027 - 55,000,901 (-)	NCBI		T2T-CHM13v2.0

Lrtm1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	28,740,165 - 28,755,599 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	14	28,740,165 - 28,755,602 (+)	Ensembl		GRCm39 Ensembl
GRCm38	14	29,018,208 - 29,033,642 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	29,018,208 - 29,033,645 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	14	29,831,394 - 29,846,828 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	14	27,845,265 - 27,854,891 (+)	NCBI		MGSCv36	mm8
Celera	14	25,271,616 - 25,287,049 (+)	NCBI		Celera
Cytogenetic Map	14	A3	NCBI
cM Map	14	16.8	NCBI

Lrtm1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	16	4,216,947 - 4,224,447 (+)	NCBI		GRCr8
mRatBN7.2	16	4,210,343 - 4,217,843 (+)	NCBI	mRatBN7.2	mRatBN7.2
Rnor_6.0	16	4,993,728 - 5,005,110 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	4,997,461 - 5,003,066 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	4,934,436 - 4,945,500 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	4,285,032 - 4,293,657 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	16	10,954,321 - 10,965,702 (-)	NCBI		Celera
Cytogenetic Map	16	p16	NCBI

LRTM1
(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	2	54,911,383 - 54,921,629 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	54,916,154 - 54,926,400 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	54,858,452 - 54,868,183 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	56,078,743 - 56,127,798 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	56,078,764 - 56,085,634 (-)	Ensembl	panpan1.1		panPan2

LRTM1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	20	35,220,954 - 35,236,425 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	35,221,951 - 35,231,943 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	35,151,325 - 35,162,968 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	20	35,494,882 - 35,506,518 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	20	35,496,155 - 35,508,172 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	20	34,937,103 - 34,948,750 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	20	35,296,361 - 35,308,008 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	20	35,511,795 - 35,523,447 (+)	NCBI		UU_Cfam_GSD_1.0

Lrtm1
(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_024405118	172,339,906 - 172,353,124 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936473	5,481,929 - 5,491,858 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936473	5,478,481 - 5,491,689 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LRTM1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	36,869,494 - 36,881,013 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	36,870,269 - 36,881,586 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	40,235,908 - 40,247,046 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LRTM1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Vero_WHO_p1.0	NW_023666041	150,591,981 - 150,605,509 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Lrtm1
(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_004624822	2,343,967 - 2,354,525 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624822	2,343,968 - 2,354,038 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005387378	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01029249	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDI01251545	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCLAT00000011722 ⟹ ENSCLAP00000011585

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955430	4,784,367 - 4,794,372 (-)	Ensembl

RefSeq Acc Id:

XM_005387378 ⟹ XP_005387435

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955430	4,784,643 - 4,794,318 (-)	NCBI

Sequence:

show sequence

CCTGACAAACATTCTTTATGCGGCTCGCCATCTGAATGAGAACAGCAGGGATGAGCGGGCCGGG
GGTGGAGGGGAGAATGACACTTTAAGAAAGAGAAGAGACACAATCAAATGATCCTCTTCTGGAA
AGCAATCCCAGCCAGATGGAGACAAGGGGACAGGCTGCGTAAATAACTGGTCTGCCGAACACTT
TGCTGTTTTCTGAACAAGCAGGATTCAGGAAAAGTGAATGAGAAGCTGGGCTCCAAGCTTCCAT
GCTCTTGGTTCGCTGATCTGTGAACTAATAAGGGTGGGCTACGTGTGCAGCCCAGGGATACTCA
GCCATGAAAGGTGAGCTGCTGTTGCTTTCAAGCATGATCTTCTTACTGCAGGGGGCCTGTGGCT
GCCCAGAGAAGTGCTTCTGTCACTCATCTTCAAACTCTGTAGACTGCAGCCGCCAAGGTCTGGC
TGAAATCCCTCCCGACCTGCCTCCTGAGACACTAACACTGCTCCTGCAAGATAACCAGATATGC
CAGCTTCCTGCTCTTGCATTTCGGAGAGTGCCACGGCTCAAGATCTTAAATCTGTCCAACAATT
CCCTTTCAAACCTGGCCCCGGAAGCTTTCCACGGACTTCAGCATTTGGAGGTTTTAAATCTAAC
CCAGAACTCCCTGCTTTCCTTGGAAAGCAGACTTTTCCATTTTCTCCCGCAGCTGCGGGAGCTG
GATTTGTCATCCAACAACATAAGCCACCTACCCCAGTCCCTGGGAGAGCCCTGGGAGAATCTAA
CTGTATTTGCAGTGCAACAAAATCAGCTTCAGCATCTCAGCCGTGAGCTCCTAGAATCCATGCC
CAGGGTGAGGCTGTTACTGCTCCAGAACAACCTCTGGAAATGCAATTGCCACCTGCTTGGTCTT
AAACTCTGGCTAGAGAAATTTATCTATGAAGGGGGAATAACAGACGGCATTGTCTGTGGGTCAC
CCGACCCCTGGAGGGGGAAGGATCTCCTTAAAATCCCCCACGAGCTGTACCAGCCCTGCCCTCC
TCCTCCTCCTCCAGAGCTAGTGTCTGCCCAGGCTCCGCAGCACAGCTCTGAACACGGGGAGCTT
CGCAAGCCTCCTGAGGACCACATCCTGGGCCTGCACGATACCTCAGAGTGTGCGGTCAAACCCA
AACCAAGGCCTGCCAACCTGCGTCATGCCGTGGCTACTGTTGTGATCACCGGGGTTGTGTGTGG
CATTGTGTGCCTCATGATGCTGGCGGCTGCCATCTACGGCTGCACCTACGCAGCCATCACAGCC
CAGTACCACGGCCGACCCTCGGCTCAAACCAGTGAGTCTGGGAAGACAGGAGGGAAAGACCTGT
TTGACAACTTGCCAGCCTAACAGCATGCACCTCGAAGAGCAGTGAGCATCACAGGCTGGACAAA
AGGCCTGAGTGTCACCTGTCATTGTCTCATTTTGCTTTTTCCAAAAGGTAAAAAAAAAAAAAAA
AAAAAAAGCGTCTTTAAAATGATGTTCCTGGGAAGACATGTATGTTGAAATTTTTAAAATACCA
CAGATTAAATAGAGATGC

hide sequence

Protein Sequences


Protein RefSeqs	XP_005387435	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000011585
	ENSCLAP00000011585.1

RefSeq Acc Id:

XP_005387435 ⟸ XM_005387378

- UniProtKB:

A0A8C2VBI1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MKGELLLLSSMIFLLQGACGCPEKCFCHSSSNSVDCSRQGLAEIPPDLPPETLTLLLQDNQICQ
LPALAFRRVPRLKILNLSNNSLSNLAPEAFHGLQHLEVLNLTQNSLLSLESRLFHFLPQLRELD
LSSNNISHLPQSLGEPWENLTVFAVQQNQLQHLSRELLESMPRVRLLLLQNNLWKCNCHLLGLK
LWLEKFIYEGGITDGIVCGSPDPWRGKDLLKIPHELYQPCPPPPPPELVSAQAPQHSSEHGELR
KPPEDHILGLHDTSECAVKPKPRPANLRHAVATVVITGVVCGIVCLMMLAAAIYGCTYAAITAQ
YHGRPSAQTSESGKTGGKDLFDNLPA

hide sequence

RefSeq Acc Id:

ENSCLAP00000011585 ⟸ ENSCLAT00000011722

Protein Domains

LRRCT LRRNT

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000007983	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000011722	ENTREZGENE
	ENSCLAT00000011722.1	UniProtKB/TrEMBL
Gene3D-CATH	3.80.10.10	UniProtKB/TrEMBL
InterPro	Cys-rich_flank_reg_C	UniProtKB/TrEMBL
	Leu-rich_rpt	UniProtKB/TrEMBL
	Leu-rich_rpt_typical-subtyp	UniProtKB/TrEMBL
	LRR_dom_sf	UniProtKB/TrEMBL
	LRRNT	UniProtKB/TrEMBL
NCBI Gene	Lrtm1	ENTREZGENE
PANTHER	ANTIGEN BSP, PUTATIVE-RELATED	UniProtKB/TrEMBL
	LEUCINE RICH REPEATS AND TRANSMEMBRANE DOMAINS 2	UniProtKB/TrEMBL
Pfam	LRR_8	UniProtKB/TrEMBL
PRINTS	LEURICHRPT	UniProtKB/TrEMBL
PROSITE	LRR	UniProtKB/TrEMBL
	PROKAR_LIPOPROTEIN	UniProtKB/TrEMBL
SMART	LRR_TYP	UniProtKB/TrEMBL
	LRRCT	UniProtKB/TrEMBL
	LRRNT	UniProtKB/TrEMBL
Superfamily-SCOP	L domain-like	UniProtKB/TrEMBL
UniProt	A0A8C2VBI1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-08-03	Lrtm1	leucine rich repeats and transmembrane domains 1		leucine-rich repeats and transmembrane domains 1	Symbol and/or name change	5135510	APPROVED

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)

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