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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

LRTM1 Gene

protein-coding GIFtS: 43
GCID: GC03M054928

leucine-rich repeats and transmembrane domains 1

Explore 3 diseases affiliated with
LRTM1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Leucine-Rich Repeats And Transmembrane Domains 1¹ ²
HT017¹
Leucine-Rich Repeat And Transmembrane Domain-Containing Protein 1²

External Ids:	HGNC: 25023¹	Entrez Gene: 57408²	Ensembl: ENSG00000144771⁷	UniProtKB: Q9HBL6³

Export aliases for LRTM1 gene to outside databases

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000003.11 NC_018914.1 NT_022517.18

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the LRTM1 gene promoter:
USF1 NF-YA MyoD NF-YB CBF-A CBF-B USF-1 CP1A NF-Y CBF(2)
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: LRTM1 promoter sequence

Search SABiosciences Chromatin IP Primers for LRTM1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LRTM1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3p14.3 Ensembl cytogenetic band: 3p14.3 HGNC cytogenetic band: 3p14.3

LRTM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LRTM1 gene location

GeneLoc information about chromosome 3 GeneLoc Exon Structure

GeneLoc location for GC03M054928: view genomic region (about GC identifiers)

Start:	54,952,264 bp from pter	End:	55,001,115 bp from pter
Size:	48,852 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: LRTM1_HUMAN, Q9HBL6 (See protein sequence)

Recommended Name: Leucine-rich repeat and transmembrane domain-containing protein 1 precursor

Size: 345 amino acids; 38171 Da

Subcellular location: Membrane; Single-pass type I membrane protein (Potential)

Secondary accessions: Q8IUU2

Alternative splicing: 2 isoforms: Q9HBL6-1 Q9HBL6-2

Explore the universe of human proteins at neXtProt for LRTM1: NX_Q9HBL6

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9HBL6

LRTM1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_065729.1

ENSEMBL proteins:

ENSP00000273286 ENSP00000419772

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	Uscn Proteins for LRTM1

Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0016021	integral to membrane	IEA	--

LRTM1 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

LRTM1 for domains About GeneDecksing

4 InterPro domains/families:

IPR000483 Cys-rich_flank_reg_C

IPR001611 Leu-rich_rpt

IPR003591 Leu-rich_rpt_typical-subtyp

IPR000372 LRR-contain_N

Graphical View of Domain Structure for InterPro Entry Q9HBL6

ProtoNet protein and cluster: Q9HBL6

2 Blocks protein families:

IPB000483 Cysteine-rich flanking region

IPB001611 Leucine-rich repeat signature

UniProtKB/Swiss-Prot: LRTM1_HUMAN, Q9HBL6

Similarity: Contains 5 LRR (leucine-rich) repeats

Similarity: Contains 1 LRRCT domain

Similarity: Contains 1 LRRNT domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for LRTM1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for LRTM1
Search CenterWatch for drugs/clinical trials and news about LRTM1

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for LRTM1 gene:

NM_020678.2

Unigene Cluster for LRTM1:

Leucine-rich repeats and transmembrane domains 1

Hs.591668 [show with all ESTs]

Unigene Representative Sequence: BC040732

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000273286(uc003dhl.3) ENST00000493075

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Additional cDNA sequence:

AF225421.1 BC040732.1 BC074741.2

4 DOTS entries:

DT.100748493 DT.116604 DT.100748494 DT.95366896

24/78 AceView cDNA sequences (see all 78):

AI193267 BM706979 AA298298 AA298309 BX119799 AA298332 BC040732 AA702392

AA298392 AA298331 AA298327 AA298378 AI802922 AW959797 AI761918 AA298389

AA716035 BC074741 BM703580 AA758427 AA298395 AA757350 BX954320 AA298185

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

LRTM1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GGGGACCCTT

About this image

LRTM1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

2 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Eye

Inner Nuclear Layer

Mature Rod Bipolar Cells

Bipolar, Retina

Eye

Inner Nuclear Layer

Type1 Off Cone Bipolar Cells

Bipolar, Retina

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See LRTM1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for LRTM1

SOURCE GeneReport for Unigene cluster: Hs.591668

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In Situ
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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for LRTM1 gene from 4/10 species (see all 10) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	LRTM1⁶	Uncharacterized protein	50(a)	1 ↔ 1	12(7889891-7893474)
lizard (Anolis carolinensis)	Reptilia	LRTM1⁶	--	46(a)	1 ↔ 1	2(161387208-161395816)
zebrafish (Danio rerio)	Actinopterygii	CABZ01074188.1⁶	--	40(a)	1 ↔ 1	8(55946969-55959656)
fruit fly (Drosophila melanogaster)	Insecta	kek6⁶ kek1⁶ (see all 6)	kekkon-1 (see all 6)	8(a) 8(a) (see all 6)	many ↔ many many ↔ many (see all 6)	3R(27447858-27490368) 2L(12817000-12822787)

ENSEMBL Gene Tree for LRTM1 (if available)
TreeFam Gene Tree for LRTM1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for LRTM1 gene

LRRC26² SLIT2² ISLR² LRRC17² LRIT2² SLIT1² LRRC52² LRIT1²

LRTM2² SLIT3² LRIT3² LRRC55² ISLR2² LRRC24² LRRC38²

1 SIMAP similar gene for LRTM1 using alignment to 1 protein entry: LRTM1_HUMAN:

LRTM2

LRTM1 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 3 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs141453618^1,2	C,F,	--	54952531(+)	`TTCCCA/GGGATC`	2	P	syn¹		1		NA	4550
rs144150699^1,2	C,F	--	54952554(+)	`CAAGGG/CTCCCC`	2	/P /A	mis¹		2		NA EU	5839
rs200474589^1,2		--	54952583(+)	`TTGCCC/GCATAG`	2	A G	mis¹		0	--	--	--	--
rs146117666^1,2	C,F,	--	54952639(+)	`CCACAC/GACAAC`	2	V	syn¹		1		NA	4552
rs61735203^1,2	C,F,	--	54952644(+)	`CACAAC/TGCCAG`	2	I V	mis¹		4		NS WA NA EU	6059
rs142542421^1,2	C,F	--	54952676(+)	`CATGAC/TGCAGG`	2	H R	mis¹		1		NA	4552
rs141801857^1,2	C,F	--	54952677(+)	`ATGACG/ACAGGT`	2	/R /C	mis¹		2		NA EU	5875
rs147753980^1,2	C,F,	--	54952678(+)	`TGACGC/AAGGTT`	2	/L	syn¹		2		NA EU	5875
rs138683728^1,2	C,F	--	54952688(+)	`TGGCCG/AGCCTT`	2	/P /L	mis¹		1		NA	4552
rs11541701^1,2	C,F,H,	--	54952727(-)	`GGAGCG/TAGAAC`	2	R L	mis¹		6		NS NA	5156

HapMap Linkage Disequilibrium report for LRTM1 (54952264 - 55001115 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for LRTM1: --

SABiosciences Cancer Mutation PCR Assays

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

LRTM1 for disorders About GeneDecksing

3 diseases for LRTM1: About MalaCards

congenital diaphragmatic hernia hernia hypertrichosis

2 diseases from the University of Copenhagen DISEASES database for LRTM1:

Hypertrichosis Congenital diaphragmatic hernia

Export disorders for LRTM1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for LRTM1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with LRTM1)

Utopia: connect your pdf to the dynamic
world of online information

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)^{1, 3} Strausberg R.L....Marra M.A. (2002)
Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PubMed id 10931946)^{1, 2} Hu R.-M.... Chen J.-L. (2000)
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)¹ Olsen J.V....Mann M. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 57408	HGNC: 25023	AceView: HT017	Ensembl:ENSG00000144771	euGenes: HUgn57408
ECgene: LRTM1	H-InvDB: LRTM1

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for LRTM1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for LRTM1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for LRTM1 gene:
Search GeneIP for patents involving LRTM1

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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Advanced Cell Diagnostics
About This Section


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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LRTM1

GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes LRTM1 gene at Home site.

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LRTM1 Gene

leucine-rich repeats and transmembrane domains 1

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LRTM1 Gene

leucine-rich repeats and transmembrane domains 1

Aliasesfor LRTM1 gene

Summariesfor LRTM1 gene

Genomic Viewsfor LRTM1 gene

Proteinsfor LRTM1 gene

Protein Domains /Familiesfor LRTM1 gene

Functionfor LRTM1 gene

Pathways & Interactionsfor LRTM1 gene

Drugs & Compoundsfor LRTM1 gene

Transcriptsfor LRTM1 gene

Expression for LRTM1 gene

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Genome Databases showing LRTM1 gene

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Specialized Databases showing LRTM1 gene

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Aliases
for LRTM1 gene

Summaries
for LRTM1 gene

Genomic Views
for LRTM1 gene

Proteins
for LRTM1 gene

Protein Domains /
Families
for LRTM1 gene

Function
for LRTM1 gene

Pathways & Interactions
for LRTM1 gene

Drugs & Compounds
for LRTM1 gene

Transcripts
for LRTM1 gene

Expression
for LRTM1 gene

Orthologs
for LRTM1 gene

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for LRTM1 gene

Genomic Variants
for LRTM1 gene

Disorders / Diseases
for LRTM1 gene

Publications
for LRTM1 gene

Intellectual Property
for LRTM1 gene

Products
for LRTM1 gene