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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

LRIT1 Gene

protein-coding GIFtS: 43
GCID: GC10M085982

leucine-rich repeat, immunoglobulin-like and transmembrane...

(Previous name: leucine rich repeat containing 21 )
(Previous symbol: LRRC21)

Explore 3 diseases affiliated with
LRIT1 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 Repeat, Immunoglobulin-Like And Transmembrane Domains 1¹ ²		Photoreceptor-Associated LRR Superfamily Protein² ³
LRRC21¹ ² ³		Retina-Specific Protein PAL² ³
PAL¹ ² ³		DKFZP434K091¹
FIGLER9¹ ²		Fibronectin Type III, Immunoglobulin And Leucine Rich Repeat Domains 9²
Leucine Rich Repeat Containing 21¹ ²		Leucine-Rich Repeat, Immunoglobulin-Like Domain And Transmembrane Domain-Containing Protein 1²
Leucine-Rich Repeat-Containing Protein 21² ³

External Ids:	HGNC: 23404¹	Entrez Gene: 26103²	Ensembl: ENSG00000148602⁷	UniProtKB: Q9P2V4³

Export aliases for LRIT1 gene to outside databases

Previous GC identifer: GC10M079836

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

UniProtKB/Swiss-Prot: LRIT1_HUMAN, Q9P2V4

Function: Possible role in phototransduction

(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_000010.10 NC_018921.1 NT_030059.13

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the LRIT1 gene promoter:
GR GR-beta GR-alpha
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: LRIT1 promoter sequence

Search SABiosciences Chromatin IP Primers for LRIT1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LRIT1

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

Entrez Gene cytogenetic band: 10q23 Ensembl cytogenetic band: 10q23.1 HGNC cytogenetic band: 10q23

LRIT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LRIT1 gene location

GeneLoc information about chromosome 10 GeneLoc Exon Structure

GeneLoc location for GC10M085982: view genomic region (about GC identifiers)

Start:	85,991,276 bp from pter	End:	86,001,217 bp from pter
Size:	9,942 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: LRIT1_HUMAN, Q9P2V4 (See protein sequence)

Recommended Name: Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1

precursor

Size: 623 amino acids; 68041 Da

Subunit: Homodimer (By similarity)

Subcellular location: Endoplasmic reticulum membrane; Single-pass type I membrane protein (By similarity)

Secondary accessions: Q9Y4N7

Explore the universe of human proteins at neXtProt for LRIT1: NX_Q9P2V4

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9P2V4

LRIT1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_056428.1

ENSEMBL proteins:

ENSP00000361177

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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:0030176	integral to endoplasmic reticulum membrane	ISS	--

LRIT1 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

LRIT1 for domains About GeneDecksing

5/9 InterPro domains/families (see all 9):

IPR003598 Ig_sub2

IPR000483 Cys-rich_flank_reg_C

IPR001611 Leu-rich_rpt

IPR003961 Fibronectin_type3

IPR013098 Ig_I-set

Graphical View of Domain Structure for InterPro Entry Q9P2V4

ProtoNet protein and cluster: Q9P2V4

3 Blocks protein families:

IPB000372 Cysteine-rich flanking region

IPB000483 Cysteine-rich flanking region

IPB003598 Immunoglobulin C-2 type

UniProtKB/Swiss-Prot: LRIT1_HUMAN, Q9P2V4

Similarity: Contains 1 fibronectin type-III domain

Similarity: Contains 1 Ig-like C2-type (immunoglobulin-like) domain

Similarity: Contains 6 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

Function Summary:

UniProtKB/Swiss-Prot: LRIT1_HUMAN, Q9P2V4

Function: Possible role in phototransduction

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		hsa-miR-3934 hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-3136-5p hsa-miR-302a hsa-miR-302e hsa-miR-373

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003674	molecular_function	ND	--

LRIT1 for ontologies About GeneDecksing

(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 LRIT1

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0008150	biological_process	ND	--

LRIT1 for ontologies About GeneDecksing

(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

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(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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About This Section

REFSEQ mRNAs for LRIT1 gene:

NM_015613.2

Unigene Cluster for LRIT1:

Leucine-rich repeat, immunoglobulin-like and transmembrane domains 1

Hs.226000 [show with all ESTs]

Unigene Representative Sequence: NM_015613

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000372105(uc001kcz.1)

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		hsa-miR-3934 hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-3136-5p hsa-miR-302a hsa-miR-302e hsa-miR-373

		SwitchGear 3'UTR luciferase reporter plasmid: LRIT1 3' UTR sequence

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Additional cDNA sequence:

AB031547.1 AL080175.1 DQ426881.1 DQ426882.1

1 DOTS entry:

DT.91972920

5 AceView cDNA sequences:

AB031547 BM716666 BX510255 NM_015613 AL080175

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

LRIT1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CGGCGGGTGA

About this image

LRIT1 expression in embryonic tissues and stem cells

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

1 LifeMap In Vivo Development Anatomical Compartment/Cell

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Eye

Outer Nuclear Layer

Mature Rod Cells

Photoreceptors, Retina

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See LRIT1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for LRIT1

SOURCE GeneReport for Unigene cluster: Hs.226000

SABiosciences Custom PCR Arrays for LRIT1

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In Situ
Assay Products:

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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 LRIT1 gene from 5/12 species (see all 12) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Lrit1^{1 , 5}	leucine-rich repeat, immunoglobulin-like and transmembrane more^{1, 5}	79.35(n)¹ 78.97(a)¹		14 (21.29 cM)⁵ 239037¹ NM_146245.2¹ NP_666357.2¹ 37054830⁵
chicken (Gallus gallus)	Aves	LRIT1¹	leucine-rich repeat, immunoglobulin-like and transmembrane more	62.9(n) 57.67(a)		428935 XM_003641454.1 XP_003641502.1
lizard (Anolis carolinensis)	Reptilia	LRIT1⁶	--	54(a)	1 ↔ 1	GL343199.1(3297614-3335311)
zebrafish (Danio rerio)	Actinopterygii	lrit1b¹	leucine-rich repeat, immunoglobulin-like and transmembrane more	58.7(n) 52.06(a)		553432 NM_001042753.1 NP_001036218.1
fruit fly (Drosophila melanogaster)	Insecta	kek5⁶ kek4⁶ (see all 6)	kekkon4 (see all 6)	9(a) 14(a) (see all 6)	many ↔ many many ↔ many (see all 6)	X(19247218-19365947) 2L(13212335-13215152)

ENSEMBL Gene Tree for LRIT1 (if available)
TreeFam Gene Tree for LRIT1 (if available)

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

Paralogs for LRIT1 gene

LRRC26² SLIT2² ISLR² LRRC17² LRIT2² SLIT1² LRRC52² LRTM1²

LRTM2² ISLR2² LRIT3² LRRC55² SLIT3² LRRC24² LRRC38²

1 SIMAP similar gene for LRIT1 using alignment to 1 protein entry: LRIT1_HUMAN:

LRIT3

LRIT1 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 10 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs189494807^1,2		--	85990937(+)	`TAACCA/GTGGAT`	1	--	ds500¹		0	--	--	--	--
rs79777002^1,2	F,	--	85990982(+)	`AATTTG/TCCTAG`	1	--	ds500¹		1		NA	120
rs17103264^1,2	C,F,H,	--	85990991(+)	`AGCTGT/CGTAAT`	1	--	ds500¹		14		NA NS EA WA	926
rs181767001^1,2		--	85990992(+)	`GCTGTA/GTAATC`	1	--	ds500¹		0	--	--	--	--
rs116214762^1,2	C,F,	--	85991022(+)	`TCACTG/TTTCAG`	1	--	ds500¹		1		WA	118
rs115167911^1,2		--	85991029(+)	`TCAGCA/GCATAT`	1	--	ds500¹		1		WA	118
rs187161707^1,2		--	85991041(+)	`CCTTGC/GTCTAC`	1	--	ds500¹		0	--	--	--	--
rs7909901^1,2	C,F,A,H,	--	85991083(+)	`GCCCCG/ATCAAA`	1	--	ds500¹		16		NS EA NA WA CSA	794
rs114018165^1,2	F,	--	85991104(+)	`GCCATG/AAGACT`	1	--	ds500¹		1		WA	118
rs112935425^1,2		--	85991176(+)	`ACAGGC/TATTGC`	1	--	ds500¹		1		CSA	2

HapMap Linkage Disequilibrium report for LRIT1 (85991276 - 86001217 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for LRIT1: --

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing LRIT1

DNA2.0 Custom Variant and Variant Library Synthesis for LRIT1

(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

LRIT1 for disorders About GeneDecksing

3 diseases for LRIT1: About MalaCards

hepatitis b alzheimer's disease hepatitis

Human Genome Epidemiology (HuGE) Navigator: LRIT1 (3 documents)

Export disorders for LRIT1 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 LRIT1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with LRIT1)

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

Molecular cloning of a novel membrane glycoprotein, Pal, specifically expressed in photoreceptor cells of the retina and containing leucine- rich repeat. (PubMed id 10777785)^{1, 2, 3} Gomi F.... Tohyama M. (2000)
New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)¹ Davila S....Seielstad M. (2010)
Investigation of genetic susceptibility factors for h uman longevity - A targeted nonsynonymous SNP study. (PubMed id 20800603)¹ Flachsbart F....Nebel A. (2010)
The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)² Bechtel S.... Schupp I. (2007)
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)¹ Olsen J.V....Mann M. (2006)
A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)¹ Grupe A....Goate A. (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: 26103	HGNC: 23404	AceView: LRRC21	Ensembl:ENSG00000148602	euGenes: HUgn26103
ECgene: LRIT1	H-InvDB: LRIT1

(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 LRIT1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for LRIT1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for LRIT1 gene:
Search GeneIP for patents involving LRIT1

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),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section


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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LRIT1

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

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LRIT1 Gene

leucine-rich repeat, immunoglobulin-like and transmembrane...

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LRIT1 Gene

leucine-rich repeat, immunoglobulin-like and transmembrane...

Aliasesfor LRIT1 gene

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