Aliases for LRIT1 Gene

Aliases for LRIT1 Gene

  • Leucine Rich Repeat, Ig-Like And Transmembrane Domains 1 2 3 5
  • PAL 2 3 4
  • Leucine-Rich Repeat, Immunoglobulin-Like Domain And Transmembrane Domain-Containing Protein 1 3 4
  • Fibronectin Type III, Immunoglobulin And Leucine Rich Repeat Domains 9 2 3
  • Photoreceptor-Associated LRR Superfamily Protein 3 4
  • Leucine-Rich Repeat-Containing Protein 21 3 4
  • Leucine Rich Repeat Containing 21 2 3
  • Retina-Specific Protein PAL 3 4
  • FIGLER9 2 3
  • LRRC21 3 4
  • Leucine-Rich Repeat, Immunoglobulin-Like And Transmembrane Domains 1 3
  • DKFZP434K091 2
  • LRIT1 5

External Ids for LRIT1 Gene

Previous HGNC Symbols for LRIT1 Gene

  • LRRC21

Previous GeneCards Identifiers for LRIT1 Gene

  • GC10M085982
  • GC10M079836

Summaries for LRIT1 Gene

GeneCards Summary for LRIT1 Gene

LRIT1 (Leucine Rich Repeat, Ig-Like And Transmembrane Domains 1) is a Protein Coding gene. Diseases associated with LRIT1 include Nanophthalmos and Leukoencephalopathy With Vanishing White Matter. An important paralog of this gene is LRIT3.

UniProtKB/Swiss-Prot Summary for LRIT1 Gene

Additional gene information for LRIT1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRIT1 Gene

Genomics for LRIT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRIT1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J084241 Promoter/Enhancer 0.5 EPDnew Ensembl 600.7 +0.0 45 0.6 LRIT1 RGR piR-41084
GH10J084214 Enhancer 0.6 ENCODE 22.4 +26.8 26796 0.1 CTCF PRDM10 JUND RAD21 SMC3 NR2F1 NR2F6 CEBPB FOXK2 CHD1 LRIT1 GHITM CDHR1 LRIT2
GH10J084156 Enhancer 1.1 Ensembl ENCODE dbSUPER 10.7 +82.5 82545 8 TEAD4 POLR2A JUND ZIC2 PKNOX1 HDAC1 SOX6 NRF1 MGA CEBPB piR-57137-005 CDHR1 LRIT2 GHITM LRIT1 RNU1-65P C10orf99 ENSG00000271933 CCSER2 MN309191
GH10J084264 Enhancer 1 Ensembl ENCODE 11.9 -23.4 -23420 0.9 CTCF TEAD4 FOXA1 PRDM1 ZNF143 ZIC2 POLR2A REST RAD21 TRIM22 LRIT1 LRIT2 CDHR1 RGR LINC00858 HSALNG0079322 CCSER2
GH10J084269 Enhancer 0.7 Ensembl ENCODE 12 -28.3 -28255 1.2 CEBPB FOS BHLHE40 USF2 ATF4 JUND CEBPG lnc-RGR-2 RGR LRIT1 LRIT2 LINC00858 CCSER2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRIT1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRIT1

Top Transcription factor binding sites by QIAGEN in the LRIT1 gene promoter:
  • GR
  • GR-alpha
  • GR-beta

Genomic Locations for LRIT1 Gene

Genomic Locations for LRIT1 Gene
chr10:84,231,520-84,241,546
(GRCh38/hg38)
Size:
10,027 bases
Orientation:
Minus strand
chr10:85,991,276-86,001,217
(GRCh37/hg19)
Size:
9,942 bases
Orientation:
Minus strand

Genomic View for LRIT1 Gene

Genes around LRIT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRIT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRIT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRIT1 Gene

Proteins for LRIT1 Gene

  • Protein details for LRIT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P2V4-LRIT1_HUMAN
    Recommended name:
    Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1
    Protein Accession:
    Q9P2V4
    Secondary Accessions:
    • Q0QD41
    • Q9Y4N7

    Protein attributes for LRIT1 Gene

    Size:
    623 amino acids
    Molecular mass:
    68041 Da
    Quaternary structure:
    • Homodimer.

neXtProt entry for LRIT1 Gene

Post-translational modifications for LRIT1 Gene

  • Glycosylation at Asn156, Asn296, and Asn455
  • Modification sites at PhosphoSitePlus

Other Protein References for LRIT1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRIT1 Gene

Domains & Families for LRIT1 Gene

Gene Families for LRIT1 Gene

Protein Domains for LRIT1 Gene

InterPro:
Blocks:
  • Immunoglobulin C-2 type
  • Cysteine-rich flanking region, N-terminal
  • Cysteine-rich flanking region, C-terminal
ProtoNet:

Suggested Antigen Peptide Sequences for LRIT1 Gene

GenScript: Design optimal peptide antigens:
  • Retina-specific protein PAL (LRIT1_HUMAN)
  • Leucine rich repeat containing 21 (Q0QD41_HUMAN)
  • Leucine rich repeat containing 21 (Q0QD42_HUMAN)
genes like me logo Genes that share domains with LRIT1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LRIT1 Gene

Function for LRIT1 Gene

Molecular function for LRIT1 Gene

UniProtKB/Swiss-Prot Function:
Possible role in phototransduction.

Phenotypes From GWAS Catalog for LRIT1 Gene

Gene Ontology (GO) - Molecular Function for LRIT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with LRIT1: view
genes like me logo Genes that share phenotypes with LRIT1: view

Animal Models for LRIT1 Gene

MGI Knock Outs for LRIT1:
  • Lrit1 Lrit1<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

miRNA for LRIT1 Gene

miRTarBase miRNAs that target LRIT1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRIT1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LRIT1 Gene

Localization for LRIT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRIT1 Gene

Endoplasmic reticulum membrane. Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRIT1 gene
Compartment Confidence
endoplasmic reticulum 4
plasma membrane 3
extracellular 2
lysosome 1
mitochondrion 0
peroxisome 0
golgi apparatus 0

Gene Ontology (GO) - Cellular Components for LRIT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030176 integral component of endoplasmic reticulum membrane ISS --
genes like me logo Genes that share ontologies with LRIT1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRIT1 Gene

Pathways & Interactions for LRIT1 Gene

PathCards logo

SuperPathways for LRIT1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRIT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with LRIT1: view

No data available for Pathways by source and SIGNOR curated interactions for LRIT1 Gene

Drugs & Compounds for LRIT1 Gene

No Compound Related Data Available

Transcripts for LRIT1 Gene

mRNA/cDNA for LRIT1 Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRIT1

Alternative Splicing Database (ASD) splice patterns (SP) for LRIT1 Gene

No ASD Table

Relevant External Links for LRIT1 Gene

GeneLoc Exon Structure for
LRIT1

Expression for LRIT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRIT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRIT1 Gene

This gene is overexpressed in Testis (x49.3).

Protein differential expression in normal tissues from HIPED for LRIT1 Gene

This gene is overexpressed in Vitreous humor (50.3) and Retina (16.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRIT1 Gene



Protein tissue co-expression partners for LRIT1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRIT1

SOURCE GeneReport for Unigene cluster for LRIT1 Gene:

Hs.226000

Evidence on tissue expression from TISSUES for LRIT1 Gene

  • Eye(4.4)
genes like me logo Genes that share expression patterns with LRIT1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRIT1 Gene

Orthologs for LRIT1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRIT1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRIT1 30 31
  • 98.61 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRIT1 30 31
  • 82.85 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lrit1 30 17 31
  • 79.35 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lrit1 30
  • 79.24 (n)
Dog
(Canis familiaris)
Mammalia LRIT1 31
  • 75 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LRIT1 31
  • 60 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LRIT1 31
  • 48 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LRIT1 30 31
  • 63.64 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRIT1 31
  • 54 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lrit1 30
  • 57.27 (n)
Zebrafish
(Danio rerio)
Actinopterygii lrit1b 30 31
  • 58.7 (n)
OneToMany
lrit1a 31
  • 47 (a)
OneToMany
Species where no ortholog for LRIT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for LRIT1 Gene

ENSEMBL:
Gene Tree for LRIT1 (if available)
TreeFam:
Gene Tree for LRIT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRIT1: view image

Paralogs for LRIT1 Gene

(1) SIMAP similar genes for LRIT1 Gene using alignment to 1 proteins:

  • LRIT1_HUMAN
genes like me logo Genes that share paralogs with LRIT1: view

Variants for LRIT1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRIT1 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs11200933 - p.Leu154Met
rs12262099 - p.Pro389Thr
rs3814211 - p.Ser591Gly
rs7090059 - p.Pro258Gln

Additional dbSNP identifiers (rs#s) for LRIT1 Gene

Structural Variations from Database of Genomic Variants (DGV) for LRIT1 Gene

Variant ID Type Subtype PubMed ID
nsv1046749 CNV gain 25217958
nsv1141879 OTHER inversion 24896259
nsv551745 CNV gain 21841781

Variation tolerance for LRIT1 Gene

Residual Variation Intolerance Score: 81.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.96; 74.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRIT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRIT1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRIT1 Gene

Disorders for LRIT1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LRIT1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
nanophthalmos
  • nanophthalmia
leukoencephalopathy with vanishing white matter
  • cle
fundus dystrophy
  • retinal dystrophy
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search LRIT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LRIT1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LRIT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRIT1 Gene

Publications for LRIT1 Gene

  1. Molecular cloning of a novel membrane glycoprotein, pal, specifically expressed in photoreceptor cells of the retina and containing leucine-rich repeat. (PMID: 10777785) Gomi F … Tohyama M (The Journal of neuroscience : the official journal of the Society for Neuroscience 2000) 2 3 4
  2. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 41
  3. Mapping of transcription start sites of human retina expressed genes. (PMID: 17286855) Roni V … Wissinger B (BMC genomics 2007) 3 4
  4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 41
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3

Products for LRIT1 Gene

Sources for LRIT1 Gene