Human Gene LRIT3 (uc031sgv.1) Description and Page Index
  Description: Homo sapiens leucine-rich repeat, immunoglobulin-like and transmembrane domains 3 (LRIT3), mRNA.
RefSeq Summary (NM_198506): This gene encodes a protein that has a fibronectin type III domain and a C-terminal transmembrane domain, as well as a leucine-rich repeat domain and immunoglobulin-like domain near the N-terminus. The encoded protein may regulate fibroblast growth factor receptors and affect the modification of these receptors, which are glycosylated differently in the Golgi and endoplasmic reticulum. Mutations in this gene are associated with congenital stationary night blindness, type 1F. [provided by RefSeq, May 2013]. Sequence Note: This RefSeq record was created from partial transcripts and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by orthologous alignment from mouse (NP_001192031.1). ##Evidence-Data-START## RNAseq introns :: single sample supports all introns SAMN01820689, SAMN01820691 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr4:110,769,340-110,793,471 Size: 24,132 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr4:110,769,358-110,791,945 Size: 22,588 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:110,769,340-110,793,471)mRNA (may differ from genome)Protein (679 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSCGAP
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIneXtProtOMIM
PubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: LRIT3_HUMAN
DESCRIPTION: RecName: Full=Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3;
SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).
SIMILARITY: Contains 1 fibronectin type-III domain.
SIMILARITY: Contains 1 Ig-like (immunoglobulin-like) domain.
SIMILARITY: Contains 4 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 LRRCT domain.
SEQUENCE CAUTION: Sequence=AAI04038.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LRIT3
CDC HuGE Published Literature: LRIT3
Positive Disease Associations: Blood Pressure , Cholesterol, HDL , Exercise Test , Triglycerides
Related Studies:
  1. Blood Pressure
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.
  2. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  3. Exercise Test
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: LRIT3
Diseases sorted by gene-association score: night blindness, congenital stationary , 1f, autosomal recessive* (1300), congenital stationary night blindness* (151), night blindness (18), night blindness, congenital stationary , 1b, autosomal recessive (13)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.70 RPKM in Brain - Cerebellum
Total median expression: 12.25 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -2.2018-0.122 Picture PostScript Text
3' UTR -396.181526-0.260 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003961 - Fibronectin_type3
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003598 - Ig_sub2
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp

Pfam Domains:
PF00560 - Leucine Rich Repeat
PF07679 - Immunoglobulin I-set domain
PF12799 - Leucine Rich repeats (2 copies)
PF13306 - Leucine rich repeats (6 copies)
PF13855 - Leucine rich repeat
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin
49265 - Fibronectin type III
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

ModBase Predicted Comparative 3D Structure on Q3SXY7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007601 visual perception
GO:0040036 regulation of fibroblast growth factor receptor signaling pathway
GO:0050896 response to stimulus

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030425 dendrite
GO:0042995 cell projection
GO:0043204 perikaryon


-  Descriptions from all associated GenBank mRNAs
  JQ354981 - Homo sapiens leucine-rich repeat immunoglobulin-like domain and transmembrane domain-containing protein 3 (LRIT3) mRNA, partial cds.
AK126648 - Homo sapiens cDNA FLJ44691 fis, clone BRACE3013874.
BC104037 - Homo sapiens leucine-rich repeat, immunoglobulin-like and transmembrane domains 3, mRNA (cDNA clone MGC:120618 IMAGE:40026462), complete cds.
KJ904214 - Synthetic construct Homo sapiens clone ccsbBroadEn_13608 LRIT3 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: C9J1C2, LRIT3_HUMAN, NM_198506, NP_940908, Q3SXY7, Q6ZTG1, uc003hzx.4
UCSC ID: uc031sgv.1
RefSeq Accession: NM_198506
Protein: Q3SXY7 (aka LRIT3_HUMAN)
CCDS: CCDS3688.3

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198506.4
exon count: 4CDS single in 3' UTR: no RNA size: 3601
ORF size: 2040CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4271.00frame shift in genome: no % Coverage: 99.53
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.