Human Gene LRRC7 (uc001dep.3) Description and Page Index
  Description: Homo sapiens leucine rich repeat containing 7 (LRRC7), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:70,225,858-70,589,171 Size: 363,314 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr1:70,225,888-70,587,570 Size: 361,683 Coding Exon Count: 25 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:70,225,858-70,589,171)mRNA (may differ from genome)Protein (1537 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: LRRC7_HUMAN
DESCRIPTION: RecName: Full=Leucine-rich repeat-containing protein 7; AltName: Full=Densin-180; Short=Densin; AltName: Full=Protein LAP1;
FUNCTION: Required for normal synaptic spine architecture and function. Necessary for DISC1 and GRM5 localization to postsynaptic density complexes and for both N-methyl D-aspartate receptor-dependent and metabotropic glutamate receptor-dependent long term depression.
SUBUNIT: Interacts with CAMKII, CNKSR2 and DLG4 (By similarity). Interacts with CTNND2/Catenin delta-2. Forms a complex with N- cadherin through CTNND2.
SUBCELLULAR LOCATION: Cytoplasm. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density (By similarity).
TISSUE SPECIFICITY: Brain-specific. Isoform 3 is ubiquitously expressed.
SIMILARITY: Belongs to the LAP (LRR and PDZ) protein family.
SIMILARITY: Contains 17 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SEQUENCE CAUTION: Sequence=AAP06801.1; Type=Erroneous initiation; Sequence=BAA92603.1; Type=Frameshift; Positions=665; Sequence=CAH70975.1; Type=Erroneous initiation; Sequence=CAH73692.1; Type=Erroneous initiation; Sequence=CAH74019.1; Type=Erroneous initiation; Sequence=CAI22426.1; Type=Erroneous initiation; Sequence=CAI23423.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LRRC7
CDC HuGE Published Literature: LRRC7
Positive Disease Associations: Attention Deficit Disorder with Hyperactivity , Body Height , Hypertension
Related Studies:
  1. Attention Deficit Disorder with Hyperactivity
    Eric Mick et al. Journal of the American Academy of Child and Adolescent Psychiatry 2011, Genome-wide association study of the child behavior checklist dysregulation profile., Journal of the American Academy of Child and Adolescent Psychiatry. [PubMed 21784300]
    We found suggestive evidence for developmentally expressed genes operant in hippocampal dependent memory and learning with the CBCL-DP.
  2. Body Height
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Hypertension
    Se Joong Kim et al. Circulation journal 2012, Genetic association of short sleep duration with hypertension incidence--a 6-year follow-up in the Korean genome and epidemiology study., Circulation journal : official journal of the Japanese Circulation Society. [PubMed 22322875]
    This prospective communitywide study showed that premenopausal women with short sleep duration had an increased risk of incident HT, and found associations with specific genomic markers.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: LRRC7
Diseases sorted by gene-association score: dental pulp necrosis (9), dental pulp disease (4)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.21 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 43.66 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -7.0030-0.233 Picture PostScript Text
3' UTR -347.891601-0.217 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
IPR001611 - Leu-rich_rpt
IPR025875 - Leu-rich_rpt_2_copies
IPR001478 - PDZ

Pfam Domains:
PF00595 - PDZ domain (Also known as DHR or GLGF)
PF13306 - Leucine rich repeats (6 copies)
PF13855 - Leucine rich repeat

SCOP Domains:
50156 - PDZ domain-like
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1

ModBase Predicted Comparative 3D Structure on Q96NW7
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
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007165 signal transduction
GO:0010976 positive regulation of neuron projection development
GO:0043312 neutrophil degranulation

Cellular Component:
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030054 cell junction
GO:0035580 specific granule lumen
GO:0043005 neuron projection
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  AK294206 - Homo sapiens cDNA FLJ54846 complete cds, highly similar to Leucine-rich repeat-containing protein 7.
AF498274 - Homo sapiens densin-180 like protein mRNA, complete cds.
AF434715 - Homo sapiens densin-180 mRNA, complete cds.
BC128989 - Homo sapiens leucine rich repeat containing 7, mRNA (cDNA clone MGC:144918 IMAGE:8381584), complete cds.
CR749629 - Homo sapiens mRNA; cDNA DKFZp686I1147 (from clone DKFZp686I1147).
AB037786 - Homo sapiens mRNA for KIAA1365 protein, partial cds.
AX786956 - Sequence 1 from Patent WO03006493.
BX648943 - Homo sapiens mRNA; cDNA DKFZp686O2344 (from clone DKFZp686O2344).
JD114484 - Sequence 95508 from Patent EP1572962.
JD563015 - Sequence 544039 from Patent EP1572962.
JD504078 - Sequence 485102 from Patent EP1572962.
JD093937 - Sequence 74961 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96NW7 (Reactome details) participates in the following event(s):

R-HSA-6798749 Exocytosis of specific granule lumen proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA1365, LAP1, LRRC7_HUMAN, NM_020794, NP_065845, Q5VXC2, Q5VXC3, Q68D07, Q86VE8, Q8WX20, Q96NW7, Q9P2I2
UCSC ID: uc001dep.3
RefSeq Accession: NM_020794
Protein: Q96NW7 (aka LRRC7_HUMAN or LAP1_HUMAN)
CCDS: CCDS645.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020794.2
exon count: 25CDS single in 3' UTR: no RNA size: 6313
ORF size: 4614CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9428.00frame shift in genome: no % Coverage: 98.92
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: 16# 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.