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Aliases for LRCH4 Gene

Aliases for LRCH4 Gene

  • Leucine Rich Repeats And Calponin Homology Domain Containing 4 2 3 5
  • Leucine-Rich Repeats And Calponin Homology (CH) Domain Containing 4 2 3
  • Leucine-Rich Neuronal Protein 3 4
  • LRRN1 3 4
  • LRRN4 3 4
  • LRN 3 4
  • Leucine-Rich Repeat And Calponin Homology Domain-Containing Protein 4 3
  • Leucine-Rich Repeat Neuronal Protein 4 4
  • Leucine Rich Repeat Neuronal 4 3
  • PP14183 3

External Ids for LRCH4 Gene

Previous HGNC Symbols for LRCH4 Gene

  • LRN
  • LRRN1

Previous GeneCards Identifiers for LRCH4 Gene

  • GC07M099782
  • GC07M099814
  • GC07M100009
  • GC07M100172
  • GC07M094803

Summaries for LRCH4 Gene

Entrez Gene Summary for LRCH4 Gene

  • This gene encodes a protein that contains leucine-rich repeats (LRR) at its amino terminus and that is known to be involved in ligand binding. The carboxyl terminus may act as a membrane anchor. Identified structural elements suggest that the encoded protein resembles a receptor. [provided by RefSeq, Jul 2008]

GeneCards Summary for LRCH4 Gene

LRCH4 (Leucine Rich Repeats And Calponin Homology Domain Containing 4) is a Protein Coding gene. An important paralog of this gene is LRCH1.

Gene Wiki entry for LRCH4 Gene

Additional gene information for LRCH4 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRCH4 Gene

Genomics for LRCH4 Gene

GeneHancer (GH) Regulatory Elements for LRCH4 Gene

Promoters and enhancers for LRCH4 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
GH07J100581 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 661 +1.5 1521 5.9 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC ZFP41 MEF2D SSRP1 ZNF610 FBXO24 LRCH4 ZSCAN25 AP4M1 SRRT ZSCAN21 SAP25 MEPCE PPP1R35 GIGYF1
GH07J100538 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 33 +41.6 41575 12.6 CLOCK MLX DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 AGFG2 SRRT PPP1R35 ZSCAN25 SAP25 GIGYF1 MEPCE AP4M1 LRCH4 ENSG00000242798
GH07J101116 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.1 -537.6 -537555 15.1 CLOCK MLX DMAP1 IRF4 YY1 ZNF143 MEF2D SSRP1 ZNF610 GLIS1 SERPINE1 SRRT GIGYF1 ENSG00000242798 PPP1R35 STAG3L5P MEPCE PCOLCE-AS1 PILRB LRCH4
GH07J100427 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 21.3 +153.0 152989 10.8 CLOCK ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 PPP1R35 MEPCE ZCWPW1 PIR54054 ZSCAN25 SRRT TRIM4 GIGYF1 ZNF3 PILRA
GH07J100475 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 19.1 +108.4 108433 4.4 HDGF PKNOX1 FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 ZNF2 TSC22D4 ZSCAN25 SRRT TRIM4 GIGYF1 ZNF655 ZNF3 ENSG00000242798 STAG3L5P PPP1R35
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRCH4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRCH4 gene promoter:
  • PPAR-gamma2
  • PPAR-gamma1
  • FAC1
  • Pax-3
  • Nkx2-5
  • Sp1
  • c-Myb
  • Sox5
  • GATA-1
  • NF-kappaB

Genomic Locations for LRCH4 Gene

Genomic Locations for LRCH4 Gene
chr7:100,574,011-100,586,188
(GRCh38/hg38)
Size:
12,178 bases
Orientation:
Minus strand
chr7:100,169,855-100,183,776
(GRCh37/hg19)
Size:
13,922 bases
Orientation:
Minus strand

Genomic View for LRCH4 Gene

Genes around LRCH4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRCH4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRCH4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRCH4 Gene

Proteins for LRCH4 Gene

  • Protein details for LRCH4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75427-LRCH4_HUMAN
    Recommended name:
    Leucine-rich repeat and calponin homology domain-containing protein 4
    Protein Accession:
    O75427
    Secondary Accessions:
    • A4D2D5
    • Q8WV85
    • Q96ID0

    Protein attributes for LRCH4 Gene

    Size:
    683 amino acids
    Molecular mass:
    73450 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC78793.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for LRCH4 Gene

Post-translational modifications for LRCH4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LRCH4 Gene

No data available for DME Specific Peptides for LRCH4 Gene

Domains & Families for LRCH4 Gene

Gene Families for LRCH4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for LRCH4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LRCH4: view

No data available for UniProtKB/Swiss-Prot for LRCH4 Gene

Function for LRCH4 Gene

Phenotypes From GWAS Catalog for LRCH4 Gene

Gene Ontology (GO) - Molecular Function for LRCH4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with LRCH4: view
genes like me logo Genes that share phenotypes with LRCH4: view

Animal Model Products

miRNA for LRCH4 Gene

miRTarBase miRNAs that target LRCH4

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRCH4 Gene

Localization for LRCH4 Gene

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 LRCH4 gene
Compartment Confidence
nucleus 5
plasma membrane 3
cytosol 3
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Focal adhesion sites (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRCH4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016323 basolateral plasma membrane IBA --
GO:0016605 PML body IDA 16449650
genes like me logo Genes that share ontologies with LRCH4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LRCH4 Gene

Pathways & Interactions for LRCH4 Gene

SuperPathways for LRCH4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRCH4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IBA --
GO:0007399 nervous system development TAS 9799793
GO:0045199 maintenance of epithelial cell apical/basal polarity IBA --
genes like me logo Genes that share ontologies with LRCH4: view

No data available for Pathways by source and SIGNOR curated interactions for LRCH4 Gene

Drugs & Compounds for LRCH4 Gene

No Compound Related Data Available

Transcripts for LRCH4 Gene

mRNA/cDNA for LRCH4 Gene

Unigene Clusters for LRCH4 Gene

Leucine-rich repeats and calponin homology (CH) domain containing 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRCH4 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b · 16c ^ 17a ·
SP1: - - - - -
SP2: - - - -
SP3:
SP4:
SP5:
SP6: - -
SP7:
SP8:
SP9:
SP10: -
SP11:

ExUns: 17b ^ 18a · 18b ^ 19a · 19b · 19c ^ 20 ^ 21a · 21b ^ 22a · 22b ^ 23 ^ 24 ^ 25
SP1: -
SP2: -
SP3: - -
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for LRCH4 Gene

GeneLoc Exon Structure for
LRCH4
ECgene alternative splicing isoforms for
LRCH4

Expression for LRCH4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRCH4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRCH4 Gene

This gene is overexpressed in Whole Blood (x7.2).

Protein differential expression in normal tissues from HIPED for LRCH4 Gene

This gene is overexpressed in Amniocyte (26.5), Peripheral blood mononuclear cells (12.3), and Monocytes (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LRCH4 Gene



Protein tissue co-expression partners for LRCH4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRCH4 Gene:

LRCH4

SOURCE GeneReport for Unigene cluster for LRCH4 Gene:

Hs.125742

Evidence on tissue expression from TISSUES for LRCH4 Gene

  • Liver(4.2)
  • Muscle(4.2)
  • Skin(4.2)
  • Nervous system(3.9)
genes like me logo Genes that share expression patterns with LRCH4: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRCH4 Gene

Orthologs for LRCH4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRCH4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRCH4 34 33
  • 99.51 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LRCH4 34 33
  • 87.43 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRCH4 34 33
  • 86.97 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gm20605 34
  • 86 (a)
OneToMany
Lrch4 16 34 33
  • 84.85 (n)
rat
(Rattus norvegicus)
Mammalia Lrch4 33
  • 84.16 (n)
oppossum
(Monodelphis domestica)
Mammalia LRCH4 34
  • 63 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRCH4 34
  • 38 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC100535148 33
  • 57.55 (n)
LRCH4 (2 of 2) 34
  • 46 (a)
OneToMany
lrch4 34
  • 45 (a)
OneToMany
Species where no ortholog for LRCH4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • chicken (Gallus gallus)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRCH4 Gene

ENSEMBL:
Gene Tree for LRCH4 (if available)
TreeFam:
Gene Tree for LRCH4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRCH4: view image

Paralogs for LRCH4 Gene

(4) SIMAP similar genes for LRCH4 Gene using alignment to 3 proteins:

  • LRCH4_HUMAN
  • C9JYK0_HUMAN
  • H7C5D9_HUMAN
genes like me logo Genes that share paralogs with LRCH4: view

Variants for LRCH4 Gene

Sequence variations from dbSNP and Humsavar for LRCH4 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs1000004142 -- 100,579,437(-) A/G intron_variant
rs1000083112 -- 100,587,590(-) A/C upstream_transcript_variant
rs1000116950 -- 100,574,325(-) T/C 3_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1000446188 -- 100,574,090(-) T/C 3_prime_UTR_variant
rs1000870684 -- 100,584,604(-) G/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LRCH4 Gene

Variant ID Type Subtype PubMed ID
esv2734888 CNV deletion 23290073
nsv5868 CNV deletion 18451855
nsv607932 CNV loss 21841781
nsv831072 CNV loss 17160897
nsv951386 CNV deletion 24416366

Variation tolerance for LRCH4 Gene

Residual Variation Intolerance Score: 7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.76; 66.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRCH4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRCH4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRCH4 Gene

Disorders for LRCH4 Gene

Additional Disease Information for LRCH4

No disorders were found for LRCH4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRCH4 Gene

Publications for LRCH4 Gene

  1. Large-scale sequencing of two regions in human chromosome 7q22: analysis of 650 kb of genomic sequence around the EPO and CUTL1 loci reveals 17 genes. (PMID: 9799793) Glöckner G … Rosenthal A (Genome research 1998) 2 3 4 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase. (PMID: 25332235) Kim TY … Major MB (Molecular and cellular biology 2015) 3 58

Products for LRCH4 Gene

Sources for LRCH4 Gene

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