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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

LRCH4 Gene

protein-coding   GIFtS: 48
GCID: GC07M100172

leucine-rich repeats and calponin homology (CH) domain containing...


(Previous symbols: LRN, LRRN1)
 Explore 2 diseases affiliated with
LRCH4 via our new
 Human Malady Compendium 
Biological research products
for LRCH4
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Leucine-Rich Repeats And Calponin Homology (CH) Domain Containing 41 2     LRRN42 3
LRN1 2 3     PP141832
LRRN11 2 3     Leucine Rich Repeat Neuronal 42
Leucine-Rich Neuronal Protein2 3     Leucine-Rich Repeat And Calponin Homology Domain-Containing Protein 42
Leucine-Rich Repeat Neuronal Protein 42 3     

External Ids:    HGNC: 66911   Entrez Gene: 40342   Ensembl: ENSG000000774547   UniProtKB: O754273   

Export aliases for LRCH4 gene to outside databases

Previous GC identifers: GC07M099782 GC07M099814 GC07M100009 GC07M094803


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

Entrez Gene summary for LRCH4:
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)

Gene Wiki entry for LRCH4


(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_000007.13  NC_018918.1  NT_007933.15  NT_079595.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LRCH4 gene promoter:
         Sox5   Sp1   Nkx2-5   NF-kappaB   GATA-1   PPAR-gamma1   FAC1   Pax-3   c-Myb   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): LRCH4 promoter sequence
   Search SABiosciences Chromatin IP Primers for LRCH4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LRCH4


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

Entrez Gene cytogenetic band: 7q22   Ensembl cytogenetic band:  7q22.1   HGNC cytogenetic band: 7q22

LRCH4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LRCH4 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M100172:  view genomic region     (about GC identifiers)

Start:
100,169,855 bp from pter      End:
100,183,776 bp from pter
Size:
13,922 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 99,531,269-99,543,409     

(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: LRCH4_HUMAN, O75427 (See protein sequence)
Recommended Name: Leucine-rich repeat and calponin homology domain-containing protein 4  
Size: 683 amino acids; 73450 Da
Sequence caution: Sequence=AAC78793.1; Type=Erroneous gene model prediction;
Secondary accessions: A4D2D5 Q8WV85 Q96ID0

Explore the universe of human proteins at neXtProt for LRCH4: NX_O75427

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O75427

  • LRCH4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_002310.2  
    ENSEMBL proteins: 
     ENSP00000419674   ENSP00000309689   ENSP00000419870  

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    Uscn Proteins for LRCH4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016605PML body IDA16449650


    LRCH4 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

    LRCH4 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR001611 Leu-rich_rpt
     IPR003591 Leu-rich_rpt_typical-subtyp
     IPR001715 CH-domain

    Graphical View of Domain Structure for InterPro Entry O75427

    ProtoNet protein and cluster: O75427

    2 Blocks protein families:
    IPB001611 Leucine-rich repeat signature
    IPB001715 Calponin-like actin-binding


    UniProtKB/Swiss-Prot: LRCH4_HUMAN, O75427
    Similarity: Contains 1 CH (calponin-homology) domain
    Similarity: Contains 9 LRR (leucine-rich) repeats


    (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

    miRNA
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    hsa-miR-485-5p hsa-miR-185* hsa-miR-503 hsa-miR-759 hsa-miR-340 hsa-miR-877* hsa-miR-511 hsa-miR-1265
    SwitchGear 3'UTR luciferase reporter plasmidLRCH4 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LRCH4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19060904


    LRCH4 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 CentralTM Interacting Genes and Proteins Networks for LRCH4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    5/6 Interacting proteins for LRCH4 (O754271, 3 ENSP000003096894) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MDFIQ997501, 3, ENSP000002303214EBI-718707,EBI-724076 I2D: score=4 STRING: ENSP00000230321
    RTN4Q9NQC33, ENSP000003378384I2D: score=4 STRING: ENSP00000337838
    RBBP6Q7Z6E93, ENSP000003178724I2D: score=2 STRING: ENSP00000317872
    TADA2AO754783, ENSP000002253964I2D: score=1 STRING: ENSP00000225396
    SIN3AQ96ST33, ENSP000003536224I2D: score=1 STRING: ENSP00000353622
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007399nervous system development TAS9799793


    LRCH4 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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for LRCH4
    Search CenterWatch for drugs/clinical trials and news about LRCH4 

    (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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for LRCH4 gene: 
    NM_002319.3  

    Unigene Cluster for LRCH4:

    Leucine-rich repeats and calponin homology (CH) domain containing 4
    Hs.125742  [show with all ESTs]
    Unigene Representative Sequence: NM_002319
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000485071(uc003uvh.3 uc010lgz.3 uc003uvi.3 uc011kjw.1)
    ENST00000485554 ENST00000467201 ENST00000310300(uc003uvj.3 uc011kjx.1)
    ENST00000476881 ENST00000497245 ENST00000490359 ENST00000498539 ENST00000487697
    ENST00000470184 ENST00000485583

    miRNA
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    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat LRCH4
    8/31 QIAGEN miScript miRNA Assays for microRNAs that regulate LRCH4 (see all 31):
    hsa-miR-485-5p hsa-miR-185* hsa-miR-503 hsa-miR-759 hsa-miR-340 hsa-miR-877* hsa-miR-511 hsa-miR-1265
    SwitchGear 3'UTR luciferase reporter plasmidLRCH4 3' UTR sequence
    Inhib. RNA
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    OriGene shRNA RFP: LRCH4
    OriGene siRNA: LRCH4
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat LRCH4
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    Additional cDNA sequence: 

    AF459638.1 AK074833.1 AK097420.1 BC007634.1 BC018529.1 FR717257.1 HQ401361.1 

    17 DOTS entries:

    DT.446923  DT.95366153  DT.100779313  DT.100835466  DT.95344174  DT.100779311  DT.91942699  DT.121039567 
    DT.121039618  DT.100779312  DT.40132404  DT.95155267  DT.95366149  DT.95366150  DT.100684627  DT.100680477 
    DT.100779315 

    24/211 AceView cDNA sequences (see all 211):

    BC018529 AK097420 BU621579 BI829556 BM680894 AK074833 AI026884 BI910714 
    BI826492 BQ635892 CA489881 CR610208 AI919053 BF797367 BM712742 BU527456 
    BG392369 AW176705 BM715063 AI992313 CN478530 AI377238 BI835263 BM741494 

    GeneLoc Exon Structure

    5/11 Alternative Splicing Database (ASD) splice patterns (SP) for LRCH4 (see all 11)    About this scheme

    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:                                                                                                                                                            

    ExUns: 17b ^ 18a · 18b ^ 19a · 19b · 19c ^ 20 ^ 21a · 21b ^ 22a · 22b ^ 23 ^ 24 ^ 25
    SP1:              -                                                                     
    SP2:              -                                                                     
    SP3:                                                  -     -                           
    SP4:              -                                                                     
    SP5:                                                                                    


    ECgene alternative splicing isoforms for LRCH4

    (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

    LRCH4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTCCCGGAGC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See LRCH4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LRCH4

    SOURCE GeneReport for Unigene cluster: Hs.125742
        SABiosciences Custom PCR Arrays for LRCH4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LRCH4

    (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 LRCH4 gene from 3/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia LRCH46
    --
    32(a)
    1 ↔ 1
    GL344413.1(1007-21127)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1005351481 leucine-rich repeat and calponin homology domain-containing more 57.78(n)
    55.97(a)
      100535148  XM_003199005.1  XP_003199053.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Lrch6
    Leucine-rich-repeats and calponin homology domain ...
    18(a)
    1 → many
    2L(17367509-17384147)


    ENSEMBL Gene Tree for LRCH4 (if available)
    TreeFam Gene Tree for LRCH4 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for LRCH4 gene
    RSU12  LRCH22  LRSAM12  LRCH32  LRCH12  
    5 SIMAP similar genes for LRCH4 using alignment to 3 protein entries:     LRCH4_HUMAN (see all proteins):
    LRCH2    LRCH1    LRCH3    CNN3    LRRC57

    LRCH4 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

    10/285 NCBI SNPs in LRCH4 are shown (see all 285    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs26868121,2
    C,H--100171167(-) CATGCC/GTTCAC 2 -- int1 ds50016Minor allele frequency- G:0.00NS EA NA 420
    rs26868111,2
    C--100171186(-) GACAGC/AGACTG 2 -- ds5001 int11Minor allele frequency- A:0.00NA 2
    rs610525981,2
    C,--100171198(+) CCCCAA/CGGCTC 2 -- int1 ds50010--------
    rs1480461691,2
    --100171444(+) GGCGCC/GGCGCG 2 -- ds5001 us2k10--------
    rs1124601861,2
    C,F,--100171658(+) AGAGGG/ACTTCT 2 -- us2k1 ut311Minor allele frequency- A:0.01EU 571
    rs772213731,2
    C,F,--100171733(+) GACCCC/TAGAGG 2 -- ut31 us2k11Minor allele frequency- T:0.03WA 118
    rs737111361,2
    C,F,--100171788(+) CACCAC/AGTGCT 2 -- ut31 us2k14Minor allele frequency- A:0.11WA CSA NA 242
    rs1894852561,2
    --100172069(+) ATCACC/TGTGCG 2 -- us2k1 ut310--------
    rs602478891,2
    C,--100172084(+) GGGCTC/TGGCGA 2 -- us2k1 ut313Minor allele frequency- T:0.14WA NA 240
    rs1810696081,2
    --100172111(+) AAGCTA/GTCAGC 2 -- ut31 us2k10--------

    HapMap Linkage Disequilibrium report for LRCH4 (100169855 - 100183776 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for LRCH4
         1 CNV: 4550

    SABiosciences Cancer Mutation PCR Assays
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    (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

    LRCH4 for disorders           About GeneDecksing

    2 diseases for LRCH4:    About MalaCards
    atrioventricular septal defect    neuronitis


    Export disorders for LRCH4 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 LRCH4 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with LRCH4)
        Utopia: connect your pdf to the dynamic
    world of online information

    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. (PubMed id 9799793)1, 2, 3 Gloeckner G.... Rosenthal A. (1998)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)1, 2 Scherer S.W.... Tsui L.-C. (2003)
    4. LRCH proteins: a novel family of cytoskeletal regulat ors. (PubMed id 20805893)1 Foussard H....Payre F. (2010)
    5. ATAC and Mediator coactivators form a stable complex and regulate a set of non-coding RNA genes. (PubMed id 20508642)1 Krebs A.R....Tora L. (2010)
    6. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (2009)
    7. An empirical framework for binary interactome mapping . (PubMed id 19060904)1 Venkatesan K....Vidal M. (2009)
    8. RBBP6 interacts with multifunctional protein YB-1 through its RING finger domain, leading to ubiquitination and proteosomal degradation of YB-1. (PubMed id 18851979)1 Chibi M....Pugh D.J. (2008)
    9. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    10. Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex. (PubMed id 16449650)1 Shiio Y.... Eisenman R.N. (2006)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 4034 HGNC: 6691 AceView: LRCH4 Ensembl:ENSG00000077454 euGenes: HUgn4034
    ECgene: LRCH4 H-InvDB: LRCH4

    (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
    NameDescription
    PharmGKB entry for LRCH4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LRCH4 gene:
    Search GeneIP for patents involving LRCH4

    GeneCards and IP:
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