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    LRCH4 leucine rich repeats and calponin homology domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 4034, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LRCH4provided by HGNC
    Official Full Name
    leucine rich repeats and calponin homology domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:6691
    See related
    Ensembl:ENSG00000077454 MIM:620165; AllianceGenome:HGNC:6691
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LRN; LRRN1; LRRN4; PP14183
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 33.5), spleen (RPKM 31.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRCH4 in Genome Data Viewer
    Location:
    7q22.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100574011..100586129, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101814094..101826212, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100171634..100183752, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100168785-100169455 Neighboring gene insulin receptor substrate 3, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100172387-100172941 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100172942-100173495 Neighboring gene Sin3A associated protein 25 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100181227-100181915 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100182061-100182574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100182575-100183088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18447 Neighboring gene F-box protein 24 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100187581-100188381 Neighboring gene PCOLCE antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100201095-100201887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18449 Neighboring gene procollagen C-endopeptidase enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26376

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ40101, FLJ46315

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in membrane raft assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of toll-like receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in PML body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat and calponin homology domain-containing protein 4
    Names
    leucine rich repeat neuronal 4
    leucine-rich neuronal protein
    leucine-rich repeats and calponin homology (CH) domain containing 4

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001289934.2 → NP_001276863.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001276863.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AI491709, BC007634, BC018529, DC397219, DR422652
      Consensus CDS
      CCDS94156.1
      UniProtKB/TrEMBL
      H7C5D9
      Related
      ENSP00000419674.2, ENST00000485554.6
      Conserved Domains (5) summary
      cd00116
      Location:103 → 245
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:46 → 69
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:537 → 630
      CH; Calponin homology (CH) domain
      pfam12799
      Location:92 → 131
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:138 → 194
      LRR_8; Leucine rich repeat

    2. NM_002319.5 → NP_002310.2  leucine-rich repeat and calponin homology domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_002310.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AI491709, BC007634, BC018529, DC397219, DR422652
      Consensus CDS
      CCDS34706.1
      UniProtKB/Swiss-Prot
      A4D2D5, O75427, Q8WV85, Q96ID0
      Related
      ENSP00000309689.6, ENST00000310300.11
      Conserved Domains (5) summary
      cd00116
      Location:103 → 245
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:46 → 69
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:537 → 627
      CH; Calponin homology (CH) domain
      pfam12799
      Location:92 → 131
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:138 → 194
      LRR_8; Leucine rich repeat

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      100574011..100586129 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420389.1 → XP_047276345.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X11

    2. XM_047420384.1 → XP_047276340.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X7

    3. XM_047420390.1 → XP_047276346.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X12

    4. XM_047420388.1 → XP_047276344.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X10

    5. XM_047420387.1 → XP_047276343.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X9

    6. XM_047420383.1 → XP_047276339.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X6

    7. XM_047420378.1 → XP_047276334.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X1

    8. XM_047420379.1 → XP_047276335.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X2

    9. XM_047420381.1 → XP_047276337.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X4

    10. XM_047420385.1 → XP_047276341.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X8

    11. XM_047420380.1 → XP_047276336.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X3

    12. XM_047420382.1 → XP_047276338.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X5

    13. XM_047420395.1 → XP_047276351.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X16

    14. XM_047420392.1 → XP_047276348.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X14

    15. XM_047420397.1 → XP_047276353.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X17

    16. XM_047420391.1 → XP_047276347.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X13

    17. XM_047420398.1 → XP_047276354.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X17

    18. XM_047420394.1 → XP_047276350.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X15

    19. XM_047420396.1 → XP_047276352.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X17

    20. XM_047420393.1 → XP_047276349.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X15

    RNA

    1. XR_007060035.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      101814094..101826212 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358242.1 → XP_054214217.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X11

    2. XM_054358237.1 → XP_054214212.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X7

    3. XM_054358243.1 → XP_054214218.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X12

    4. XM_054358241.1 → XP_054214216.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X10

    5. XM_054358240.1 → XP_054214215.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X9

    6. XM_054358236.1 → XP_054214211.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X6

    7. XM_054358231.1 → XP_054214206.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X1

    8. XM_054358238.1 → XP_054214213.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X18

    9. XM_054358232.1 → XP_054214207.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X2

    10. XM_054358234.1 → XP_054214209.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X4

    11. XM_054358239.1 → XP_054214214.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X8

    12. XM_054358233.1 → XP_054214208.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X3

    13. XM_054358235.1 → XP_054214210.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X5

    14. XM_054358248.1 → XP_054214223.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X16

    15. XM_054358245.1 → XP_054214220.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X14

    16. XM_054358250.1 → XP_054214225.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X17

      UniProtKB/TrEMBL
      B4DYF8

    17. XM_054358244.1 → XP_054214219.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X13

    18. XM_054358251.1 → XP_054214226.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X17

      UniProtKB/TrEMBL
      B4DYF8

    19. XM_054358247.1 → XP_054214222.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X15

    20. XM_054358249.1 → XP_054214224.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X17

      UniProtKB/TrEMBL
      B4DYF8

    21. XM_054358246.1 → XP_054214221.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X15

    RNA

    1. XR_008487616.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75427.2 GenPept UniProtKB/Swiss-Prot:O75427

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