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    LRCH2 leucine rich repeats and calponin homology domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 57631, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LRCH2provided by HGNC
    Official Full Name
    leucine rich repeats and calponin homology domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:29292
    See related
    Ensembl:ENSG00000130224 AllianceGenome:HGNC:29292
    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
    dA204F4.4
    Summary
    This gene encodes a member of the leucine-rich repeat and calponin homology domain-containing protein family. These family members contain multiple N-terminal leucine-rich repeats, in addition to a C-terminal calponin homology domain, a type of domain that mediates interactions with actin filaments. These proteins are conserved across animal species, and studies of a similar Drosophila protein indicate a function as a cytoskeletal scaffolding protein. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2011]
    Expression
    Broad expression in prostate (RPKM 3.7), brain (RPKM 2.9) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRCH2 in Genome Data Viewer
    Location:
    Xq23
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (115110616..115234096, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (113519325..113642681, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (114345179..114468659, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene zinc finger protein 670 pseudogene Neighboring gene YAP1 pseudogene 2 Neighboring gene small nucleolar RNA, H/ACA box 35B Neighboring gene TMSB4X pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:114424095-114424596 Neighboring gene RBMX like 3 Neighboring gene ribosomal protein L36 pseudogene 18 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:114552544-114553121 Neighboring gene leucine zipper protein 4 Neighboring gene uncharacterized LOC107985681 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:114579651-114580150 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:114606578-114607435 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:114607575-114608077

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Leucine-rich repeat (LRR) proteins: integrators of pattern recognition and signaling in immunity. Ng A, et al. Autophagy, 2011 Sep. PMID 21606681, Free PMC Article
    2. Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. Ng AC, et al. Proc Natl Acad Sci U S A, 2011 Mar 15. PMID 20616063, Free PMC Article
    3. LRCH proteins: a novel family of cytoskeletal regulators. Foussard H, et al. PLoS One, 2010 Aug 18. PMID 20805893, Free PMC Article
    4. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
    5. The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics. O'Loughlin T, et al. EMBO Rep, 2018 Apr. PMID 29467281, Free PMC Article

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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

    • KIAA1495, MGC150671

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    leucine-rich repeat and calponin homology domain-containing protein 2
    Names
    leucine-rich repeats and calponin homology (CH) domain containing 2

    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.

    Genomic

    1. NG_021299.2 RefSeqGene

      Range
      4977..128457
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243963.2 → NP_001230892.1  leucine-rich repeat and calponin homology domain-containing protein 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AC239923, BC125224, BX647193
      Consensus CDS
      CCDS59175.1
      UniProtKB/Swiss-Prot
      Q5VUJ6
      Related
      ENSP00000439366.1, ENST00000538422.2
      Conserved Domains (5) summary
      cd00116
      Location:136 → 237
      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:92 → 112
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:627 → 734
      CH; Calponin homology (CH) domain
      pfam12799
      Location:136 → 173
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:181 → 237
      LRR_8; Leucine rich repeat

    2. NM_020871.4 → NP_065922.3  leucine-rich repeat and calponin homology domain-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_065922.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB040928, AC239923, BG541540, BX647193
      Consensus CDS
      CCDS48155.1
      UniProtKB/Swiss-Prot
      F5H2T1, Q08AD5, Q5VUJ6, Q9HA88, Q9P233
      Related
      ENSP00000325091.8, ENST00000317135.13
      Conserved Domains (5) summary
      cd00116
      Location:136 → 237
      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:92 → 112
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:644 → 751
      CH; Calponin homology (CH) domain
      pfam12799
      Location:136 → 173
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:181 → 237
      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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      115110616..115234096 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006724724.4 → XP_006724787.2  leucine-rich repeat and calponin homology domain-containing protein 2 isoform X1

      Conserved Domains (5) summary
      cd00116
      Location:136 → 237
      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:92 → 112
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00307
      Location:637 → 744
      CH; Calponin homology (CH) domain
      pfam12799
      Location:136 → 173
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:181 → 237
      LRR_8; Leucine rich repeat

    2. XM_017029696.3 → XP_016885185.1  leucine-rich repeat and calponin homology domain-containing protein 2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      113519325..113642681 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327463.1 → XP_054183438.1  leucine-rich repeat and calponin homology domain-containing protein 2 isoform X1

    2. XM_054327464.1 → XP_054183439.1  leucine-rich repeat and calponin homology domain-containing protein 2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VUJ6.2 GenPept UniProtKB/Swiss-Prot:Q5VUJ6

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