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    LRCH3 leucine rich repeats and calponin homology domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 84859, updated on 5-May-2024

    Summary

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    Official Symbol
    LRCH3provided by HGNC
    Official Full Name
    leucine rich repeats and calponin homology domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:28637
    See related
    Ensembl:ENSG00000186001 AllianceGenome:HGNC:28637
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Involved in septin cytoskeleton organization. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in ovary (RPKM 3.8), lymph node (RPKM 3.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3q29
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197791226..197888436)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (200523608..200620895)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (197518097..197615307)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene rubicon autophagy regulator Neighboring gene microRNA 922 Neighboring gene MPRA-validated peak4996 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21112 Neighboring gene Sharpr-MPRA regulatory region 8415 Neighboring gene Sharpr-MPRA regulatory region 6653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197463053-197463900 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197466398-197466530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15092 Neighboring gene forty-two-three domain containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197504526-197504699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197517785-197518499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21120 Neighboring gene uncharacterized LOC124909482 Neighboring gene uncharacterized LOC105374310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21121 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:197581553-197582752 Neighboring gene ribosomal protein L17 pseudogene 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:197594026-197594561 Neighboring gene NUP98-IQCG recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:197626412-197627184 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197628168-197628668 Neighboring gene uncharacterized LOC124906330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15094 Neighboring gene RNA, U6 small nuclear 858, pseudogene Neighboring gene IQ motif containing G

    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
    • 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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    Related articles in PubMed

    1. LRCH proteins: a novel family of cytoskeletal regulators. Foussard H, et al. PLoS One, 2010 Aug 18. PMID 20805893, Free PMC Article
    2. DDX39B drives colorectal cancer progression by promoting the stability and nuclear translocation of PKM2. Zhao G, et al. Signal Transduct Target Ther, 2022 Aug 17. PMID 35973989, Free PMC Article
    3. DYRK1A regulates the recruitment of 53BP1 to the sites of DNA damage in part through interaction with RNF169. Menon VR, et al. Cell Cycle, 2019 Mar. PMID 30773093, Free PMC Article
    4. 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
    5. Targeting RICTOR Sensitizes SMAD4-Negative Colon Cancer to Irinotecan. Wong CK, et al. Mol Cancer Res, 2020 Mar. PMID 31932471, Free PMC Article

    See all (49) citations in PubMed

    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC4126, FLJ20994, FLJ43245, FLJ44976

    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 septin cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IC
    Inferred by Curator
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    DISP complex protein LRCH3
    Names
    leucine-rich repeat and calponin homology domain-containing protein 3
    leucine-rich repeats and calponin homology (CH) domain containing 3

    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_001363887.1 → NP_001350816.1  DISP complex protein LRCH3 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC055764, AC135893, AC144530
      Consensus CDS
      CCDS87193.1
      UniProtKB/TrEMBL
      B4DEQ7
      Related
      ENSP00000394763.2, ENST00000428136.2
      Conserved Domains (3) summary
      smart00033
      Location:660 → 762
      CH; Calponin homology domain
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    2. NM_001365715.1 → NP_001352644.1  DISP complex protein LRCH3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC055764, AC135893, AC144530
      Consensus CDS
      CCDS93456.1
      UniProtKB/Swiss-Prot
      B4E0T7, Q96FP9, Q96II8, Q9NT52
      UniProtKB/TrEMBL
      B4DEQ7
      Related
      ENSP00000393579.2, ENST00000425562.7
      Conserved Domains (3) summary
      smart00033
      Location:660 → 734
      CH; Calponin homology domain
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    3. NM_001365716.1 → NP_001352645.1  DISP complex protein LRCH3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC055764, AC135893, AC144530
      UniProtKB/TrEMBL
      B4DEQ7
      Conserved Domains (3) summary
      smart00033
      Location:624 → 726
      CH; Calponin homology domain
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    4. NM_001365717.1 → NP_001352646.1  DISP complex protein LRCH3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC055764, AC135893, AC144530
      UniProtKB/TrEMBL
      B4DEQ7
      Conserved Domains (3) summary
      smart00033
      Location:636 → 710
      CH; Calponin homology domain
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    5. NM_001365718.1 → NP_001352647.1  DISP complex protein LRCH3 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC055764, AC135893, AC144530
      UniProtKB/TrEMBL
      B4DEQ7
      Conserved Domains (3) summary
      smart00033
      Location:624 → 698
      CH; Calponin homology domain
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    6. NM_001365719.2 → NP_001352648.1  DISP complex protein LRCH3 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC055764, AC144530
      Conserved Domains (2) summary
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    7. NM_032773.4 → NP_116162.1  DISP complex protein LRCH3 isoform 2

      See identical proteins and their annotated locations for NP_116162.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK300466, BC007504, DB454969
      Consensus CDS
      CCDS3330.1
      UniProtKB/TrEMBL
      B4DEQ7
      Related
      ENSP00000334375.4, ENST00000334859.8
      Conserved Domains (3) summary
      smart00033
      Location:660 → 708
      CH; Calponin homology domain
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    RNA

    1. NR_158582.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC055764, AC135893, AC144530

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      197791226..197888436
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005269367.4 → XP_005269424.1  DISP complex protein LRCH3 isoform X1

      UniProtKB/TrEMBL
      B4DEQ7
      Conserved Domains (3) summary
      smart00033
      Location:600 → 702
      CH; Calponin homology domain
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    2. XM_047449082.1 → XP_047305038.1  DISP complex protein LRCH3 isoform X4

    3. XM_047449081.1 → XP_047305037.1  DISP complex protein LRCH3 isoform X2

    4. XM_017007352.3 → XP_016862841.1  DISP complex protein LRCH3 isoform X3

      UniProtKB/TrEMBL
      B4DEQ7
      Conserved Domains (4) summary
      smart00033
      Location:582 → 684
      CH; Calponin homology domain
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]
      pfam05917
      Location:427 → 590
      DUF874; Helicobacter pylori protein of unknown function (DUF874)

    5. XM_047449083.1 → XP_047305039.1  DISP complex protein LRCH3 isoform X5

    6. XM_011513242.4 → XP_011511544.1  DISP complex protein LRCH3 isoform X6

      Conserved Domains (2) summary
      COG4886
      Location:77 → 285
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:61 → 83
      LRR_RI; leucine-rich repeat [structural motif]

    7. XM_047449084.1 → XP_047305040.1  DISP complex protein LRCH3 isoform X7

    RNA

    1. XR_007095758.1 RNA Sequence

    2. XR_007095759.1 RNA Sequence

    3. XR_007095760.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      200523608..200620895
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348135.1 → XP_054204110.1  DISP complex protein LRCH3 isoform X1

    2. XM_054348138.1 → XP_054204113.1  DISP complex protein LRCH3 isoform X4

    3. XM_054348136.1 → XP_054204111.1  DISP complex protein LRCH3 isoform X2

    4. XM_054348137.1 → XP_054204112.1  DISP complex protein LRCH3 isoform X3

    5. XM_054348139.1 → XP_054204114.1  DISP complex protein LRCH3 isoform X5

    6. XM_054348140.1 → XP_054204115.1  DISP complex protein LRCH3 isoform X6

    7. XM_054348141.1 → XP_054204116.1  DISP complex protein LRCH3 isoform X7

    RNA

    1. XR_008486846.1 RNA Sequence

    2. XR_008486844.1 RNA Sequence

    3. XR_008486845.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96II8.2 GenPept UniProtKB/Swiss-Prot:Q96II8

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