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    Limch1 LIM and calponin homology domains 1 [ Mus musculus (house mouse) ]

    Gene ID: 77569, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Limch1provided by MGI
    Official Full Name
    LIM and calponin homology domains 1provided by MGI
    Primary source
    MGI:MGI:1924819
    See related
    Ensembl:ENSMUSG00000037736 AllianceGenome:MGI:1924819
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    mKIAA1102; 3732412D22Rik
    Summary
    Predicted to enable myosin II head/neck binding activity. Predicted to be involved in several processes, including cytoplasmic actin-based contraction involved in cell motility; positive regulation of stress fiber assembly; and regulation of focal adhesion assembly. Predicted to be located in cytoplasm. Predicted to be part of myosin II complex. Predicted to be active in stress fiber. Is expressed in several structures, including cardiovascular system; gonad; gut; hemolymphoid system gland; and nervous system. Orthologous to human LIMCH1 (LIM and calponin homology domains 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in lung adult (RPKM 20.3), heart adult (RPKM 7.0) and 11 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Limch1 in Genome Data Viewer
    Location:
    5 C3.1; 5 35.95 cM
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (66903232..67214502)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (66745889..67057159)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene amyloid beta precursor protein binding family B member 2 Neighboring gene predicted gene, 52775 Neighboring gene ubiquitin carboxy-terminal hydrolase L1, opposite strand Neighboring gene STARR-seq mESC enhancer starr_13303 Neighboring gene STARR-seq mESC enhancer starr_13304 Neighboring gene ubiquitin carboxy-terminal hydrolase L1 Neighboring gene STARR-seq mESC enhancer starr_13305 Neighboring gene STARR-seq mESC enhancer starr_13306 Neighboring gene eukaryotic translation elongation factor 1 gamma pseudogene Neighboring gene STARR-seq mESC enhancer starr_13307 Neighboring gene predicted gene 6517 Neighboring gene STARR-seq mESC enhancer starr_13308 Neighboring gene STARR-seq mESC enhancer starr_13309 Neighboring gene STARR-seq mESC enhancer starr_13310 Neighboring gene predicted gene, 33040 Neighboring gene STARR-seq mESC enhancer starr_13312 Neighboring gene predicted gene, 33167 Neighboring gene paired-like homeobox 2b Neighboring gene predicted gene, 33293

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. The role of Limch1 alternative splicing in skeletal muscle function. Penna MS, et al. Life Sci Alliance, 2023 Jun. PMID 36977593, Free PMC Article
    2. Subtype-Specific Genes that Characterize Subpopulations of Callosal Projection Neurons in Mouse Identify Molecularly Homologous Populations in Macaque Cortex. Fame RM, et al. Cereb Cortex, 2017 Mar 1. PMID 26874185, Free PMC Article
    3. Excitatory projection neuron subtypes control the distribution of local inhibitory interneurons in the cerebral cortex. Lodato S, et al. Neuron, 2011 Feb 24. PMID 21338885, Free PMC Article
    4. Cyclical expression of the Notch/Wnt regulator Nrarp requires modulation by Dll3 in somitogenesis. Sewell W, et al. Dev Biol, 2009 May 15. PMID 19268448, Free PMC Article
    5. ESRP1 Mutations Cause Hearing Loss due to Defects in Alternative Splicing that Disrupt Cochlear Development. Rohacek AM, et al. Dev Cell, 2017 Nov 6. PMID 29107558, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The role of Limch1 alternative splicing in skeletal muscle function.
      Title: The role of Limch1 alternative splicing in skeletal muscle function.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2)  1 citation
    • Targeted (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables actin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables myosin II head/neck binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables myosin II head/neck binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables myosin II head/neck binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in actomyosin structure organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cytoplasmic actin-based contraction involved in cell motility ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of protein phosphorylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of protein phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of stress fiber assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of stress fiber assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of stress fiber assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of focal adhesion assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of focal adhesion assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of focal adhesion assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of myosin II complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of myosin II complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in stress fiber ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in stress fiber ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    LIM and calponin homology domains-containing protein 1

    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_001001980.3 → NP_001001980.2  LIM and calponin homology domains-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001001980.2

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994
      Consensus CDS
      CCDS39102.1
      UniProtKB/Swiss-Prot
      Q3UH68, Q6DIC3, Q80TK1
      UniProtKB/TrEMBL
      A0A5F8MPN3
      Related
      ENSMUSP00000098723.5, ENSMUST00000101164.11
      Conserved Domains (4) summary
      smart00132
      Location:987 → 1044
      LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
      cd00014
      Location:26 → 138
      CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
      pfam15949
      Location:250 → 417
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:771 → 808
      GBP_C; Guanylate-binding protein, C-terminal domain

    2. NM_001256122.3 → NP_001243051.1  LIM and calponin homology domains-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001243051.1

      Status: VALIDATED

      Source sequence(s)
      AC119834
      Consensus CDS
      CCDS57347.1
      UniProtKB/TrEMBL
      A0A5F8MPN3
      Related
      ENSMUSP00000043163.8, ENSMUST00000038188.14
      Conserved Domains (3) summary
      smart00132
      Location:831 → 888
      LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
      pfam15949
      Location:94 → 261
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:615 → 652
      GBP_C; Guanylate-binding protein, C-terminal domain

    3. NM_001368863.1 → NP_001355792.1  LIM and calponin homology domains-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC158994
      Consensus CDS
      CCDS89925.1
      UniProtKB/TrEMBL
      A0A5F8MPN3, D3Z589
      Conserved Domains (3) summary
      smart00132
      Location:828 → 885
      LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
      pfam15949
      Location:91 → 259
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:612 → 649
      GBP_C; Guanylate-binding protein, C-terminal domain

    4. NM_001401410.1 → NP_001388339.1  LIM and calponin homology domains-containing protein 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994
      UniProtKB/TrEMBL
      A0A571BG24
      Related
      ENSMUSP00000158661.2, ENSMUST00000238785.2

    5. NM_001401411.1 → NP_001388340.1  LIM and calponin homology domains-containing protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994

    6. NM_001401412.1 → NP_001388341.1  LIM and calponin homology domains-containing protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994

    7. NM_001401413.1 → NP_001388342.1  LIM and calponin homology domains-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994
      UniProtKB/TrEMBL
      D3Z589

    8. NM_001401414.1 → NP_001388343.1  LIM and calponin homology domains-containing protein 1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994

    9. NM_001401415.1 → NP_001388344.1  LIM and calponin homology domains-containing protein 1 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994

    10. NM_001401416.1 → NP_001388345.1  LIM and calponin homology domains-containing protein 1 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994

    11. NM_001401417.1 → NP_001388346.1  LIM and calponin homology domains-containing protein 1 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994

    12. NM_001401418.1 → NP_001388347.1  LIM and calponin homology domains-containing protein 1 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994
      UniProtKB/TrEMBL
      D3YU22
      Related
      ENSMUSP00000112732.2, ENSMUST00000118242.8

    13. NM_001401419.1 → NP_001388348.1  LIM and calponin homology domains-containing protein 1 isoform 13

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994

    14. NM_001401420.1 → NP_001388349.1  LIM and calponin homology domains-containing protein 1 isoform 14

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC158994

    15. NM_001401421.1 → NP_001388350.1  LIM and calponin homology domains-containing protein 1 isoform 15

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC158994

    16. NM_001401422.1 → NP_001388351.1  LIM and calponin homology domains-containing protein 1 isoform 16

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC158994

    17. NM_001401423.1 → NP_001388352.1  LIM and calponin homology domains-containing protein 1 isoform 17

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC158994

    18. NM_001401424.1 → NP_001388353.1  LIM and calponin homology domains-containing protein 1 isoform 18

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC158994

    19. NM_001401425.1 → NP_001388354.1  LIM and calponin homology domains-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC158994
      UniProtKB/TrEMBL
      D3Z589
      Related
      ENSMUSP00000113544.3, ENSMUST00000117601.8

    20. NM_001401426.1 → NP_001388355.1  LIM and calponin homology domains-containing protein 1 isoform 19

      Status: VALIDATED

      Source sequence(s)
      AC119834

    21. NM_001401427.1 → NP_001388356.1  LIM and calponin homology domains-containing protein 1 isoform 20

      Status: VALIDATED

      Source sequence(s)
      AC119834

    22. NM_001403508.1 → NP_001390437.1  LIM and calponin homology domains-containing protein 1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC119834

    23. NM_001403509.1 → NP_001390438.1  LIM and calponin homology domains-containing protein 1 isoform 21

      Status: VALIDATED

      Source sequence(s)
      AC119834

    RNA

    1. NR_174705.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC119834, AC152416, AC158994

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      66903232..67214502
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036165606.1 → XP_036021499.1  LIM and calponin homology domains-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A5F8MPN3
      Conserved Domains (4) summary
      smart00132
      Location:957 → 1014
      LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
      pfam15949
      Location:220 → 388
      DUF4757; Domain of unknown function (DUF4757)
      cl00030
      Location:3 → 110
      CH_SF; calponin homology (CH) domain superfamily
      cl20817
      Location:741 → 778
      GBP_C; Guanylate-binding protein, C-terminal domain

    2. XM_036165607.1 → XP_036021500.1  LIM and calponin homology domains-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      A0A5F8MPN3
      Conserved Domains (4) summary
      smart00132
      Location:945 → 1002
      LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
      pfam15949
      Location:220 → 376
      DUF4757; Domain of unknown function (DUF4757)
      cl00030
      Location:3 → 110
      CH_SF; calponin homology (CH) domain superfamily
      cl20817
      Location:729 → 766
      GBP_C; Guanylate-binding protein, C-terminal domain

    3. XM_036165604.1 → XP_036021497.1  LIM and calponin homology domains-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A5F8MPN3, D3Z589
      Conserved Domains (3) summary
      smart00132
      Location:828 → 885
      LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
      pfam15949
      Location:91 → 259
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:612 → 649
      GBP_C; Guanylate-binding protein, C-terminal domain

    4. XM_036165601.1 → XP_036021494.1  LIM and calponin homology domains-containing protein 1 isoform X2

      Conserved Domains (2) summary
      pfam15949
      Location:580 → 713
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:1066 → 1103
      GBP_C; Guanylate-binding protein, C-terminal domain

    5. XM_036165612.1 → XP_036021505.1  LIM and calponin homology domains-containing protein 1 isoform X12

      UniProtKB/TrEMBL
      D3YU59, Q8CGB7
      Related
      ENSMUSP00000112651.3, ENSMUST00000119854.8
      Conserved Domains (3) summary
      smart00132
      Location:726 → 783
      LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
      pfam15949
      Location:1 → 157
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:510 → 547
      GBP_C; Guanylate-binding protein, C-terminal domain

    6. XM_036165602.1 → XP_036021495.1  LIM and calponin homology domains-containing protein 1 isoform X3

      Conserved Domains (3) summary
      smart00132
      Location:1285 → 1342
      LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
      pfam15949
      Location:583 → 716
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:1069 → 1106
      GBP_C; Guanylate-binding protein, C-terminal domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3UH68.2 GenPept UniProtKB/Swiss-Prot:Q3UH68

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