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

Gene ID: 77569, updated on 9-Dec-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, Dec 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
    UniProtKB/TrEMBL
    A0A5F8MPN3

  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
    UniProtKB/TrEMBL
    A0A5F8MPN3

  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
    A0A5F8MPN3, 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
    UniProtKB/TrEMBL
    A0A5F8MPN3

  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
    UniProtKB/TrEMBL
    A0A5F8MPN3

  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
    A0A5F8MPN3, 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
    UniProtKB/TrEMBL
    A0A5F8MPN3

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

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC158994
    UniProtKB/TrEMBL
    A0A5F8MPN3

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

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC158994
    UniProtKB/TrEMBL
    A0A5F8MPN3

  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
    A0A5F8MPN3, 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
    UniProtKB/TrEMBL
    D3YU59

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

    Status: VALIDATED

    Source sequence(s)
    AC119834
    UniProtKB/TrEMBL
    A0A5F8MPN3

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

    Status: VALIDATED

    Source sequence(s)
    AC119834
    UniProtKB/TrEMBL
    A0A5F8MPN3

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

    Status: VALIDATED

    Source sequence(s)
    AC119834
    UniProtKB/TrEMBL
    D3YU59

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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