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    Limch1 LIM and calponin homology domains 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 305332, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Limch1provided by RGD
    Official Full Name
    LIM and calponin homology domains 1provided by RGD
    Primary source
    RGD:1305269
    See related
    EnsemblRapid:ENSRNOG00000002318 AllianceGenome:RGD:1305269
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1305269
    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 part of myosin II complex. Predicted to be active in stress fiber. Orthologous to human LIMCH1 (LIM and calponin homology domains 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 747.2), Muscle (RPKM 168.9) and 4 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Limch1 in Genome Data Viewer
    Location:
    14p11
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (41466433..41779477, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (41112579..41425001, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (42760363..43072976, complement)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481746 Neighboring gene paired-like homeobox 2b Neighboring gene uncharacterized LOC120096605 Neighboring gene U2 spliceosomal RNA Neighboring gene uncharacterized LOC134481847 Neighboring gene U6 spliceosomal RNA Neighboring gene ubiquitin C-terminal hydrolase L1 Neighboring gene amyloid beta precursor protein binding family B member 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Expression and localization of an agmatinase-like protein in the rat brain. Mella C, et al. Histochem Cell Biol, 2010 Aug. PMID 20607275
    2. Cloning and functional expression of a rodent brain cDNA encoding a novel protein with agmatinase activity, but not belonging to the arginase family. Uribe E, et al. Arch Biochem Biophys, 2007 May 1. PMID 17291445
    3. LIMCH1 regulates nonmuscle myosin-II activity and suppresses cell migration. Lin YH, et al. Mol Biol Cell, 2017 Apr 15. PMID 28228547, Free PMC Article
    4. Association of connexin43 with E3 ubiquitin ligase TRIM21 reveals a mechanism for gap junction phosphodegron control. Chen VC, et al. J Proteome Res, 2012 Dec 7. PMID 23106098
    5. FMRP recruitment of β-catenin to the translation pre-initiation complex represses translation. Ehyai S, et al. EMBO Rep, 2018 Dec. PMID 30361391, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    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
    		  
    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 positive regulation of protein phosphorylation ISO
    Inferred from Sequence Orthology
    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 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
    		  
    Component Evidence Code Pubs
    part_of myosin II complex ISO
    Inferred from Sequence Orthology
    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
    		  

    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_001191678.2 → NP_001178607.1  LIM and calponin homology domains-containing protein 1 isoform l

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A0A8I6ASI2
      Conserved Domains (4) summary
      smart00132
      Location:1015 → 1072
      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:772 → 809
      GBP_C; Guanylate-binding protein, C-terminal domain

    2. NM_001401560.1 → NP_001388489.1  LIM and calponin homology domains-containing protein 1 isoform a

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      Related
      ENSRNOP00000076732.2, ENSRNOT00000095221.2

    3. NM_001401561.1 → NP_001388490.1  LIM and calponin homology domains-containing protein 1 isoform b

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    4. NM_001401562.1 → NP_001388491.1  LIM and calponin homology domains-containing protein 1 isoform c

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    5. NM_001401563.1 → NP_001388492.1  LIM and calponin homology domains-containing protein 1 isoform d

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      Related
      ENSRNOP00000087540.2, ENSRNOT00000118493.2

    6. NM_001401564.1 → NP_001388493.1  LIM and calponin homology domains-containing protein 1 isoform e

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    7. NM_001401565.1 → NP_001388494.1  LIM and calponin homology domains-containing protein 1 isoform f

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      Related
      ENSRNOP00000093427.2, ENSRNOT00000103342.2

    8. NM_001401566.1 → NP_001388495.1  LIM and calponin homology domains-containing protein 1 isoform g

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A0A8I6AJT8

    9. NM_001401567.1 → NP_001388496.1  LIM and calponin homology domains-containing protein 1 isoform h

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      Related
      ENSRNOP00000097815.2, ENSRNOT00000097408.2

    10. NM_001401568.1 → NP_001388497.1  LIM and calponin homology domains-containing protein 1 isoform i

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    11. NM_001401569.1 → NP_001388498.1  LIM and calponin homology domains-containing protein 1 isoform j

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      Related
      ENSRNOP00000063345.4, ENSRNOT00000064263.4

    12. NM_001401570.1 → NP_001388499.1  LIM and calponin homology domains-containing protein 1 isoform k

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      F1M392

    13. NM_001401572.1 → NP_001388501.1  LIM and calponin homology domains-containing protein 1 isoform m

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      Related
      ENSRNOP00000096454.2, ENSRNOT00000100682.2

    14. NM_001401573.1 → NP_001388502.1  LIM and calponin homology domains-containing protein 1 isoform n

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A0A8I6A611

    15. NM_001401574.1 → NP_001388503.1  LIM and calponin homology domains-containing protein 1 isoform o

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      Related
      ENSRNOP00000093239.1, ENSRNOT00000114959.2

    16. NM_001401575.1 → NP_001388504.1  LIM and calponin homology domains-containing protein 1 isoform p

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    17. NM_001401577.1 → NP_001388506.1  LIM and calponin homology domains-containing protein 1 isoform q

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    18. NM_001401578.1 → NP_001388507.1  LIM and calponin homology domains-containing protein 1 isoform r

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    19. NM_001401579.1 → NP_001388508.1  LIM and calponin homology domains-containing protein 1 isoform s

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    20. NM_001401580.1 → NP_001388509.1  LIM and calponin homology domains-containing protein 1 isoform s

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086032.1 Reference GRCr8

      Range
      41466433..41779477 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063273093.1 → XP_063129163.1  LIM and calponin homology domains-containing protein 1 isoform X9

    2. XM_063273091.1 → XP_063129161.1  LIM and calponin homology domains-containing protein 1 isoform X7

    3. XM_063273092.1 → XP_063129162.1  LIM and calponin homology domains-containing protein 1 isoform X8

    4. XM_063273088.1 → XP_063129158.1  LIM and calponin homology domains-containing protein 1 isoform X4

    5. XM_063273089.1 → XP_063129159.1  LIM and calponin homology domains-containing protein 1 isoform X5

    6. XM_063273090.1 → XP_063129160.1  LIM and calponin homology domains-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      A0A8I5XVC5

    7. XM_063273087.1 → XP_063129157.1  LIM and calponin homology domains-containing protein 1 isoform X3

    8. XM_063273085.1 → XP_063129155.1  LIM and calponin homology domains-containing protein 1 isoform X1

    9. XM_063273086.1 → XP_063129156.1  LIM and calponin homology domains-containing protein 1 isoform X2

    10. XM_063273099.1 → XP_063129169.1  LIM and calponin homology domains-containing protein 1 isoform X15

    11. XM_063273098.1 → XP_063129168.1  LIM and calponin homology domains-containing protein 1 isoform X14

    12. XM_063273095.1 → XP_063129165.1  LIM and calponin homology domains-containing protein 1 isoform X11

    13. XM_063273097.1 → XP_063129167.1  LIM and calponin homology domains-containing protein 1 isoform X13

    14. XM_063273096.1 → XP_063129166.1  LIM and calponin homology domains-containing protein 1 isoform X12

    15. XM_063273094.1 → XP_063129164.1  LIM and calponin homology domains-containing protein 1 isoform X10

    16. XM_063273100.1 → XP_063129170.1  LIM and calponin homology domains-containing protein 1 isoform X16

    17. XM_063273101.1 → XP_063129171.1  LIM and calponin homology domains-containing protein 1 isoform X17

    Nucleotide Protein Strain
    Heading Accession and Version

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