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

Gene ID: 305332, updated on 13-Apr-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
Ensembl: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 active in stress fiber. Orthologous to human LIMCH1 (LIM and calponin homology domains 1). [provided by Alliance of Genome Resources, Apr 2022]
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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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
  • 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 (7) 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
    Related
    ENSRNOP00000096454.1, ENSRNOT00000100682.1
    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

  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

  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

  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
    Related
    ENSRNOP00000093427.1, ENSRNOT00000103342.1

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

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000014

  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

  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
    Related
    ENSRNOP00000063345.3, ENSRNOT00000064263.3

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

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000014

  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
    Related
    ENSRNOP00000087540.1, ENSRNOT00000118493.1

  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, ENSRNOT00000114959.1

  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
    Related
    ENSRNOP00000097815.1, ENSRNOT00000097408.1

  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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