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

Gene ID: 77569, updated on 8-May-2024

Summary

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 and cytoskeleton. Predicted to be part of myosin II complex. Predicted to be active in stress fiber. Is expressed in several structures, including eye; gonad; gut; hemolymphoid system gland; and nervous system. Orthologous to human LIMCH1 (LIM and calponin homology domains 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in lung adult (RPKM 20.3), heart adult (RPKM 7.0) and 11 other tissues See more
Orthologs
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Genomic context

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

Expression

  • 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

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
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

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_001001980.3NP_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:9871044
    LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
    cd00014
    Location:26138
    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:250417
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:771808
    GBP_C; Guanylate-binding protein, C-terminal domain
  2. NM_001256122.3NP_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:831888
    LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
    pfam15949
    Location:94261
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:615652
    GBP_C; Guanylate-binding protein, C-terminal domain
  3. NM_001368863.1NP_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:828885
    LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
    pfam15949
    Location:91259
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:612649
    GBP_C; Guanylate-binding protein, C-terminal domain
  4. NM_001401410.1NP_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_001401411.1NP_001388340.1  LIM and calponin homology domains-containing protein 1 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC152416, AC158994
  6. NM_001401412.1NP_001388341.1  LIM and calponin homology domains-containing protein 1 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC152416, AC158994
  7. NM_001401413.1NP_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_001401414.1NP_001388343.1  LIM and calponin homology domains-containing protein 1 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC152416, AC158994
  9. NM_001401415.1NP_001388344.1  LIM and calponin homology domains-containing protein 1 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC152416, AC158994
  10. NM_001401416.1NP_001388345.1  LIM and calponin homology domains-containing protein 1 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC152416, AC158994
  11. NM_001401417.1NP_001388346.1  LIM and calponin homology domains-containing protein 1 isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC152416, AC158994
  12. NM_001401418.1NP_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_001401419.1NP_001388348.1  LIM and calponin homology domains-containing protein 1 isoform 13

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC152416, AC158994
  14. NM_001401420.1NP_001388349.1  LIM and calponin homology domains-containing protein 1 isoform 14

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC158994
  15. NM_001401421.1NP_001388350.1  LIM and calponin homology domains-containing protein 1 isoform 15

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC158994
  16. NM_001401422.1NP_001388351.1  LIM and calponin homology domains-containing protein 1 isoform 16

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC158994
  17. NM_001401423.1NP_001388352.1  LIM and calponin homology domains-containing protein 1 isoform 17

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC158994
  18. NM_001401424.1NP_001388353.1  LIM and calponin homology domains-containing protein 1 isoform 18

    Status: VALIDATED

    Source sequence(s)
    AC119834, AC158994
  19. NM_001401425.1NP_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_001401426.1NP_001388355.1  LIM and calponin homology domains-containing protein 1 isoform 19

    Status: VALIDATED

    Source sequence(s)
    AC119834
  21. NM_001401427.1NP_001388356.1  LIM and calponin homology domains-containing protein 1 isoform 20

    Status: VALIDATED

    Source sequence(s)
    AC119834
  22. NM_001403508.1NP_001390437.1  LIM and calponin homology domains-containing protein 1 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC119834
  23. NM_001403509.1NP_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_036165606.1XP_036021499.1  LIM and calponin homology domains-containing protein 1 isoform X7

    UniProtKB/TrEMBL
    A0A5F8MPN3
    Conserved Domains (4) summary
    smart00132
    Location:9571014
    LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
    pfam15949
    Location:220388
    DUF4757; Domain of unknown function (DUF4757)
    cl00030
    Location:3110
    CH_SF; calponin homology (CH) domain superfamily
    cl20817
    Location:741778
    GBP_C; Guanylate-binding protein, C-terminal domain
  2. XM_036165607.1XP_036021500.1  LIM and calponin homology domains-containing protein 1 isoform X8

    UniProtKB/TrEMBL
    A0A5F8MPN3
    Conserved Domains (4) summary
    smart00132
    Location:9451002
    LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
    pfam15949
    Location:220376
    DUF4757; Domain of unknown function (DUF4757)
    cl00030
    Location:3110
    CH_SF; calponin homology (CH) domain superfamily
    cl20817
    Location:729766
    GBP_C; Guanylate-binding protein, C-terminal domain
  3. XM_036165604.1XP_036021497.1  LIM and calponin homology domains-containing protein 1 isoform X5

    UniProtKB/TrEMBL
    A0A5F8MPN3, D3Z589
    Conserved Domains (3) summary
    smart00132
    Location:828885
    LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
    pfam15949
    Location:91259
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:612649
    GBP_C; Guanylate-binding protein, C-terminal domain
  4. XM_036165601.1XP_036021494.1  LIM and calponin homology domains-containing protein 1 isoform X2

    Conserved Domains (2) summary
    pfam15949
    Location:580713
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:10661103
    GBP_C; Guanylate-binding protein, C-terminal domain
  5. XM_036165612.1XP_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:726783
    LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
    pfam15949
    Location:1157
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:510547
    GBP_C; Guanylate-binding protein, C-terminal domain
  6. XM_036165602.1XP_036021495.1  LIM and calponin homology domains-containing protein 1 isoform X3

    Conserved Domains (3) summary
    smart00132
    Location:12851342
    LIM; Zinc-binding domain present in Lin-11, Isl-1, Mec-3
    pfam15949
    Location:583716
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:10691106
    GBP_C; Guanylate-binding protein, C-terminal domain