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Clmn calmin [ Mus musculus (house mouse) ]

Gene ID: 94040, updated on 5-Mar-2024

Summary

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Official Symbol
Clmnprovided by MGI
Official Full Name
calminprovided by MGI
Primary source
MGI:MGI:2136957
See related
Ensembl:ENSMUSG00000021097 AllianceGenome:MGI:2136957
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
mKIAA1188; 9330188N17Rik
Summary
Predicted to enable actin filament binding activity. Acts upstream of or within negative regulation of cell population proliferation and neuron projection development. Located in cytoplasm. Is expressed in several structures, including alimentary system; brain; limb; metanephros; and nose. Orthologous to human CLMN (calmin). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis adult (RPKM 13.1), colon adult (RPKM 8.0) and 22 other tissues See more
Orthologs
human all
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Genomic context

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Location:
12 E; 12 54.91 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (104729373..104831335, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (104763114..104865082, complement)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 31573 Neighboring gene dicer 1, ribonuclease type III Neighboring gene STARR-positive B cell enhancer ABC_E7176 Neighboring gene STARR-seq mESC enhancer starr_33151 Neighboring gene predicted gene, 53761 Neighboring gene STARR-seq mESC enhancer starr_33155 Neighboring gene spectrin repeat containing, nuclear envelope family member 3 Neighboring gene STARR-positive B cell enhancer ABC_E1453 Neighboring gene STARR-seq mESC enhancer starr_33158 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:106251266-106251483 Neighboring gene STARR-positive B cell enhancer ABC_E7177 Neighboring gene predicted gene, 31742 Neighboring gene small Cajal body-specific RNA 13 Neighboring gene microRNA 3069 Neighboring gene small nucleolar RNA host gene 10

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. Expression of calmin, a novel developmentally regulated brain protein with calponin-homology domains. Takaishi M, et al. Brain Res Mol Brain Res, 2003 Apr 10. PMID 12670712
  2. The all-trans retinoic acid (atRA)-regulated gene Calmin (Clmn) regulates cell cycle exit and neurite outgrowth in murine neuroblastoma (Neuro2a) cells. Marzinke MA, et al. Exp Cell Res, 2012 Jan 1. PMID 22001116
  3. Calmin, a protein with calponin homology and transmembrane domains expressed in maturing spermatogenic cells. Ishisaki Z, et al. Genomics, 2001 Jun 1. PMID 11386753
  4. Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways. Thiagarajan RD, et al. PLoS One, 2011 Feb 28. PMID 21386911, Free PMC Article
  5. Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Trinidad JC, et al. Mol Cell Proteomics, 2006 May. PMID 16452087

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1188

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables actin binding IEA
Inferred from Electronic Annotation
more info
  
enables actin filament binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of cell population proliferation IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within negative regulation of cell population proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within neuron projection development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear migration IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
part_of meiotic nuclear membrane microtubule tethering complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
is_active_in nuclear outer membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
calmin
Names
calponin-like transmembrane domain protein

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_001040682.1 → NP_001035772.1  calmin isoform b

    See identical proteins and their annotated locations for NP_001035772.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (b) lacks an internal segment, compared to isoform a.
    Source sequence(s)
    AC124364, AC133077, AK077023
    Consensus CDS
    CCDS36540.1
    UniProtKB/TrEMBL
    B9EJ15
    Related
    ENSMUSP00000105562.2, ENSMUST00000109936.3
    Conserved Domains (1) summary
    pfam00307
    Location:33 → 134
    CH; Calponin homology (CH) domain

  2. NM_053155.2 → NP_444385.2  calmin isoform a

    See identical proteins and their annotated locations for NP_444385.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AC124364, AC133077, AK077023
    Consensus CDS
    CCDS36541.1
    UniProtKB/Swiss-Prot
    Q8C5W0, Q91V71, Q91XT7, Q91XT8, Q91XU9
    UniProtKB/TrEMBL
    B9EJ15
    Related
    ENSMUSP00000105563.2, ENSMUST00000109937.9
    Conserved Domains (1) summary
    pfam00307
    Location:33 → 134
    CH; Calponin homology (CH) domain

RNA

  1. NR_104435.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has an additional exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC124364, AC133077, AW494443

  2. NR_104436.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) has an additional exon and an alternate splice site and also lacks an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC124364, AC133077, AW494443

  3. NR_104437.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) has an additional exon and also lacks an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC124364, AC133077, AW494443

  4. NR_104438.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an additional exon and an alternate splice site in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC124364, AC133077, AW494443

  5. NR_104439.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) has an alternate splice site and also lacks an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC124364, AC133077, AW494443

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_000078.7 Reference GRCm39 C57BL/6J

    Range
    104729373..104831335 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001780506.3 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8C5W0.2 GenPept UniProtKB/Swiss-Prot:Q8C5W0

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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