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    CLMN calmin [ Homo sapiens (human) ]

    Gene ID: 79789, updated on 27-Nov-2024

    Summary

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    Official Symbol
    CLMNprovided by HGNC
    Official Full Name
    calminprovided by HGNC
    Primary source
    HGNC:HGNC:19972
    See related
    Ensembl:ENSG00000165959 MIM:611121; AllianceGenome:HGNC:19972
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable actin filament binding activity. Predicted to be involved in negative regulation of cell population proliferation and nuclear migration. Predicted to act upstream of or within neuron projection development. Predicted to be located in membrane. Predicted to be part of meiotic nuclear membrane microtubule tethering complex. Predicted to be active in cytoplasm and nuclear outer membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 7.5), kidney (RPKM 7.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLMN in Genome Data Viewer
    Location:
    14q32.13
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (95181940..95319908, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (89412156..89550109, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (95648277..95786245, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene dicer 1, ribonuclease III Neighboring gene microRNA 3173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8948 Neighboring gene DICER1 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:95662653-95662819 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:95665195-95666123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95719574-95720500 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:95720501-95721426 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:95721427-95722352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95725084-95725755 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95725756-95726426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95727628-95728254 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:95731514-95732713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:95769323-95769824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6045 Neighboring gene uncharacterized LOC105370637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8956 Neighboring gene uncharacterized LOC124903371 Neighboring gene long intergenic non-protein coding RNA 2292

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Calmin, a protein with calponin homology and transmembrane domains expressed in maturing spermatogenic cells. Ishisaki Z, et al. Genomics, 2001 Jun 1. PMID 11386753
    2. Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. Adkins DE, et al. Mol Psychiatry, 2011 Mar. PMID 20195266, Free PMC Article
    3. α-catenin interaction with YAP/FoxM1/TEAD-induced CEP55 supports liver cancer cell migration. Tang Y, et al. Cell Commun Signal, 2023 Jun 28. PMID 37381005, Free PMC Article
    4. Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. Sherva R, et al. Alzheimers Dement, 2014 Jan. PMID 23535033, Free PMC Article
    5. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. Seki N, et al. DNA Res, 1997 Oct 31. PMID 9455484

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetic variants associated with breast size also influence breast cancer risk.
    EBI GWAS Catalog
    Genome-wide association of lipid-lowering response to statins in combined study populations.
    EBI GWAS Catalog
    Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    EBI GWAS Catalog
    Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of calmin (CLMN) in primary human brain microvascular endothelial cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12383, FLJ43048, KIAA0500, KIAA1188

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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
    		  
    involved_in neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    part_of meiotic nuclear membrane microtubule tethering complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    calmin (calponin-like, transmembrane)
    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_024734.4 → NP_079010.2  calmin

      Status: VALIDATED

      Source sequence(s)
      AB007969, AB047979, AL356017, BC068482, CB155696
      Consensus CDS
      CCDS9933.1
      UniProtKB/Swiss-Prot
      B2RAR7, Q96JQ2, Q9H713, Q9HA23, Q9HA57, Q9UFP4, Q9ULN2
      UniProtKB/TrEMBL
      Q6NUQ2
      Related
      ENSP00000298912.3, ENST00000298912.9
      Conserved Domains (1) summary
      pfam00307
      Location:33 → 134
      CH; Calponin homology (CH) domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      95181940..95319908 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011537158.2 → XP_011535460.1  calmin isoform X1

      UniProtKB/TrEMBL
      Q6NUQ2
      Conserved Domains (1) summary
      pfam00307
      Location:33 → 134
      CH; Calponin homology (CH) domain

    2. XM_017021646.2 → XP_016877135.1  calmin isoform X2

      UniProtKB/TrEMBL
      Q6NUQ2

    3. XM_011537159.3 → XP_011535461.1  calmin isoform X3

      UniProtKB/TrEMBL
      Q6NUQ2
      Conserved Domains (1) summary
      pfam00307
      Location:33 → 134
      CH; Calponin homology (CH) domain

    4. XM_047431774.1 → XP_047287730.1  calmin isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      89412156..89550109 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376718.1 → XP_054232693.1  calmin isoform X1

    2. XM_054376719.1 → XP_054232694.1  calmin isoform X2

    3. XM_054376721.1 → XP_054232696.1  calmin isoform X3

    4. XM_054376722.1 → XP_054232697.1  calmin isoform X4

    5. XM_054376720.1 → XP_054232695.1  calmin isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96JQ2.1 GenPept UniProtKB/Swiss-Prot:Q96JQ2

    Gene LinkOut

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

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