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    MICAL3 microtubule associated monooxygenase, calponin and LIM domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 57553, updated on 2-Nov-2024

    Summary

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    Official Symbol
    MICAL3provided by HGNC
    Official Full Name
    microtubule associated monooxygenase, calponin and LIM domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:24694
    See related
    Ensembl:ENSG00000243156 MIM:608882; AllianceGenome:HGNC:24694
    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
    Also known as
    MICAL-3
    Summary
    Enables actin binding activity and molecular adaptor activity. Involved in actin filament depolymerization. Located in several cellular components, including Flemming body; intercellular bridge; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 5.1), brain (RPKM 4.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MICAL3 in Genome Data Viewer
    Location:
    22q11.21
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (17787649..18024561, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (18455325..18695978, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (18270415..18507327, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13442 Neighboring gene BH3 interacting domain death agonist Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18633 Neighboring gene microRNA 3198-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18262368-18263275 Neighboring gene nonconserved acetylation island sequence 74 enhancer Neighboring gene VISTA enhancer hs2543 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:18271287-18271499 Neighboring gene long intergenic non-protein coding RNA 528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18277231-18277730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18641 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:18286544-18287743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18291439-18292235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18298181-18298960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18338757-18339640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18341985-18342486 Neighboring gene uncharacterized LOC124905075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18368270-18368770 Neighboring gene Sharpr-MPRA regulatory region 8921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:18424525-18425300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18435745-18436351 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18438647-18439148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18439149-18439648 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:18443505-18444221 Neighboring gene Sharpr-MPRA regulatory region 15525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18456361-18456913 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:18462205-18462583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18474404-18474908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18474909-18475413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18476614-18477114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18477115-18477615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13444 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:18484257-18484953 Neighboring gene microRNA 648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18646 Neighboring gene long intergenic non-protein coding RNA 1634 Neighboring gene RHEB pseudogene 3 Neighboring gene uncharacterized LOC105372853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:18544003-18544503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13447 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:18552873-18554072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18647

    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 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. Structural and kinetic insights into flavin-containing monooxygenase and calponin-homology domains in human MICAL3. Kim J, et al. IUCrJ, 2020 Jan 1. PMID 31949908, Free PMC Article
    2. Allelic expression analysis of the osteoarthritis susceptibility locus that maps to MICAL3. Ratnayake M, et al. BMC Med Genet, 2012 Mar 2. PMID 22385522, Free PMC Article
    3. MICAL3 Flavoprotein Monooxygenase Forms a Complex with Centralspindlin and Regulates Cytokinesis. Liu Q, et al. J Biol Chem, 2016 Sep 23. PMID 27528609, Free PMC Article
    4. Semaphorin signaling via MICAL3 induces symmetric cell division to expand breast cancer stem-like cells. Tominaga K, et al. Proc Natl Acad Sci U S A, 2019 Jan 8. PMID 30587593, Free PMC Article
    5. Rab6, Rab8, and MICAL3 cooperate in controlling docking and fusion of exocytotic carriers. Grigoriev I, et al. Curr Biol, 2011 Jun 7. PMID 21596566

    See all (68) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the niche factor Sema3-stimulated NP1/MICAL3/CRMP2/Numb axis appears to expand Cancer stem-like cells (CSCs) at least partly through increased frequency of MICAL3-mediated symmetric division of CSCs.
      Title: Semaphorin signaling via MICAL3 induces symmetric cell division to expand breast cancer stem-like cells.
    2. MICAL3 acts as a midbody-associated scaffold for vesicle targeting, which promotes maturation of the intercellular bridge and abscission.
      Title: MICAL3 Flavoprotein Monooxygenase Forms a Complex with Centralspindlin and Regulates Cytokinesis.
    3. Further exploration of the NINL-associated interactome identifies MICAL3, a protein known to interact with Rab8 and to play an important role in vesicle docking and fusion.
      Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking.
    4. a novel link wherein placenta growth factor-mediated downregulation of paired box protein 5 attenuates miR-648 expression leading to increased endothelin-1 levels that are known to induce Pulmonary hypertension in sickle cell anemia
      Title: MicroRNA 648 Targets ET-1 mRNA and is cotranscriptionally regulated with MICAL3 by PAX5.
    5. data do not support our hypothesis that the association between rs2277831 and primary osteoarthriti is due to the effect this SNP has on MICAL3, BCL2L13 or BID gene expression
      Title: Allelic expression analysis of the osteoarthritis susceptibility locus that maps to MICAL3.
    6. The monooxygenase activity of MICAL3 is required to regulate its own turnover and the concomitant remodeling of vesicle-docking protein complexes.
      Title: Rab6, Rab8, and MICAL3 cooperate in controlling docking and fusion of exocytotic carriers.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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
    Gene network analysis in a pediatric cohort identifies novel lung function genes.
    EBI GWAS Catalog
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    EBI GWAS Catalog
    Genome-wide association study of antiphospholipid antibodies.
    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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of microtubule associated monoxygenase, calponin and LIM domain containing 3 (MICAL3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ37503, KIAA0819, MGC189703

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables F-actin monooxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables FAD binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables actin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables actin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables molecular adaptor activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actin filament depolymerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in actin filament depolymerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cytoskeleton organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in exocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Flemming body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cell cortex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intercellular bridge IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in spindle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    [F-actin]-monooxygenase MICAL3
    Names
    [F-actin]-methionine sulfoxide oxidase MICAL3
    flavoprotein oxidoreductase MICAL3
    molecule interacting with CasL protein 3
    protein MICAL-3
    protein-methionine sulfoxide oxidase MICAL3
    NP_001116203.1
    NP_001129476.1
    NP_056056.2

    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_001122731.2 → NP_001116203.1  [F-actin]-monooxygenase MICAL3 isoform 3

      See identical proteins and their annotated locations for NP_001116203.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains multiple differences in the UTRs and coding region, including the lack of multiple 3' coding exons, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AB037785, BC085009, BX647382, DA531335
      Consensus CDS
      CCDS46660.1
      UniProtKB/TrEMBL
      A0A5F9ZHV5
      Related
      ENSP00000383406.2, ENST00000400561.6
      Conserved Domains (4) summary
      cd09439
      Location:764 → 818
      LIM_Mical; The LIM domain of Mical (molecule interacting with CasL)
      pfam00307
      Location:524 → 619
      CH; Calponin homology (CH) domain
      pfam01494
      Location:87 → 274
      FAD_binding_3; FAD binding domain
      pfam13450
      Location:91 → 119
      NAD_binding_8; NAD(P)-binding Rossmann-like domain

    2. NM_001136004.3 → NP_001129476.1  [F-actin]-monooxygenase MICAL3 isoform 2

      See identical proteins and their annotated locations for NP_001129476.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains multiple differences in the UTRs and coding region, including the lack of multiple 3' coding exons, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC016026, BC157876, BU617485, DA531335, KC877929
      Consensus CDS
      CCDS46661.1
      UniProtKB/TrEMBL
      A0A5F9ZHV5
      Related
      ENSP00000462033.1, ENST00000585038.1
      Conserved Domains (4) summary
      cd09439
      Location:888 → 942
      LIM_Mical; The LIM domain of Mical (molecule interacting with CasL)
      pfam00307
      Location:524 → 619
      CH; Calponin homology (CH) domain
      pfam01494
      Location:87 → 274
      FAD_binding_3; FAD binding domain
      pfam13450
      Location:91 → 119
      NAD_binding_8; NAD(P)-binding Rossmann-like domain

    3. NM_015241.3 → NP_056056.2  [F-actin]-monooxygenase MICAL3 isoform 1

      See identical proteins and their annotated locations for NP_056056.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB020626, AC016026, AC016027, BC035213, CR456364, DA531335, DR731344
      Consensus CDS
      CCDS46659.1
      UniProtKB/Swiss-Prot
      B2RXJ5, E9PEF0, O94909, Q5U4P4, Q6ICK4, Q7RTP6, Q96DF2, Q9P2I3
      Related
      ENSP00000416015.2, ENST00000441493.7
      Conserved Domains (5) summary
      cd09439
      Location:764 → 818
      LIM_Mical; The LIM domain of Mical (molecule interacting with CasL)
      pfam00307
      Location:524 → 619
      CH; Calponin homology (CH) domain
      pfam01494
      Location:87 → 274
      FAD_binding_3; FAD binding domain
      pfam12130
      Location:1850 → 1971
      DUF3585; Protein of unknown function (DUF3585)
      pfam13450
      Location:91 → 119
      NAD_binding_8; NAD(P)-binding Rossmann-like 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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      17787649..18024561 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      18455325..18695978 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_020793.1: Suppressed sequence

      Description
      NM_020793.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7RTP6.2 GenPept UniProtKB/Swiss-Prot:Q7RTP6

    Gene LinkOut

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

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