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

Gene ID: 57553, updated on 7-Apr-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. Involved in actin filament depolymerization. Located in several cellular components, including Flemming body; intercellular bridge; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
22q11.21
Exon count:
37
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (17787649..18024561, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (18455325..18695978, complement)
105.20220307 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
  • 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. 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
  2. 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
  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. Rab6, Rab8, and MICAL3 cooperate in controlling docking and fusion of exocytotic carriers. Grigoriev I, et al. Curr Biol, 2011 Jun 7. PMID 21596566
  5. MicroRNA 648 Targets ET-1 mRNA and is cotranscriptionally regulated with MICAL3 by PAX5. Li C, et al. Mol Cell Biol, 2015 Feb. PMID 25403488, Free PMC Article

See all (61) 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 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
  
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 cycle IEA
Inferred from Electronic Annotation
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
  
involved_in localization EXP
Inferred from Experiment
more info
 PubMed 
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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NEW Try the new Transcript table

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_2023_10

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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