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

Summary

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

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_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of antiphospholipid antibodies. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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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

A005C33 (e-PCR)
- UniSTS:6407

D11S2921 (e-PCR)
- UniSTS:152074

SGC32325 (e-PCR)
- UniSTS:99851

G63345 (e-PCR)
- UniSTS:140312

A005R08 (e-PCR)
- UniSTS:56361

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

RH93600 (e-PCR)
- UniSTS:87369

A006A19 (e-PCR)
- UniSTS:63817

RH77783 (e-PCR)
- UniSTS:7755

SGC30622 (e-PCR)
- UniSTS:58194

RH80619 (e-PCR)
- UniSTS:88915

STS-Z41052 (e-PCR)
- UniSTS:40533

D22S1584 (e-PCR)
- UniSTS:473695

D10S16 (e-PCR)
- UniSTS:155756

GDB:313731 (e-PCR)
- UniSTS:17519

D1S1423 (e-PCR)
- UniSTS:149619

G32276 (e-PCR)
- UniSTS:116874

G63573 (e-PCR)
- UniSTS:140684

D11S3114 (e-PCR)
- UniSTS:152207

stD22S181 (e-PCR)
- UniSTS:146576

SHGC-145298 (e-PCR)
- UniSTS:174503

G32312 (e-PCR)
- UniSTS:116906

D22S627 (e-PCR)
- UniSTS:45743

SHGC-78815 (e-PCR)
- UniSTS:95694

SHGC-78836 (e-PCR)
- UniSTS:100830

RH77815 (e-PCR)
- UniSTS:45051

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

EC 1.14.13.225

NP_001129476.1

EC 1.14.13.225

NP_056056.2

EC 1.14.13.225

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)

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
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
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

NC_000022.11 Reference GRCh38.p14 Primary Assembly

Range

17787649..18024561 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

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.