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Aliases for MATR3 Gene

Aliases for MATR3 Gene

  • Matrin 3 2 3 5
  • Vocal Cord And Pharyngeal Weakness With Distal Myopathy 3
  • Myopathy, Distal 2 2
  • Matrin-3 3
  • KIAA0723 4
  • ALS21 3
  • VCPDM 3
  • MPD2 3

External Ids for MATR3 Gene

Previous HGNC Symbols for MATR3 Gene

  • MPD2

Previous GeneCards Identifiers for MATR3 Gene

  • GC05P138504
  • GC05P139284
  • GC05P138640
  • GC05P138705
  • GC05P138657
  • GC05P138609

Summaries for MATR3 Gene

Entrez Gene Summary for MATR3 Gene

  • This gene encodes a nuclear matrix protein, which is proposed to stabilize certain messenger RNA species. Mutations of this gene are associated with distal myopathy 2, which often includes vocal cord and pharyngeal weakness. Alternatively spliced transcript variants, including read-through transcripts composed of the upstream small nucleolar RNA host gene 4 (non-protein coding) and matrin 3 gene sequence, have been identified. Pseudogenes of this gene are located on chromosomes 1 and X. [provided by RefSeq, Aug 2013]

GeneCards Summary for MATR3 Gene

MATR3 (Matrin 3) is a Protein Coding gene. Diseases associated with MATR3 include Amyotrophic Lateral Sclerosis 21 and Distal Myopathy With Vocal Cord Weakness. GO annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is ENSG00000280987.

UniProtKB/Swiss-Prot for MATR3 Gene

  • May play a role in transcription or may interact with other nuclear matrix proteins to form the internal fibrogranular network. In association with the SFPQ-NONO heteromer may play a role in nuclear retention of defective RNAs.

Gene Wiki entry for MATR3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MATR3 Gene

Genomics for MATR3 Gene

Regulatory Elements for MATR3 Gene

Enhancers for MATR3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G139310 1.3 Ensembl ENCODE dbSUPER 12.5 +37.2 37159 0.8 KLF1 ZNF2 RAD21 ZFHX2 ZNF366 SMC3 FOS ZNF600 PRDM10 EGR2 MATR3 PAIP2 SNORA74A SLC23A1 HSPA9 ENSG00000222937 SNORD63 PIR61462 RN7SKP64
GH05G139131 1.5 Ensembl ENCODE dbSUPER 10 -141.3 -141271 2.7 HNRNPUL1 AGO1 SIN3A TAF15 KAT8 SMARCA4 HNF4A KDM1A SP7 LEF1 LOC105379194 CDC23 KDM3B MATR3 SIL1 GC05P139103 GC05P139105 GC05P139106 GC05P139104 GC05P139102
GH05G139147 1.4 Ensembl ENCODE dbSUPER 10.7 -124.7 -124661 4.0 HDAC1 PKNOX1 FOXA2 CBX3 TBL1XR1 RAD21 TCF12 GATA2 FOS ZNF548 LOC105379194 CDC23 KDM3B CTNNA1 MATR3 SIL1 GC05P139163 GC05P139162 GC05P139102 GC05P139103
GH05G139297 1.2 Ensembl dbSUPER 11.9 +23.9 23949 0.2 ATF1 PKNOX1 CREB3L1 ZNF76 SIN3A FEZF1 ZNF2 ZBTB40 RAD21 YY1 ENSG00000252213 MATR3 PAIP2 SLC23A1 GC05P139300 SIL1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around MATR3 on UCSC Golden Path with GeneCards custom track

Promoters for MATR3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187617 748 1801 PKNOX1 MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143

Genomic Location for MATR3 Gene

139,273,752 bp from pter
139,331,677 bp from pter
57,926 bases
Plus strand

Genomic View for MATR3 Gene

Genes around MATR3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MATR3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MATR3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MATR3 Gene

Proteins for MATR3 Gene

  • Protein details for MATR3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B7ZAV5
    • D3DQC3
    • Q9UHW0
    • Q9UQ27

    Protein attributes for MATR3 Gene

    847 amino acids
    Molecular mass:
    94623 Da
    Quaternary structure:
    • Part of a complex consisting of SFPQ, NONO and MATR3. Interacts with AGO1 and AGO2. Part of a complex composed at least of ASCL2, EMSY, HCFC1, HSPA8, CCAR2, MATR3, MKI67, RBBP5, TUBB2A, WDR5 and ZNF335; this complex may have a histone H3-specific methyltransferase activity. Interacts with TARDBP.
    • Sequence=AAF17217.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=BAA34443.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for MATR3 Gene


neXtProt entry for MATR3 Gene

Post-translational modifications for MATR3 Gene

  • Ubiquitination at posLast=132132, posLast=146146, posLast=181181, Lys245, Lys515, Lys522, and Lys555
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for MATR3 Gene

Domains & Families for MATR3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with MATR3: view

No data available for Gene Families and UniProtKB/Swiss-Prot for MATR3 Gene

Function for MATR3 Gene

Molecular function for MATR3 Gene

GENATLAS Biochemistry:
matrin 3
UniProtKB/Swiss-Prot Function:
May play a role in transcription or may interact with other nuclear matrix proteins to form the internal fibrogranular network. In association with the SFPQ-NONO heteromer may play a role in nuclear retention of defective RNAs.

Gene Ontology (GO) - Molecular Function for MATR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,IDA 22658674
GO:0005198 structural molecule activity TAS 2033075
GO:0005515 protein binding IPI 17932509
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with MATR3: view
genes like me logo Genes that share phenotypes with MATR3: view

Human Phenotype Ontology for MATR3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for MATR3 Gene

Localization for MATR3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MATR3 Gene

Nucleus matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MATR3 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for MATR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005637 nuclear inner membrane TAS 2033075
GO:0016020 membrane IDA 19946888
GO:0016363 nuclear matrix IEA --
genes like me logo Genes that share ontologies with MATR3: view

Pathways & Interactions for MATR3 Gene

SuperPathways for MATR3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for MATR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010608 posttranscriptional regulation of gene expression IDA 21771347
genes like me logo Genes that share ontologies with MATR3: view

No data available for Pathways by source and SIGNOR curated interactions for MATR3 Gene

Drugs & Compounds for MATR3 Gene

(1) Drugs for MATR3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with MATR3: view

Transcripts for MATR3 Gene

Unigene Clusters for MATR3 Gene

Matrin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for MATR3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b · 10c ^ 11 ^
SP1: - - -
SP2: - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - - -
SP4: - - - -
SP5: - - - - - - - - - - - - -
SP8: - - - - - - - - - - - - - - - -
SP11: -
SP16: - - - - - - -
SP17: - - - - - - - -
SP18: - - - - - - - - - - - -
SP19: - - - - - -
SP20: - - - - -
SP21: - - - - - - - - - -
SP22: - - - -
SP23: - -
SP24: -

ExUns: 12a · 12b · 12c ^ 13 ^ 14a · 14b · 14c ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18 ^ 19a · 19b ^ 20 ^ 21a · 21b ^ 22a · 22b
SP1: - - -
SP2: -
SP3: -
SP4: -
SP6: -
SP7: - -
SP8: - - - - -
SP12: -

Relevant External Links for MATR3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MATR3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MATR3 Gene

Protein differential expression in normal tissues from HIPED for MATR3 Gene

This gene is overexpressed in Fetal Brain (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for MATR3 Gene

Protein tissue co-expression partners for MATR3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of MATR3 Gene:


SOURCE GeneReport for Unigene cluster for MATR3 Gene:


Evidence on tissue expression from TISSUES for MATR3 Gene

  • Nervous system(5)
  • Liver(4.7)
  • Skin(4.6)
  • Blood(4.3)
  • Muscle(4.2)
  • Kidney(3.1)
  • Eye(3)
  • Lung(2.9)
  • Intestine(2.8)
  • Bone marrow(2.1)
  • Heart(2.1)
  • Lymph node(2.1)
  • Thyroid gland(2.1)
  • Adrenal gland(2)
  • Gall bladder(2)
  • Spleen(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for MATR3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • epiglottis
  • face
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • skull
  • tongue
  • vocal cord
  • bronchus
  • clavicle
  • esophagus
  • heart
  • lung
  • scapula
  • trachea
  • biliary tract
  • liver
  • stomach
  • arm
  • digit
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • shin
  • shoulder
  • thigh
  • toe
  • upper limb
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with MATR3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for MATR3 Gene

Orthologs for MATR3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for MATR3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia MATR3 34 35
  • 99.8 (n)
(Canis familiaris)
Mammalia MATR3 34 35
  • 96.26 (n)
(Bos Taurus)
Mammalia -- 35
  • 96 (a)
MATR3 34
  • 95.16 (n)
-- 35
  • 92 (a)
(Mus musculus)
Mammalia Matr3 34 16 35
  • 94.84 (n)
(Rattus norvegicus)
Mammalia Matr3 34
  • 94.83 (n)
(Monodelphis domestica)
Mammalia MATR3 35
  • 89 (a)
(Ornithorhynchus anatinus)
Mammalia MATR3 35
  • 80 (a)
(Gallus gallus)
Aves MATR3 34 35
  • 81.22 (n)
(Anolis carolinensis)
Reptilia MATR3 35
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia matr3 34
  • 65.82 (n)
Str.6585 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.7663 34
(Danio rerio)
Actinopterygii matr3l1.1 35
  • 18 (a)
MATR3 (2 of 2) 35
  • 16 (a)
Species where no ortholog for MATR3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for MATR3 Gene

Gene Tree for MATR3 (if available)
Gene Tree for MATR3 (if available)

Paralogs for MATR3 Gene

Variants for MATR3 Gene

Sequence variations from dbSNP and Humsavar for MATR3 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs121434591 other, Amyotrophic lateral sclerosis 21 (ALS21) [MIM:606070] 139,307,669(+) GCAGT(C/G)TATAT intron-variant, reference, missense
rs587777300 Pathogenic, Amyotrophic lateral sclerosis 21 (ALS21) [MIM:606070] 139,307,759(+) CAGCT(G/T)TGGTC intron-variant, reference, missense
rs587777301 Pathogenic, Amyotrophic lateral sclerosis 21 (ALS21) [MIM:606070] 139,322,683(+) GTTCA(A/G)CCGAA reference, missense
rs587777302 Pathogenic, Amyotrophic lateral sclerosis 21 (ALS21) [MIM:606070] 139,307,875(+) AAGGC(C/T)CTACC intron-variant, reference, missense
VAR_074067 Amyotrophic lateral sclerosis 21 (ALS21) [MIM:606070]

Structural Variations from Database of Genomic Variants (DGV) for MATR3 Gene

Variant ID Type Subtype PubMed ID
esv2730825 CNV deletion 23290073
esv2730826 CNV deletion 23290073
esv2730827 CNV deletion 23290073
esv3566711 CNV deletion 23714750
esv3606937 CNV loss 21293372
nsv1148119 CNV deletion 26484159
nsv1149796 CNV deletion 26484159
nsv1150239 CNV deletion 26484159
nsv1152166 CNV deletion 26484159
nsv950409 CNV duplication 24416366
nsv980731 CNV duplication 23825009

Variation tolerance for MATR3 Gene

Residual Variation Intolerance Score: 4.16% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.88; 18.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for MATR3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MATR3 Gene

Disorders for MATR3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for MATR3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis 21
  • amyotrophic lateral sclerosis type 21
distal myopathy with vocal cord weakness
  • distal myopathy 2
amyotrophic lateral sclerosis 1
  • amyotrophic lateral sclerosis
aortic coarctation
  • coarctation of the aorta
patent ductus arteriosus
  • ductus arteriosus, patent
- elite association - COSMIC cancer census association via MalaCards
Search MATR3 in MalaCards View complete list of genes associated with diseases


  • Amyotrophic lateral sclerosis 21 (ALS21) [MIM:606070]: A neurodegenerative disorder affecting upper and lower motor neurons, resulting in muscle weakness and respiratory failure. Some patients may develop myopathic features or dementia. {ECO:0000269 PubMed:19344878, ECO:0000269 PubMed:24686783, ECO:0000269 PubMed:25771394}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for MATR3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with MATR3: view

No data available for Genatlas for MATR3 Gene

Publications for MATR3 Gene

  1. Autosomal-dominant distal myopathy associated with a recurrent missense mutation in the gene encoding the nuclear matrix protein, matrin 3. (PMID: 19344878) Senderek J. … Jackson C.E. (Am. J. Hum. Genet. 2009) 2 3 4 22 64
  2. Molecular cloning of matrin 3. A 125-kilodalton protein of the nuclear matrix contains an extensive acidic domain. (PMID: 2033075) Belgrader P. … Berezney R. (J. Biol. Chem. 1991) 2 3 4 22 64
  3. Mutational analysis of MATR3 in Taiwanese patients with amyotrophic lateral sclerosis. (PMID: 25771394) Lin K.P. … Lee Y.C. (Neurobiol. Aging 2015) 3 4 64
  4. Mutations in the matrin 3 gene cause familial amyotrophic lateral sclerosis. (PMID: 24686783) Johnson J.O. … Traynor B.J. (Nat. Neurosci. 2014) 3 4 64
  5. Genetic susceptibility to distinct bladder cancer subphenotypes. (PMID: 19692168) Guey L.T. … Malats N. (Eur. Urol. 2010) 3 46 64

Products for MATR3 Gene

  • Addgene plasmids for MATR3

Sources for MATR3 Gene

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