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Aliases for SYNM Gene

Aliases for SYNM Gene

  • Synemin 2 3 3 5
  • Desmuslin 2 3 4
  • Synemin, Intermediate Filament Protein 2 3
  • Synemin Alpha 2 3
  • Synemin Beta 2 3
  • SYN 3 4
  • DMN 3 4
  • EC 2.6.1.16 56
  • EC 1.4.99.1 56
  • KIAA0353 4

External Ids for SYNM Gene

Previous HGNC Symbols for SYNM Gene

  • DMN

Previous GeneCards Identifiers for SYNM Gene

  • GC15P097463
  • GC15P099645
  • GC15P075774

Summaries for SYNM Gene

Entrez Gene Summary for SYNM Gene

  • The protein encoded by this gene is an intermediate filament (IF) family member. IF proteins are cytoskeletal proteins that confer resistance to mechanical stress and are encoded by a dispersed multigene family. This protein has been found to form a linkage between desmin, which is a subunit of the IF network, and the extracellular matrix, and provides an important structural support in muscle. Two alternatively spliced variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SYNM Gene

SYNM (Synemin) is a Protein Coding gene. Diseases associated with SYNM include Alexander Disease and Epidermolysis Bullosa Simplex With Muscular Dystrophy. Among its related pathways are Cytoskeleton remodeling Neurofilaments. Gene Ontology (GO) annotations related to this gene include structural molecule activity and structural constituent of muscle. An important paralog of this gene is NES.

UniProtKB/Swiss-Prot for SYNM Gene

  • Type-VI intermediate filament (IF) which plays an important cytoskeletal role within the muscle cell cytoskeleton. It forms heteropolymeric IFs with desmin and/or vimentin, and via its interaction with cytoskeletal proteins alpha-dystrobrevin, dystrophin, talin-1, utrophin and vinculin, is able to link these heteropolymeric IFs to adherens-type junctions, such as to the costameres, neuromuscular junctions, and myotendinous junctions within striated muscle cells.

Additional gene information for SYNM Gene

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

Genomics for SYNM Gene

GeneHancer (GH) Regulatory Elements for SYNM Gene

Promoters and enhancers for SYNM Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15I099104 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 566.3 +8.1 8102 3.8 HDGF ARNT ARID4B SIN3A ZNF2 ZNF48 ZNF143 RUNX3 SP3 NFYC SYNM LOC105371016 PIR44206 ENSG00000261616 TTC23 LRRC28
GH15I099097 Enhancer 0.2 dbSUPER 565.1 -0.1 -71 2 SYNM LRRC28 LOC105371016 GC15M099019
GH15I099122 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 27 +26.4 26356 4.2 ARID4B SIN3A FEZF1 ZNF2 ZNF48 GLIS2 ZNF213 FOS TSHZ1 SMARCB1 SYNM ENSG00000261616 ENSG00000261054 TTC23 LRRC28 PIR61097 LOC105371016
GH15I099167 Enhancer 1 Ensembl ENCODE dbSUPER 31.3 +71.2 71174 4.7 CTCF ZNF687 EBF1 RELA POLR2A SCRT2 IKZF1 RUNX3 IKZF2 SPI1 SYNM LRRC28 ENSG00000261616 ENSG00000261054 TTC23 ENSG00000259921 GC15M099193
GH15I099180 Enhancer 1.1 Ensembl ENCODE dbSUPER 21.2 +83.1 83112 1.1 SOX13 CLOCK FOXA2 SAP130 ZIC2 GATA3 FOS NFE2L2 GATAD2A SOX5 SYNM ENSG00000259921 GC15M099193 TTC23
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SYNM on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SYNM gene promoter:

Genomic Locations for SYNM Gene

Genomic Locations for SYNM Gene
chr15:99,098,217-99,135,595
(GRCh38/hg38)
Size:
37,379 bases
Orientation:
Plus strand
chr15:99,638,420-99,675,800
(GRCh37/hg19)

Genomic View for SYNM Gene

Genes around SYNM on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SYNM Gene

Proteins for SYNM Gene

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

    Protein Symbol:
    O15061-SYNEM_HUMAN
    Recommended name:
    Synemin
    Protein Accession:
    O15061
    Secondary Accessions:
    • A7E2Y2
    • Q2TBJ4
    • Q5NJJ9
    • Q8TE61
    • Q8TE62

    Protein attributes for SYNM Gene

    Size:
    1565 amino acids
    Molecular mass:
    172768 Da
    Quaternary structure:
    • Interacts with GFAP and VIM (By similarity). Isoform 1 interacts with TLN1 and VCL. Isoform 2 interacts with DES and DTNA. Isoform 1 and isoform 2 interact with DMD and UTRN.
    SequenceCaution:
    • Sequence=AAI10067.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA20810.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SYNM Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYNM Gene

Selected DME Specific Peptides for SYNM Gene

O15061:
  • STIARES
  • GGDLSQA

Post-translational modifications for SYNM Gene

No Post-translational modifications

Other Protein References for SYNM Gene

Domains & Families for SYNM Gene

Gene Families for SYNM Gene

Protein Domains for SYNM Gene

Suggested Antigen Peptide Sequences for SYNM Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O15061

UniProtKB/Swiss-Prot:

SYNEM_HUMAN :
  • Belongs to the intermediate filament family.
Family:
  • Belongs to the intermediate filament family.
genes like me logo Genes that share domains with SYNM: view

Function for SYNM Gene

Molecular function for SYNM Gene

UniProtKB/Swiss-Prot Function:
Type-VI intermediate filament (IF) which plays an important cytoskeletal role within the muscle cell cytoskeleton. It forms heteropolymeric IFs with desmin and/or vimentin, and via its interaction with cytoskeletal proteins alpha-dystrobrevin, dystrophin, talin-1, utrophin and vinculin, is able to link these heteropolymeric IFs to adherens-type junctions, such as to the costameres, neuromuscular junctions, and myotendinous junctions within striated muscle cells.

Enzyme Numbers (IUBMB) for SYNM Gene

Phenotypes From GWAS Catalog for SYNM Gene

Gene Ontology (GO) - Molecular Function for SYNM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005200 structural constituent of cytoskeleton IEA,IDA 11737198
GO:0005515 protein binding IPI 11353857
GO:0008307 structural constituent of muscle IEA,IDA 11737198
GO:0017166 vinculin binding IDA 18028034
GO:0019215 intermediate filament binding ISS,IEA --
genes like me logo Genes that share ontologies with SYNM: view
genes like me logo Genes that share phenotypes with SYNM: view

Animal Models for SYNM Gene

MGI Knock Outs for SYNM:
  • Synm tm1.1(KOMP)Vlcg

Animal Model Products

CRISPR Products

miRNA for SYNM Gene

miRTarBase miRNAs that target SYNM

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SYNM

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYNM Gene

Localization for SYNM Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNM Gene

Cytoplasm, cytoskeleton. Cell junction, adherens junction. Note=There are at least two distinct SYNM subpopulations, one in which SYMN interacts with DES within the Z-lines, and another in which it interacts with both DTNA and DES at the costamere.

Subcellular locations from

COMPARTMENTS
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 SYNM gene
Compartment Confidence
cytoskeleton 5
plasma membrane 3
nucleus 3
cytosol 2

Gene Ontology (GO) - Cellular Components for SYNM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0005882 intermediate filament IEA,NAS 11353857
GO:0005912 adherens junction IEA,IDA 16777071
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SYNM: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SYNM Gene

Pathways & Interactions for SYNM Gene

genes like me logo Genes that share pathways with SYNM: view

Pathways by source for SYNM Gene

1 GeneGo (Thomson Reuters) pathway for SYNM Gene

Gene Ontology (GO) - Biological Process for SYNM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031443 fast-twitch skeletal muscle fiber contraction IEA --
GO:0045104 intermediate filament cytoskeleton organization IEA,TAS 16777071
genes like me logo Genes that share ontologies with SYNM: view

No data available for SIGNOR curated interactions for SYNM Gene

Drugs & Compounds for SYNM Gene

No Compound Related Data Available

Transcripts for SYNM Gene

Unigene Clusters for SYNM Gene

Synemin, intermediate filament protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SYNM

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP1:
SP2:

Relevant External Links for SYNM Gene

GeneLoc Exon Structure for
SYNM
ECgene alternative splicing isoforms for
SYNM

Expression for SYNM Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYNM Gene

This gene is overexpressed in Esophagus - Muscularis (x8.1), Esophagus - Gastroesophageal Junction (x6.3), Colon - Sigmoid (x6.1), Bladder (x4.5), and Muscle - Skeletal (x4.3).

Protein differential expression in normal tissues from HIPED for SYNM Gene

This gene is overexpressed in Urinary Bladder (32.0), Colon muscle (13.6), and Colon (6.0).

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



Protein tissue co-expression partners for SYNM Gene

NURSA nuclear receptor signaling pathways regulating expression of SYNM Gene:

SYNM

SOURCE GeneReport for Unigene cluster for SYNM Gene:

Hs.207106

mRNA Expression by UniProt/SwissProt for SYNM Gene:

O15061-SYNEM_HUMAN
Tissue specificity: Isoform 2 is strongly detected in adult heart, fetal skeletal muscles and fetal heart. Isoform 1 is weakly detected in fetal heart and also in fetal skeletal muscle. Isoform 1 and isoform 2 are detected in adult bladder (at protein level). The mRNA is predominantly expressed in heart and muscle with some expression in brain which may be due to tissue-specific isoforms.

Evidence on tissue expression from TISSUES for SYNM Gene

  • Muscle(4.7)
  • Nervous system(4.7)
  • Liver(4.2)
  • Heart(2.9)
  • Intestine(2.7)
  • Eye(2.3)
  • Gall bladder(2.1)
genes like me logo Genes that share expression patterns with SYNM: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNM Gene

Orthologs for SYNM Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYNM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYNM 33 34
  • 98.93 (n)
cow
(Bos Taurus)
Mammalia SYNM 33 34
  • 79.47 (n)
rat
(Rattus norvegicus)
Mammalia Synm 33
  • 76.91 (n)
mouse
(Mus musculus)
Mammalia Synm 33 16 34
  • 76.88 (n)
dog
(Canis familiaris)
Mammalia SYNM 34
  • 64 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SYNM 34
  • 51 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYNM 34
  • 46 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYNM 33 34
  • 54.49 (n)
lizard
(Anolis carolinensis)
Reptilia SYNM 34
  • 26 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia synm 33
  • 48.37 (n)
zebrafish
(Danio rerio)
Actinopterygii synm 33 34
  • 47.8 (n)
Species where no ortholog for SYNM was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 SYNM Gene

ENSEMBL:
Gene Tree for SYNM (if available)
TreeFam:
Gene Tree for SYNM (if available)

Paralogs for SYNM Gene

Paralogs for SYNM Gene

(2) SIMAP similar genes for SYNM Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SYNM: view

Variants for SYNM Gene

Sequence variations from dbSNP and Humsavar for SYNM Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs370914226 likely-benign, not specified 99,131,474(+) C/T coding_sequence_variant, synonymous_variant
rs60530833 benign, not specified 99,105,902(+) G/GG coding_sequence_variant, frameshift
rs1000075766 -- 99,106,284(+) C/G intron_variant
rs1000119573 -- 99,125,789(+) T/C intron_variant
rs1000350384 -- 99,125,240(+) C/T intron_variant

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

Variant ID Type Subtype PubMed ID
dgv4767n54 CNV loss 21841781
dgv4768n54 CNV gain 21841781
esv22082 CNV loss 19812545
esv22522 CNV loss 19812545
esv2667911 CNV deletion 23128226
esv2750111 CNV deletion 23290073
esv3211568 CNV deletion 24192839
esv3552929 CNV deletion 23714750
esv3637420 CNV loss 21293372
esv3892741 CNV gain 25118596
esv4381 CNV loss 18987735
esv9228 CNV loss 19470904
esv987621 CNV deletion 20482838
nsv1036320 CNV loss 25217958
nsv1045124 CNV gain 25217958
nsv1055008 CNV gain 25217958
nsv1686 CNV insertion 18451855
nsv474812 CNV novel sequence insertion 20440878
nsv476611 CNV novel sequence insertion 20440878
nsv479175 CNV novel sequence insertion 20440878
nsv480439 CNV novel sequence insertion 20440878
nsv509583 CNV insertion 20534489
nsv512412 CNV loss 21212237
nsv570716 CNV gain 21841781
nsv570717 CNV loss 21841781
nsv570718 CNV loss 21841781
nsv570719 CNV loss 21841781
nsv570720 CNV gain+loss 21841781
nsv570723 CNV gain 21841781
nsv570726 CNV loss 21841781
nsv570727 CNV loss 21841781

Variation tolerance for SYNM Gene

Gene Damage Index Score: 13.39; 95.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYNM Gene

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

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

Disorders for SYNM Gene

MalaCards: The human disease database

(5) MalaCards diseases for SYNM Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
alexander disease
  • alxdrd
epidermolysis bullosa simplex with muscular dystrophy
  • ebsmd
myopathy of extraocular muscle
  • myopathy of extraocular muscles
bladder exstrophy-epispadias-cloacal exstrophy complex
  • exstrophy-epispadias complex
exstrophy of bladder
  • bladder exstrophy
- elite association - COSMIC cancer census association via MalaCards
Search SYNM in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYNM

genes like me logo Genes that share disorders with SYNM: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYNM Gene

Publications for SYNM Gene

  1. Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3. (PMID: 11454237) Mizuno Y … Kunkel LM (BMC genetics 2001) 2 3 4 22 58
  2. Human synemin gene generates splice variants encoding two distinct intermediate filament proteins. (PMID: 11737198) Titeux M … Li Z (European journal of biochemistry 2001) 2 3 4 22 58
  3. Human alpha-synemin interacts directly with vinculin and metavinculin. (PMID: 18028034) Sun N … Robson RM (The Biochemical journal 2008) 3 4 22 58
  4. Identification of a repeated domain within mammalian alpha-synemin that interacts directly with talin. (PMID: 18342854) Sun N … Robson RM (Experimental cell research 2008) 3 4 22 58
  5. Interactions of intermediate filament protein synemin with dystrophin and utrophin. (PMID: 16777071) Bhosle RC … Robson RM (Biochemical and biophysical research communications 2006) 3 4 22 58

Products for SYNM Gene

Sources for SYNM Gene

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