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Aliases for SYNM Gene

Aliases for SYNM Gene

  • Synemin 2 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 63
  • EC 1.4.99.1 63
  • 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 alveolar soft-tissue sarcoma and alexander disease. Among its related pathways are Cytoskeleton remodeling Neurofilaments. 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.

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

Genomics for SYNM Gene

Regulatory Elements for SYNM Gene

Enhancers for SYNM Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SYNM on UCSC Golden Path with GeneCards custom track

Genomic Location for SYNM Gene

Chromosome:
15
Start:
99,098,217 bp from pter
End:
99,135,595 bp from pter
Size:
37,379 bases
Orientation:
Plus strand

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

Proteomics data for SYNM Gene at MOPED

Selected DME Specific Peptides for SYNM Gene

Post-translational modifications for SYNM Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYNM Gene

Domains & Families for SYNM Gene

Protein Domains for SYNM Gene

InterPro:
ProtoNet:

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

Gene Ontology (GO) - Molecular Function for SYNM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0017166 vinculin binding IDA 18028034
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

miRNA for SYNM Gene

miRTarBase miRNAs that target 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
Jensen Localization Image for SYNM Gene COMPARTMENTS Subcellular localization image for SYNM gene
Compartment Confidence
cytoskeleton 5
nucleus 3
cytosol 2
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SYNM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0043034 costamere IDA 16777071
genes like me logo Genes that share ontologies with SYNM: view

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

None

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:

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 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, MOPED, and MaxQB for SYNM Gene



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.
genes like me logo Genes that share expression patterns with SYNM: view

Protein tissue co-expression partners for SYNM Gene

Primer Products

Orthologs for SYNM Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYNM Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SYNM 35
  • 79.47 (n)
  • 72.49 (a)
SYNM 36
  • 70 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Synm 35
  • 76.88 (n)
  • 70.26 (a)
Synm 16
Synm 36
  • 68 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SYNM 35
  • 98.93 (n)
  • 98.52 (a)
SYNM 36
  • 96 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Synm 35
  • 76.91 (n)
  • 69.72 (a)
dog
(Canis familiaris)
Mammalia SYNM 36
  • 64 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SYNM 36
  • 51 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYNM 36
  • 46 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYNM 35
  • 54.49 (n)
  • 42 (a)
SYNM 36
  • 34 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYNM 36
  • 26 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia synm 35
  • 48.37 (n)
  • 37.25 (a)
zebrafish
(Danio rerio)
Actinopterygii synm 35
  • 47.8 (n)
  • 34.72 (a)
synm 36
  • 25 (a)
OneToOne
Species with no ortholog for SYNM:
  • 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 Sequence Context AA Info Type
VAR_012295 -
VAR_012296 -
VAR_012297 -
VAR_012298 -
VAR_012299 -

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

Variant ID Type Subtype PubMed ID
nsv509583 CNV Insertion 20534489
nsv904543 CNV Gain 21882294
nsv904544 CNV Gain 21882294
nsv1686 CNV Insertion 18451855
esv22522 CNV Loss 19812545
nsv512412 CNV Loss 21212237
esv4381 CNV Deletion 18987735
esv2750111 CNV Deletion 23290073
esv22082 CNV Loss 19812545
esv2667911 CNV Deletion 23128226
esv9228 CNV Loss 19470904
esv987621 CNV Deletion 20482838

Variation tolerance for SYNM Gene

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

Relevant External Links for SYNM Gene

HapMap Linkage Disequilibrium report
SYNM
Human Gene Mutation Database (HGMD)
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: DISEASES and GeneCards

Disorder Aliases PubMed IDs
alveolar soft-tissue sarcoma
  • alveolar soft-part sarcoma
alexander disease
  • alexander's disease
pleomorphic xanthoastrocytoma
  • pleomorphic xantho-astrocytoma
diabetic autonomic neuropathy
  • diabetic neuropathies
inflammatory myofibroblastic tumor
  • inflammatory fibrosarcoma
- elite association - COSMIC cancer census association via MalaCards
Search SYNM in MalaCards View complete list of genes associated with diseases

Relevant External Links for SYNM

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 L.M. (BMC Genet. 2001) 2 3 4 23 67
  2. Human synemin gene generates splice variants encoding two distinct intermediate filament proteins. (PMID: 11737198) Titeux M. … Li Z. (Eur. J. Biochem. 2001) 2 3 23
  3. Synemin interacts with the LIM domain protein zyxin and is essential for cell adhesion and migration. (PMID: 19853601) Sun N. … Robson R.M. (Exp. Cell Res. 2010) 3 23
  4. Dysbindin, syncoilin, and beta-synemin mRNA levels in dystrophic muscles. (PMID: 20199207) Wakayama Y. … Masaki H. (Int. J. Neurosci. 2010) 3 23
  5. Human alpha-synemin interacts directly with vinculin and metavinculin. (PMID: 18028034) Sun N. … Robson R.M. (Biochem. J. 2008) 3 23

Products for SYNM Gene

Sources for SYNM Gene

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