Human Gene SYNM (uc002bup.3)
  Description: Homo sapiens synemin, intermediate filament protein (SYNM), transcript variant A, mRNA.
RefSeq Summary (NM_145728): 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].
Transcript (Including UTRs)
   Position: hg19 chr15:99,645,286-99,675,800 Size: 30,515 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr15:99,645,406-99,673,263 Size: 27,858 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:99,645,286-99,675,800)mRNA (may differ from genome)Protein (1565 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYNEM_HUMAN
DESCRIPTION: RecName: Full=Synemin; AltName: Full=Desmuslin;
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.
SUBUNIT: 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.
SUBCELLULAR LOCATION: 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.
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.
DEVELOPMENTAL STAGE: In lens, first detected at 16 weeks when expression is weakly and uniformly distributed. Subsequently, expression becomes much stronger in the epithelium of the anterior part at 25 weeks and later. In retina, weakly expressed at 15 weeks in the nerve fiber and ganglion cell layers (NFL and GCL). From 25 weeks onwards, much stronger expression is observed in the endfeet of Mueller cells, the NFL, and GCL, and much lower expression is observed in a minor subpopulation of cells in the inner cell layer (INL). At 30 and 36 weeks, expression remains in the neural retina, and subsequently becomes stronger in the NFL, GCL, and INL and is decreased in Mueller cells. At 36 weeks, also expressed at the external border of the outer nuclear layer (ONL) (at protein level).
SIMILARITY: Belongs to the intermediate filament family.
SEQUENCE CAUTION: Sequence=AAI10067.1; Type=Erroneous initiation; Sequence=BAA20810.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SYNM
Diseases sorted by gene-association score: alexander disease (10), epidermolysis bullosa simplex with muscular dystrophy (6), bladder exstrophy-epispadias-cloacal exstrophy complex (5), myopathy of extraocular muscle (5), exstrophy of bladder (5), walker-warburg syndrome (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 430.38 RPKM in Esophagus - Muscularis
Total median expression: 2173.12 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -56.80120-0.473 Picture PostScript Text
3' UTR -761.382537-0.300 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016044 - F
IPR001664 - IF
IPR018039 - Intermediate_filament_CS

Pfam Domains:
PF00038 - Intermediate filament protein

ModBase Predicted Comparative 3D Structure on O15061
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity
GO:0005200 structural constituent of cytoskeleton
GO:0005515 protein binding
GO:0008307 structural constituent of muscle
GO:0017166 vinculin binding
GO:0019215 intermediate filament binding

Biological Process:
GO:0031443 fast-twitch skeletal muscle fiber contraction
GO:0045104 intermediate filament cytoskeleton organization

Cellular Component:
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005882 intermediate filament
GO:0005912 adherens junction
GO:0016020 membrane
GO:0030054 cell junction
GO:0042383 sarcolemma
GO:0043034 costamere
GO:0060053 neurofilament cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  AL833262 - Homo sapiens mRNA; cDNA DKFZp451C2210 (from clone DKFZp451C2210).
LF207710 - JP 2014500723-A/15213: Polycomb-Associated Non-Coding RNAs.
LF212113 - JP 2014500723-A/19616: Polycomb-Associated Non-Coding RNAs.
BC151243 - Homo sapiens synemin, intermediate filament protein, mRNA (cDNA clone MGC:167837 IMAGE:8860516), complete cds.
AB002351 - Homo sapiens mRNA for KIAA0353 gene.
AJ310521 - Homo sapiens mRNA for synemin (SYN gene), isoform M.
AJ310522 - Homo sapiens mRNA for synemin (SYN gene), isoform H.
AJ697971 - Homo sapiens mRNA for synemin (SYN gene), isoform L.
AF359284 - Homo sapiens desmuslin mRNA, complete cds.
JD458862 - Sequence 439886 from Patent EP1572962.
JD462630 - Sequence 443654 from Patent EP1572962.
JD395316 - Sequence 376340 from Patent EP1572962.
JD172636 - Sequence 153660 from Patent EP1572962.
AB383857 - Synthetic construct DNA, clone: pF1KSDA0353, Homo sapiens DMN gene for desmuslin, complete cds, without stop codon, in Flexi system.
LF368179 - JP 2014500723-A/175682: Polycomb-Associated Non-Coding RNAs.
DQ599986 - Homo sapiens piRNA piR-38052, complete sequence.
DQ580367 - Homo sapiens piRNA piR-48479, complete sequence.
DQ582360 - Homo sapiens piRNA piR-32472, complete sequence.
DQ581412 - Homo sapiens piRNA piR-49524, complete sequence.
DQ597130 - Homo sapiens piRNA piR-35196, complete sequence.
DQ590900 - Homo sapiens piRNA piR-58012, complete sequence.
DQ590233 - Homo sapiens piRNA piR-57345, complete sequence.
AK026420 - Homo sapiens cDNA: FLJ22767 fis, clone KAIA1191.
BC110066 - Homo sapiens synemin, intermediate filament protein, mRNA (cDNA clone IMAGE:40027592), partial cds.
JD147167 - Sequence 128191 from Patent EP1572962.
JD447429 - Sequence 428453 from Patent EP1572962.
JD289809 - Sequence 270833 from Patent EP1572962.
JD357378 - Sequence 338402 from Patent EP1572962.
JD535098 - Sequence 516122 from Patent EP1572962.
DQ584815 - Homo sapiens piRNA piR-51927, complete sequence.
JD283529 - Sequence 264553 from Patent EP1572962.
JD428854 - Sequence 409878 from Patent EP1572962.
BC063699 - Homo sapiens cDNA clone IMAGE:4704709, partial cds.
JD353832 - Sequence 334856 from Patent EP1572962.
JD274002 - Sequence 255026 from Patent EP1572962.
JD372049 - Sequence 353073 from Patent EP1572962.
JD370805 - Sequence 351829 from Patent EP1572962.
JD454568 - Sequence 435592 from Patent EP1572962.
JD056646 - Sequence 37670 from Patent EP1572962.
JD452411 - Sequence 433435 from Patent EP1572962.
DQ578257 - Homo sapiens piRNA piR-46369, complete sequence.
JD147408 - Sequence 128432 from Patent EP1572962.
JD248385 - Sequence 229409 from Patent EP1572962.
JD184585 - Sequence 165609 from Patent EP1572962.
JD174745 - Sequence 155769 from Patent EP1572962.
JD362535 - Sequence 343559 from Patent EP1572962.
JD367128 - Sequence 348152 from Patent EP1572962.
JD484733 - Sequence 465757 from Patent EP1572962.
BC022358 - Homo sapiens cDNA clone IMAGE:4297272.
JD549478 - Sequence 530502 from Patent EP1572962.
JD325241 - Sequence 306265 from Patent EP1572962.
MA603756 - JP 2018138019-A/175682: Polycomb-Associated Non-Coding RNAs.
MA443287 - JP 2018138019-A/15213: Polycomb-Associated Non-Coding RNAs.
MA447690 - JP 2018138019-A/19616: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A7E2Y2, DMN, KIAA0353, NM_145728, NP_663780, O15061, Q2TBJ4, Q5NJJ9, Q8TE61, Q8TE62, SYN, SYNEM_HUMAN
UCSC ID: uc002bup.3
RefSeq Accession: NM_145728
Protein: O15061 (aka SYNEM_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_145728.2
exon count: 4CDS single in 3' UTR: no RNA size: 7355
ORF size: 4697CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7184.00frame shift in genome: yes % Coverage: 99.96
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 3782# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.