Human Gene VMAC (ENST00000339485.4_4) from GENCODE V47lift37
  Description: vimentin type intermediate filament associated coiled-coil protein (from RefSeq NM_001017921.4)
Gencode Transcript: ENST00000339485.4_4
Gencode Gene: ENSG00000187650.4_8
Transcript (Including UTRs)
   Position: hg19 chr19:5,904,883-5,910,864 Size: 5,982 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr19:5,904,902-5,909,153 Size: 4,252 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:5,904,883-5,910,864)mRNA (may differ from genome)Protein (169 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VMAC_HUMAN
DESCRIPTION: RecName: Full=Vimentin-type intermediate filament-associated coiled-coil protein;
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Note=Colocalizes with vimentin-type intermediate filaments (By similarity).

-  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


-  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: 6.33 RPKM in Prostate
Total median expression: 157.70 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 -1.4019-0.074 Picture PostScript Text
3' UTR -818.401711-0.478 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
  SCOP Domains:
69979 - Eea1 homodimerisation domain
103652 - G protein-binding domain
57997 - Tropomyosin

ModBase Predicted Comparative 3D Structure on Q2NL98
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  LF210892 - JP 2014500723-A/18395: Polycomb-Associated Non-Coding RNAs.
JD144335 - Sequence 125359 from Patent EP1572962.
JD497365 - Sequence 478389 from Patent EP1572962.
AK124162 - Homo sapiens cDNA FLJ42168 fis, clone THYMU2025707.
BC110802 - Homo sapiens vimentin-type IF-associated coiled-coil protein, mRNA (cDNA clone MGC:131658 IMAGE:5108486), complete cds.
KJ896243 - Synthetic construct Homo sapiens clone ccsbBroadEn_05637 VMAC gene, encodes complete protein.
JD063325 - Sequence 44349 from Patent EP1572962.
JD273171 - Sequence 254195 from Patent EP1572962.
LF341767 - JP 2014500723-A/149270: Polycomb-Associated Non-Coding RNAs.
JD304580 - Sequence 285604 from Patent EP1572962.
JD409920 - Sequence 390944 from Patent EP1572962.
JD375062 - Sequence 356086 from Patent EP1572962.
JD158487 - Sequence 139511 from Patent EP1572962.
JD088926 - Sequence 69950 from Patent EP1572962.
JD526694 - Sequence 507718 from Patent EP1572962.
JD201616 - Sequence 182640 from Patent EP1572962.
JD063862 - Sequence 44886 from Patent EP1572962.
JD245753 - Sequence 226777 from Patent EP1572962.
JD360657 - Sequence 341681 from Patent EP1572962.
JD435467 - Sequence 416491 from Patent EP1572962.
JD308174 - Sequence 289198 from Patent EP1572962.
JD435468 - Sequence 416492 from Patent EP1572962.
JD254771 - Sequence 235795 from Patent EP1572962.
JD556282 - Sequence 537306 from Patent EP1572962.
JD151643 - Sequence 132667 from Patent EP1572962.
JD522236 - Sequence 503260 from Patent EP1572962.
JD558236 - Sequence 539260 from Patent EP1572962.
JD564286 - Sequence 545310 from Patent EP1572962.
JD558235 - Sequence 539259 from Patent EP1572962.
MA577344 - JP 2018138019-A/149270: Polycomb-Associated Non-Coding RNAs.
MA446469 - JP 2018138019-A/18395: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KW55, ENST00000339485.1, ENST00000339485.2, ENST00000339485.3, NM_001017921, Q2NL98, uc317vjg.1, uc317vjg.2, VMAC_HUMAN
UCSC ID: ENST00000339485.4_4
RefSeq Accession: NM_001017921.4
Protein: Q2NL98 (aka VMAC_HUMAN)

-  Gene Model Information
  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.