Human Gene NEFM (ENST00000221166.10) Description and Page Index
  Description: Homo sapiens neurofilament medium (NEFM), transcript variant 1, mRNA. (from RefSeq NM_005382)
RefSeq Summary (NM_005382): Neurofilaments are type IV intermediate filament heteropolymers composed of light, medium, and heavy chains. Neurofilaments comprise the axoskeleton and functionally maintain neuronal caliber. They may also play a role in intracellular transport to axons and dendrites. This gene encodes the medium neurofilament protein. This protein is commonly used as a biomarker of neuronal damage. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008].
Gencode Transcript: ENST00000221166.10
Gencode Gene: ENSG00000104722.14
Transcript (Including UTRs)
   Position: hg38 chr8:24,913,761-24,919,093 Size: 5,333 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chr8:24,913,794-24,918,606 Size: 4,813 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:24,913,761-24,919,093)mRNA (may differ from genome)Protein (916 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGIneXtProtOMIMPubMed
Stanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: NFM_HUMAN
DESCRIPTION: RecName: Full=Neurofilament medium polypeptide; Short=NF-M; AltName: Full=160 kDa neurofilament protein; AltName: Full=Neurofilament 3; AltName: Full=Neurofilament triplet M protein;
FUNCTION: Neurofilaments usually contain three intermediate filament proteins: L, M, and H which are involved in the maintenance of neuronal caliber.
INTERACTION: P06400:RB1; NbExp=2; IntAct=EBI-1105035, EBI-491274; Q15796:SMAD2; NbExp=3; IntAct=EBI-1105035, EBI-1040141;
PTM: There are a number of repeats of the tripeptide K-S-P, NFM is phosphorylated on a number of the serines in this motif. It is thought that phosphorylation of NFM results in the formation of interfilament cross bridges that are important in the maintenance of axonal caliber.
PTM: Phosphorylation seems to play a major role in the functioning of the larger neurofilament polypeptides (NF-M and NF-H), the levels of phosphorylation being altered developmentally and coincidentally with a change in the neurofilament function.
PTM: Phosphorylated in the head and rod regions by the PKC kinase PKN1, leading to the inhibition of polymerization.
SIMILARITY: Belongs to the intermediate filament family.
WEB RESOURCE: Name=Human Intermediate Filament Mutation Database; URL="http://www.interfil.org";

-  MalaCards Disease Associations
  MalaCards Gene Search: NEFM
Diseases sorted by gene-association score: pineal parenchymal tumor of intermediate differentiation (6), wallerian degeneration (5), lateral sclerosis (3), motor neuron disease (2), amyotrophic lateral sclerosis 1 (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D014212 Tretinoin
  • D014635 Valproic Acid
  • C070379 1,2-bis(2-aminophenoxy)ethane N,N,N',N'-tetraacetic acid acetoxymethyl ester
  • C060229 1-(6-((3-methoxyestra-1,3,5(10)-trien-17-yl)amino)hexyl)-1H-pyrrole-2,5-dione
  • C029790 2,2',3',4,4',5-hexachlorobiphenyl
  • C011269 2,5-hexanedione
  • C093973 2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-one
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • C012587 3,5,6-trichloro-2-pyridinol
  • D018750 6-Cyano-7-nitroquinoxaline-2,3-dione
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 166.94 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 755.01 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 -6.2033-0.188 Picture PostScript Text
3' UTR -123.10487-0.253 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
IPR006821 - Intermed_filament_DNA-bd
IPR018039 - Intermediate_filament_CS
IPR002957 - Keratin_I

Pfam Domains:
PF00038 - Intermediate filament protein
PF04732 - Intermediate filament head (DNA binding) region

ModBase Predicted Comparative 3D Structure on P07197
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
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:0008017 microtubule binding

Biological Process:
GO:0033693 neurofilament bundle assembly
GO:0061564 axon development

Cellular Component:
GO:0005882 intermediate filament
GO:0005883 neurofilament
GO:0030424 axon
GO:0045111 intermediate filament cytoskeleton
GO:0097418 neurofibrillary tangle


-  Descriptions from all associated GenBank mRNAs
  BC071752 - Homo sapiens neurofilament 3 (150kDa medium), mRNA (cDNA clone IMAGE:6464368), partial cds.
EF560736 - Homo sapiens clone DKFZp686A1298 NEFM protein (NEFM) mRNA, complete cds.
AK296226 - Homo sapiens cDNA FLJ56511 complete cds, highly similar to Neurofilament triplet M protein.
EF560737 - Homo sapiens clone DKFZp686O1498 NEFM protein (NEFM) mRNA, complete cds.
BC096757 - Homo sapiens neurofilament, medium polypeptide, mRNA (cDNA clone MGC:104856 IMAGE:5442340), complete cds.
GQ129242 - Synthetic construct Homo sapiens clone HAIB:100068644; DKFZo004A0536 neurofilament, medium polypeptide 150kDa protein (NEFM) gene, partial cds.
GQ129243 - Synthetic construct Homo sapiens clone HAIB:100068548; DKFZo008A0535 neurofilament, medium polypeptide 150kDa protein (NEFM) gene, complete cds.
KJ897236 - Synthetic construct Homo sapiens clone ccsbBroadEn_06630 NEFM gene, encodes complete protein.
AB527839 - Synthetic construct DNA, clone: pF1KB8481, Homo sapiens NEF3 gene for neurofilament, medium polypeptide, without stop codon, in Flexi system.
AK294681 - Homo sapiens cDNA FLJ58361 complete cds, highly similar to Neurofilament triplet M protein.
AF181990 - Homo sapiens neurofilament-3 (150 kD medium) (NEF3) mRNA, partial cds.
JD385698 - Sequence 366722 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05014 - Amyotrophic lateral sclerosis (ALS)

-  Other Names for This Gene
  Alternate Gene Symbols: NEF3, NFM, NFM_HUMAN, NM_005382, P07197, Q4QRK6, uc003xed.1, uc003xed.2, uc003xed.3, uc003xed.4, uc003xed.5, uc003xed.6
UCSC ID: uc003xed.6
RefSeq Accession: NM_005382
Protein: P07197 (aka NFM_HUMAN)
CCDS: CCDS6046.1

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