Human Gene NEFM (ENST00000221166.10_6) from GENCODE V47lift37
  Description: neurofilament medium chain, transcript variant 1 (from RefSeq NM_005382.2)
Gencode Transcript: ENST00000221166.10_6
Gencode Gene: ENSG00000104722.14_9
Transcript (Including UTRs)
   Position: hg19 chr8:24,771,274-24,776,606 Size: 5,333 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr8:24,771,307-24,776,119 Size: 4,813 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:24,771,274-24,776,606)mRNA (may differ from genome)Protein (916 aa)
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-  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";

-  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: 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

+  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: 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

SCOP Domains:
64593 - Intermediate filament protein, coiled coil region
90257 - Myosin rod fragments
57997 - Tropomyosin

ModBase Predicted Comparative 3D Structure on P07197
FrontTopSide
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    
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-  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.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DGN2, E9PBF7, ENST00000221166.1, ENST00000221166.2, ENST00000221166.3, ENST00000221166.4, ENST00000221166.5, ENST00000221166.6, ENST00000221166.7, ENST00000221166.8, ENST00000221166.9, NEF3, NFM, NFM_HUMAN, NM_005382, P07197, Q4QRK6, uc317dai.1, uc317dai.2
UCSC ID: ENST00000221166.10_6
RefSeq Accession: NM_005382.2
Protein: P07197 (aka NFM_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.