Human Gene NTF3 (uc001qnk.4) Description and Page Index
  Description: Homo sapiens neurotrophin 3 (NTF3), transcript variant 1, mRNA.
RefSeq Summary (NM_001102654): The protein encoded by this gene is a member of the neurotrophin family, that controls survival and differentiation of mammalian neurons. This protein is closely related to both nerve growth factor and brain-derived neurotrophic factor. It may be involved in the maintenance of the adult nervous system, and may affect development of neurons in the embryo when it is expressed in human placenta. NTF3-deficient mice generated by gene targeting display severe movement defects of the limbs. The mature peptide of this protein is identical in all mammals examined including human, pig, rat and mouse. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR5189652.232075.1, SRR3476690.165428.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968540, SAMEA1968832 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000423158.4/ ENSP00000397297.2 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:5,541,280-5,604,465 Size: 63,186 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr12:5,541,491-5,604,154 Size: 62,664 Coding Exon Count: 2 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:5,541,280-5,604,465)mRNA (may differ from genome)Protein (270 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NTF3
CDC HuGE Published Literature: NTF3
Positive Disease Associations: Alzheimer's Disease , schizophrenia
Related Studies:
  1. Alzheimer's Disease
    Kunugi H et al. 1998, Possible association of missense mutation (Gly[-63]Glu) of the neurotrophin-3 gene with Alzheimer's disease in Japanese., Neuroscience letters. 1998 Jan;241(1):65-7. [PubMed 9502217]
  2. schizophrenia
    Nanko S et al. 1994, Neurotrophin-3 gene polymorphism associated with schizophrenia, Acta psychiatrica Scandinavica. 1994 Jun;89(6):390-2. [PubMed 8085468]
  3. schizophrenia
    Hattori M et al. 1995, Association of neurotrophin-3 gene variant with severe forms of schizophrenia., Biochemical and biophysical research communications. 1995 Apr;209(2):513-8. [PubMed 7733919]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NTF3
Diseases sorted by gene-association score: hypochondriasis (15), diabetic polyneuropathy (12), diabetic neuropathy (11), diabetic autonomic neuropathy (11), demyelinating disease (9), pediatric fibrosarcoma (8), neuroaxonal dystrophy (8), sensory peripheral neuropathy (7), hypoglycemic coma (6), congenital fibrosarcoma (6), bipolar disorder (5), charcot-marie-tooth disease, type 1e (5), charcot-marie-tooth disease, type 4d (4), schizophrenia (4), hydrocephalus (3), medulloblastoma (2), attention deficit-hyperactivity disorder (2), hirschsprung disease 1 (1), autistic disorder (1), parkinson disease, late-onset (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 7.62 RPKM in Artery - Tibial
Total median expression: 52.92 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 -63.82211-0.302 Picture PostScript Text
3' UTR -55.40311-0.178 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
  Pfam Domains:
PF00243 - Nerve growth factor family

SCOP Domains:
57501 - Cystine-knot cytokines

ModBase Predicted Comparative 3D Structure on P20783-2
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK293895 - Homo sapiens cDNA FLJ54849 complete cds, highly similar to Neurotrophin-3 precursor.
X53655 - H.sapiens mRNA for NGF-2.
E03081 - cDNA encoding polypeptide having human nerve growth factor activity.
E03588 - DNA encoding human NGF-like peptide.
KJ897265 - Synthetic construct Homo sapiens clone ccsbBroadEn_06659 NTF3 gene, encodes complete protein.
BC069773 - Homo sapiens neurotrophin 3, mRNA (cDNA clone MGC:97337 IMAGE:7262589), complete cds.
BC107075 - Homo sapiens neurotrophin 3, mRNA (cDNA clone MGC:129711 IMAGE:40027045), complete cds.
AB464638 - Synthetic construct DNA, clone: pF1KB9812, Homo sapiens NTF3 gene for neurotrophin 3, without stop codon, in Flexi system.
CU687004 - Synthetic construct Homo sapiens gateway clone IMAGE:100022593 5' read NTF3 mRNA.
HQ448451 - Synthetic construct Homo sapiens clone IMAGE:100071879; CCSB014027_02 neurotrophin 3 (NTF3) gene, encodes complete protein.
KJ891717 - Synthetic construct Homo sapiens clone ccsbBroadEn_01111 NTF3 gene, encodes complete protein.
CR541906 - Homo sapiens full open reading frame cDNA clone RZPDo834G0233D for gene NTF3, neurotrophin 3; complete cds, incl. stopcodon.
E03587 - DNA encoding human NGF-like peptide.
E07862 - DNA encoding the pro region,NGF2/NT-3 and its vicinity.
JD037564 - Sequence 18588 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04010 - MAPK signaling pathway
hsa04722 - Neurotrophin signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein P20783 (Reactome details) participates in the following event(s):

R-HSA-9025033 NTF3 binds NTRK2 (TRKB)
R-NUL-9025059 NTF3 binds Ntrk2
R-HSA-9026366 NTF3-bound NTRK2 dimerizes
R-NUL-9026386 NTF3-bound Ntrk2 dimerizes
R-HSA-9025046 NTF3 activates NTRK2 (TRKB) signaling
R-HSA-9006115 Signaling by NTRK2 (TRKB)
R-HSA-166520 Signaling by NTRKs
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001102654, NP_002518, P20783-2
UCSC ID: uc001qnk.4
RefSeq Accession: NM_001102654
Protein: P20783-2, splice isoform of P20783 CCDS: CCDS8538.1, CCDS44806.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001102654.1
exon count: 2CDS single in 3' UTR: no RNA size: 1349
ORF size: 813CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1793.50frame shift in genome: no % Coverage: 98.96
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# 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.