Human Gene NTF4 (ENST00000593537.2_7) from GENCODE V47lift37
  Description: neurotrophin 4, transcript variant 1 (from RefSeq NM_006179.5)
Gencode Transcript: ENST00000593537.2_7
Gencode Gene: ENSG00000225950.9_13
Transcript (Including UTRs)
   Position: hg19 chr19:49,564,385-49,568,075 Size: 3,691 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr19:49,564,622-49,565,254 Size: 633 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:49,564,385-49,568,075)mRNA (may differ from genome)Protein (210 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NTF4_HUMAN
DESCRIPTION: RecName: Full=Neurotrophin-4; Short=NT-4; AltName: Full=Neurotrophin-5; Short=NT-5; AltName: Full=Neutrophic factor 4; Flags: Precursor;
FUNCTION: Target-derived survival factor for peripheral sensory sympathetic neurons.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Highest levels in prostate, lower levels in thymus, placenta, and skeletal muscle. Expressed in embryonic and adult tissues.
DISEASE: Defects in NTF4 may be associated with susceptibility to primary open angle glaucoma type 1O (GLC1O) [MIM:613100]. A form of primary open angle glaucoma (POAG). POAG is characterized by a specific pattern of optic nerve and visual field defects. The angle of the anterior chamber of the eye is open, and usually the intraocular pressure is increased. The disease is asymptomatic until the late stages, by which time significant and irreversible optic nerve damage has already taken place.
SIMILARITY: Belongs to the NGF-beta family.

-  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: NTF4
Diseases sorted by gene-association score: glaucoma 1, open angle, 1o* (1000), hypochondriasis (22), open-angle glaucoma (11), hypertrophic pyloric stenosis (7), pyloric stenosis (7), combat disorder (7), chronic cystitis (5), juvenile glaucoma (4)
* = Manually curated disease association

-  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: 11.98 RPKM in Prostate
Total median expression: 55.37 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -531.901092-0.487 Picture PostScript Text
3' UTR -66.20237-0.279 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
IPR020408 - Nerve_growth_factor-like
IPR002072 - Nerve_growth_factor-rel
IPR019846 - Nerve_growth_factor_CS
IPR020432 - Neurotrophin-4

Pfam Domains:
PF00243 - Nerve growth factor family

SCOP Domains:
57501 - Cystine-knot cytokines

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1B8M - X-ray MuPIT 1B98 - X-ray MuPIT 1HCF - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P34130
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    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005166 neurotrophin p75 receptor binding
GO:0005515 protein binding
GO:0008083 growth factor activity

Biological Process:
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway
GO:0007202 activation of phospholipase C activity
GO:0007267 cell-cell signaling
GO:0007402 ganglion mother cell fate determination
GO:0007616 long-term memory
GO:0008052 sensory organ boundary specification
GO:0008344 adult locomotory behavior
GO:0008544 epidermis development
GO:0010469 regulation of receptor activity
GO:0042490 mechanoreceptor differentiation
GO:0043524 negative regulation of neuron apoptotic process
GO:0045664 regulation of neuron differentiation
GO:0048011 neurotrophin TRK receptor signaling pathway
GO:0048812 neuron projection morphogenesis
GO:0060384 innervation
GO:0060548 negative regulation of cell death
GO:0061193 taste bud development

Cellular Component:
GO:0005576 extracellular region
GO:0031410 cytoplasmic vesicle


-  Descriptions from all associated GenBank mRNAs
  AK297906 - Homo sapiens cDNA FLJ60732 complete cds.
BC012421 - Homo sapiens neurotrophin 4, mRNA (cDNA clone MGC:21488 IMAGE:3865300), complete cds.
JD363840 - Sequence 344864 from Patent EP1572962.
JD513836 - Sequence 494860 from Patent EP1572962.
DQ891308 - Synthetic construct clone IMAGE:100003938; FLH170957.01X; RZPDo839D06100D neurotrophin 5 (neurotrophin 4/5) (NTF5) gene, encodes complete protein.
DQ894492 - Synthetic construct Homo sapiens clone IMAGE:100008952; FLH170953.01L; RZPDo839D0699D neurotrophin 5 (neurotrophin 4/5) (NTF5) gene, encodes complete protein.
CR541900 - Homo sapiens full open reading frame cDNA clone RZPDo834C1133D for gene NTF5, neurotrophin 5 (neurotrophin 4/5); complete cds, incl. stopcodon.
KJ891718 - Synthetic construct Homo sapiens clone ccsbBroadEn_01112 NTF4 gene, encodes complete protein.
BT019368 - Homo sapiens neurotrophin 5 (neurotrophin 4/5) mRNA, complete cds.
BT019369 - Homo sapiens neurotrophin 5 (neurotrophin 4/5) mRNA, complete cds.
AB464639 - Synthetic construct DNA, clone: pF1KB9791, Homo sapiens NTF5 gene for neurotrophin 4, without stop codon, in Flexi system.
CU680318 - Synthetic construct Homo sapiens gateway clone IMAGE:100020647 5' read NTF5 mRNA.
JD332905 - Sequence 313929 from Patent EP1572962.
JD138085 - Sequence 119109 from Patent EP1572962.
JD135096 - Sequence 116120 from Patent EP1572962.
JD404497 - Sequence 385521 from Patent EP1572962.
JD525888 - Sequence 506912 from Patent EP1572962.
JD418573 - Sequence 399597 from Patent EP1572962.
JD344333 - Sequence 325357 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P34130 (Reactome details) participates in the following event(s):

R-HSA-9026358 NTF4 binds NTRK2
R-HSA-9026377 NTF4-bound NTRK2 dimerizes
R-NUL-9026433 NTF4-bound Ntrk2 dimerizes
R-HSA-9026510 NTF4-bound NTRK2 dimers trans-autophosphorylate
R-NUL-9030427 NTF4-bound Ntrk2 dimers trans-autophosphorylate
R-HSA-9026493 p-Y516 of p-5Y-NTRK2 recruits SHC1
R-HSA-9026531 p-Y817 of p-5Y-NTRK2 recruits PLCG1
R-HSA-9028730 Activated NTRK2 binds FRS2
R-HSA-9032402 Activated NTRK2 binds FRS3
R-NUL-9030433 BDNF- or NTF4-activated Ntrk2 recruits Plcg1
R-NUL-9030473 BDNF- or NTF4-activated Ntrk2 binds Shc1
R-HSA-9026890 NTRK2 phosphorylates SHC1
R-HSA-9026579 NTRK2 phosphorylates PLCG1
R-HSA-9028328 SHC1 bound to activated NTRK2 recruits GRB2:SOS1
R-HSA-9028728 NTRK2 phosphorylates FRS2
R-HSA-9031981 NTRK2-phosphorylated FRS2 binds PTPN11
R-HSA-9032426 NTRK2 phosphorylates FRS3
R-NUL-9030450 BDNF- or NTF4-activated Ntrk2 phosphorylates Plcg1
R-NUL-9031971 Ntrk2 phosphorylates Frs2
R-HSA-9026891 NTRK2 activates RAS signaling through SHC1
R-HSA-9026357 NTF4 activates NTRK2 (TRKB) signaling
R-HSA-9006115 Signaling by NTRK2 (TRKB)
R-HSA-166520 Signaling by NTRKs
R-HSA-9026519 Activated NTRK2 signals through RAS
R-HSA-9026527 Activated NTRK2 signals through PLCG1
R-HSA-9028335 Activated NTRK2 signals through PI3K
R-HSA-9028731 Activated NTRK2 signals through FRS2 and FRS3
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000593537.1, NM_006179, NTF4_HUMAN, NTF5, P34130, Q6FH56, uc326ywf.1, uc326ywf.2
UCSC ID: ENST00000593537.2_7
RefSeq Accession: NM_006179.5
Protein: P34130 (aka NTF4_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.