Human Gene NTRK2 (uc004any.1)
  Description: Homo sapiens neurotrophic tyrosine kinase, receptor, type 2 (NTRK2), transcript variant c, mRNA.
RefSeq Summary (NM_001018066): This gene encodes a member of the neurotrophic tyrosine receptor kinase (NTRK) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Signalling through this kinase leads to cell differentiation. Mutations in this gene have been associated with obesity and mood disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014].
Transcript (Including UTRs)
   Position: hg19 chr9:87,283,466-87,573,178 Size: 289,713 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr9:87,285,664-87,570,516 Size: 284,853 Coding Exon Count: 15 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:87,283,466-87,573,178)mRNA (may differ from genome)Protein (735 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCHuman Cortex Gene ExpressionLynxMalacardsMGIOMIM
PubMedReactomeTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NTRK2
CDC HuGE Published Literature: NTRK2
Positive Disease Associations: anorexia nervosa; bulimia , Bipolar Disorder , Body Height , C-Reactive Protein , Cholesterol, LDL , Echocardiography , Epilepsies, Partial , Glomerular Filtration Rate , Hip , nicotine dependence , Waist Circumference
Related Studies:
  1. anorexia nervosa; bulimia
    Ribases, M. et al. 2005, Contribution of NTRK2 to the genetic susceptibility to anorexia nervosa, harm avoidance and minimum body mass index., Molecular psychiatry. 2005 Sep;10(9):851-60. [PubMed 15838534]
    Our data support a contribution of NTRK2 to the genetic susceptibility of ED, mainly ANP, and ED-related phenotypic traits, such as Harm avoidance and minimum body mass index
  2. Bipolar Disorder
    , , . [PubMed 0]
  3. Bipolar Disorder
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NTRK2
Diseases sorted by gene-association score: obesity, hyperphagia, and developmental delay* (1229), pilocytic astrocytoma* (134), ganglioneuroma (13), dysautonomia, familial (11), obesity (10), nodular ganglioneuroblastoma (8), insensitivity to pain, congenital (8), paranoid schizophrenia (7), pulmonary large cell neuroendocrine carcinoma (7), ganglioneuroblastoma (7), status epilepticus (6), vertebral artery occlusion (6), autonomic nervous system neoplasm (5), peripheral nervous system neoplasm (5), adenocarcinoma (5), sudden infant death syndrome (3), medulloblastoma (3), attention deficit-hyperactivity disorder (2), neuroblastoma (1), schizophrenia (1), amyotrophic lateral sclerosis 1 (1)
* = Manually curated disease association

-  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: 55.05 RPKM in Brain - Amygdala
Total median expression: 529.33 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 -425.81938-0.454 Picture PostScript Text
3' UTR -781.372662-0.294 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:
PF00047 - Immunoglobulin domain
PF00069 - Protein kinase domain
PF01462 - Leucine rich repeat N-terminal domain
PF07679 - Immunoglobulin I-set domain
PF07714 - Protein tyrosine kinase
PF13306 - Leucine rich repeats (6 copies)
PF13855 - Leucine rich repeat
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain
PF16920 - Tyrosine-protein kinase receptor C2 Ig-like domain

SCOP Domains:
48726 - Immunoglobulin
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on Q16620-6
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 Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  BC075804 - Homo sapiens neurotrophic tyrosine kinase, receptor, type 2, mRNA (cDNA clone IMAGE:4939307), with apparent retained intron.
AB209118 - Homo sapiens mRNA for BDNF/NT-3 growth factors receptor precursor variant protein.
AK289904 - Homo sapiens cDNA FLJ76753 complete cds, highly similar to Homo sapiens neurotrophic tyrosine kinase, receptor, type 2 (NTRK2), transcript variant b, mRNA.
AF410900 - Homo sapiens neurotrophin receptor tyrosine kinase type 2 truncated isoform (NTRK2) mRNA, complete cds; alternatively spliced.
AF410901 - Homo sapiens neurotrophin receptor tyrosine kinase type 2 truncated isoform (NTRK2) mRNA, complete cds; alternatively spliced.
AF410899 - Homo sapiens neurotrophin receptor tyrosine kinase type 2 (NTRK2) mRNA, complete cds; alternatively spliced.
BC031835 - Homo sapiens neurotrophic tyrosine kinase, receptor, type 2, mRNA (cDNA clone MGC:24881 IMAGE:4941763), complete cds.
U12140 - Human tyrosine kinase receptor p145TRK-B (TRK-B) mRNA, complete cds.
AF400441 - Homo sapiens neurotrophic tyrosine kinase receptor type 2 (NTRK2) mRNA, complete cds.
X75958 - H.sapiens trkB mRNA for protein-tyrosine kinase.
AF508964 - Homo sapiens protein tyrosine kinase non catalytic form (NTRK2) mRNA, complete cds.
S76474 - trkB {alternatively spliced} [human, brain, mRNA, 1870 nt].
S76473 - trkB [human, brain, mRNA, 3194 nt].
KJ891719 - Synthetic construct Homo sapiens clone ccsbBroadEn_01113 NTRK2 gene, encodes complete protein.
AB489182 - Synthetic construct DNA, clone: pF1KE1054, Homo sapiens NTRK2 gene for neurotrophic tyrosine kinase, receptor, type 2, without stop codon, in Flexi system.
AB587471 - Synthetic construct DNA, clone: pF1KB8470, Homo sapiens NTRK2 gene for neurotrophic tyrosine kinase, receptor, type 2, without stop codon, in Flexi system.
AK294285 - Homo sapiens cDNA FLJ53976 complete cds, highly similar to BDNF/NT-3 growth factors receptor precursor (EC 2.7.10.1).
AF410898 - Homo sapiens clone DKFZp547L014 neurotrophin receptor tyrosine kinase type 2 truncated isoform (NTRK2) mRNA, partial cds; alternatively spliced.
JD454375 - Sequence 435399 from Patent EP1572962.
JD083755 - Sequence 64779 from Patent EP1572962.
JD137810 - Sequence 118834 from Patent EP1572962.
JD142704 - Sequence 123728 from Patent EP1572962.
JD395320 - Sequence 376344 from Patent EP1572962.
JD464594 - Sequence 445618 from Patent EP1572962.
JD141394 - Sequence 122418 from Patent EP1572962.
KC855566 - Homo sapiens strain N/A neurotrophic tyrosine receptor kinase type 2 mRNA, partial cds.

-  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 Q16620 (Reactome details) participates in the following event(s):

R-HSA-9024906 BDNF binds NTRK2 (TRKB)
R-HSA-9024967 BDNF-bound NTRK2 dimerizes
R-HSA-9025033 NTF3 binds NTRK2 (TRKB)
R-HSA-9026358 NTF4 binds NTRK2
R-HSA-9026366 NTF3-bound NTRK2 dimerizes
R-HSA-9026377 NTF4-bound NTRK2 dimerizes
R-HSA-9037040 SRC,FYN phosphorylate NTRK2
R-HSA-187661 TRKA activation by adenosine A2a receptor
R-HSA-187678 TRKA activation by PACAP type 1 receptor
R-HSA-9026464 BDNF-bound NTRK2 dimers trans-autophosphorylate
R-HSA-9026510 NTF4-bound NTRK2 dimers trans-autophosphorylate
R-HSA-9032502 Activated NTRK2 binds FYN
R-HSA-9032841 Activated NTRK2 binds CDK5
R-HSA-9033276 NTRK2 binds TIAM1
R-HSA-9032863 CDK5 phosphorylates NTRK2
R-HSA-9032854 NTRK2 phosphorylates CDK5
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-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-HSA-9033292 NTRK2 and CDK5 promote activation of RAC1 by TIAM1
R-HSA-9026891 NTRK2 activates RAS signaling through SHC1
R-HSA-9024909 BDNF activates NTRK2 (TRKB) signaling
R-HSA-9025046 NTF3 activates NTRK2 (TRKB) signaling
R-HSA-9026357 NTF4 activates NTRK2 (TRKB) signaling
R-HSA-9032500 Activated NTRK2 signals through FYN
R-HSA-187024 NGF-independant TRKA activation
R-HSA-9006115 Signaling by NTRK2 (TRKB)
R-HSA-9032845 Activated NTRK2 signals through CDK5
R-HSA-187015 Activation of TRKA receptors
R-HSA-166520 Signaling by NTRKs
R-HSA-9032759 NTRK2 activates RAC1
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-187037 Signaling by NTRK1 (TRKA)
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: AB209118, NM_001018066, NP_001018076, Q16620-6, TRKB
UCSC ID: uc004any.1
RefSeq Accession: NM_001018066
Protein: Q16620-6, splice isoform of Q16620

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AB209118.1
exon count: 18CDS single in 3' UTR: no RNA size: 5802
ORF size: 2208CDS single in intron: no Alignment % ID: 99.90
txCdsPredict score: 4500.50frame shift in genome: no % Coverage: 100.00
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: 2746# 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.