Human Gene RYK (ENST00000623711.4_8) from GENCODE V47lift37
  Description: receptor like tyrosine kinase, transcript variant 2 (from RefSeq NM_002958.4)
Gencode Transcript: ENST00000623711.4_8
Gencode Gene: ENSG00000163785.14_15
Transcript (Including UTRs)
   Position: hg19 chr3:133,875,977-133,969,701 Size: 93,725 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr3:133,876,997-133,969,496 Size: 92,500 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray 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 (chr3:133,875,977-133,969,701)mRNA (may differ from genome)Protein (606 aa)
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RYK_HUMAN
DESCRIPTION: RecName: Full=Tyrosine-protein kinase RYK; EC=2.7.10.1; Flags: Precursor;
FUNCTION: May be a coreceptor along with FZD8 of Wnt proteins, such as WNT1, WNT3, WNT3A and WNT5A. Involved in neuron differentiation, axon guidance, corpus callosum establishment and neurite outgrowth. In response to WNT3 stimulation, receptor C- terminal cleavage occurs in its transmembrane region and allows the C-terminal intracellular product to translocate from the cytoplasm to the nucleus where it plays a crucial role in neuronal development.
CATALYTIC ACTIVITY: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate.
SUBUNIT: Interacts with DVL1 (via PDZ domain).
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (By similarity). Nucleus (By similarity). Cytoplasm (By similarity). Note=In cells that have undergone neuronal differentiation, the C-terminal cleaved part is translocated from the cytoplasm to the nucleus (By similarity).
TISSUE SPECIFICITY: Observed in all the tissues examined.
DOMAIN: The extracellular WIF domain is responsible for Wnt binding (By similarity).
PTM: Proteolytically cleaved, in part by presenilin, in response to WNT3 stimulation. Cleavage occurs during neuronal differentiation.
SIMILARITY: Belongs to the protein kinase superfamily. Tyr protein kinase family.
SIMILARITY: Contains 1 protein kinase domain.
SIMILARITY: Contains 1 WIF domain.
CAUTION: According to some authors, has impaired kinase activity (PubMed:10454588).

-  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: RYK
Diseases sorted by gene-association score: multiple endocrine neoplasia iib (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -122.40205-0.597 Picture PostScript Text
3' UTR -240.501020-0.236 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
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom
IPR001245 - Ser-Thr/Tyr_kinase_cat_dom
IPR008266 - Tyr_kinase_AS
IPR020635 - Tyr_kinase_cat_dom
IPR003306 - WIF

Pfam Domains:
PF00069 - Protein kinase domain
PF02019 - WIF domain
PF07714 - Protein tyrosine and serine/threonine kinase

SCOP Domains:
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on P34925
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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:0000166 nucleotide binding
GO:0004888 transmembrane signaling receptor activity
GO:0005109 frizzled binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0017147 Wnt-protein binding
GO:0042813 Wnt-activated receptor activity
GO:1904929 coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway
GO:0004713 protein tyrosine kinase activity

Biological Process:
GO:0007165 signal transduction
GO:0007409 axonogenesis
GO:0007411 axon guidance
GO:0007416 synapse assembly
GO:0016055 Wnt signaling pathway
GO:0016310 phosphorylation
GO:0022008 neurogenesis
GO:0022038 corpus callosum development
GO:0030182 neuron differentiation
GO:0031175 neuron projection development
GO:0033278 cell proliferation in midbrain
GO:0035567 non-canonical Wnt signaling pathway
GO:0036518 chemorepulsion of dopaminergic neuron axon
GO:0043410 positive regulation of MAPK cascade
GO:0060070 canonical Wnt signaling pathway
GO:0071679 commissural neuron axon guidance
GO:1904938 planar cell polarity pathway involved in axon guidance
GO:1904948 midbrain dopaminergic neuron differentiation
GO:1904953 Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
GO:0006468 protein phosphorylation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  S59184 - Homo sapiens related to receptor tyrosine kinase (RYK) mRNA, complete cds.
X69970 - H.sapiens mRNA for h-ryk.
X96588 - H.sapiens mRNA for H-RYK receptor tyrosine kinase.
BC148614 - Synthetic construct Homo sapiens clone IMAGE:100015603, MGC:183120 RYK receptor-like tyrosine kinase (RYK) mRNA, encodes complete protein.
BC153090 - Synthetic construct Homo sapiens clone IMAGE:100016403, MGC:184320 RYK receptor-like tyrosine kinase (RYK) mRNA, encodes complete protein.
AB527382 - Synthetic construct DNA, clone: pF1KE0388, Homo sapiens RYK gene for RYK receptor-like tyrosine kinase, without stop codon, in Flexi system.
AB209405 - Homo sapiens mRNA for RYK receptor-like tyrosine kinase isoform 1 variant protein.
JD538956 - Sequence 519980 from Patent EP1572962.
BC021700 - Homo sapiens RYK receptor-like tyrosine kinase, mRNA (cDNA clone IMAGE:4052080), partial cds.
JD109892 - Sequence 90916 from Patent EP1572962.
JD300124 - Sequence 281148 from Patent EP1572962.
JD327788 - Sequence 308812 from Patent EP1572962.
JD306028 - Sequence 287052 from Patent EP1572962.
JD429349 - Sequence 410373 from Patent EP1572962.
JD168345 - Sequence 149369 from Patent EP1572962.
JD328704 - Sequence 309728 from Patent EP1572962.
JD378902 - Sequence 359926 from Patent EP1572962.
JD188619 - Sequence 169643 from Patent EP1572962.
JD049408 - Sequence 30432 from Patent EP1572962.
JD132598 - Sequence 113622 from Patent EP1572962.
JD459477 - Sequence 440501 from Patent EP1572962.
JD408540 - Sequence 389564 from Patent EP1572962.
JD281500 - Sequence 262524 from Patent EP1572962.

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

Protein P34925 (Reactome details) participates in the following event(s):

R-NUL-4551554 Wnt5a binds RYK and VANGL2
R-HSA-4551555 RYK binds WNT5A and VANGL2
R-HSA-5323545 Canonical WNT signaling through the atypical receptor RYK
R-HSA-4086400 PCP/CE pathway
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A0A087WUK1, A0A096LNL3, ENST00000623711.1, ENST00000623711.2, ENST00000623711.3, JTK5A, NM_002958, P34925, Q04696, RYK , RYK_HUMAN, uc327vlg.1, uc327vlg.2
UCSC ID: ENST00000623711.4_8
RefSeq Accession: NM_002958.4
Protein: P34925 (aka RYK_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.