LOCUS       NM_002958               3049 bp    mRNA    linear   PRI 07-APR-2024
DEFINITION  Homo sapiens receptor like tyrosine kinase (RYK), transcript
            variant 2, mRNA.
ACCESSION   NM_002958 XM_940269
VERSION     NM_002958.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3049)
  AUTHORS   Liang,Z., Liu,L., Gao,R., Che,C. and Yang,G.
  TITLE     Downregulation of exosomal miR-7-5p promotes breast cancer
            migration and invasion by targeting RYK and participating in the
            atypical WNT signalling pathway
  JOURNAL   Cell Mol Biol Lett 27 (1), 88 (2022)
   PUBMED   36210461
  REMARK    GeneRIF: Downregulation of exosomal miR-7-5p promotes breast cancer
            migration and invasion by targeting RYK and participating in the
            atypical WNT signalling pathway.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3049)
  AUTHORS   Zhou,G., Zhang,S., Jin,M. and Hu,S.
  TITLE     Comprehensive analysis reveals COPB2 and RYK associated with tumor
            stages of larynx squamous cell carcinoma
  JOURNAL   BMC Cancer 22 (1), 667 (2022)
   PUBMED   35715770
  REMARK    GeneRIF: Comprehensive analysis reveals COPB2 and RYK associated
            with tumor stages of larynx squamous cell carcinoma.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3049)
  AUTHORS   Kim,H.T., Panza,P., Kikhi,K., Nakamichi,Y., Atzberger,A.,
            Guenther,S., Ruppert,C., Guenther,A. and Stainier,D.Y.R.
  TITLE     WNT/RYK signaling functions as an antiinflammatory modulator in the
            lung mesenchyme
  JOURNAL   Proc Natl Acad Sci U S A 119 (24), e2201707119 (2022)
   PUBMED   35671428
  REMARK    GeneRIF: WNT/RYK signaling functions as an antiinflammatory
            modulator in the lung mesenchyme.
REFERENCE   4  (bases 1 to 3049)
  AUTHORS   Vaivads,M., Akota,I. and Pilmane,M.
  TITLE     PAX7, PAX9 and RYK Expression in Cleft Affected Tissue
  JOURNAL   Medicina (Kaunas) 57 (10), 1075 (2021)
   PUBMED   34684112
  REMARK    GeneRIF: PAX7, PAX9 and RYK Expression in Cleft Affected Tissue.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3049)
  AUTHORS   Sheetz,J.B., Mathea,S., Karvonen,H., Malhotra,K., Chatterjee,D.,
            Niininen,W., Perttila,R., Preuss,F., Suresh,K., Stayrook,S.E.,
            Tsutsui,Y., Radhakrishnan,R., Ungureanu,D., Knapp,S. and
            Lemmon,M.A.
  TITLE     Structural Insights into Pseudokinase Domains of Receptor Tyrosine
            Kinases
  JOURNAL   Mol Cell 79 (3), 390-405 (2020)
   PUBMED   32619402
  REMARK    GeneRIF: Structural Insights into Pseudokinase Domains of Receptor
            Tyrosine Kinases.
REFERENCE   6  (bases 1 to 3049)
  AUTHORS   Gough,N.M., Rakar,S., Hovens,C.M. and Wilks,A.
  TITLE     Localization of two mouse genes encoding the protein tyrosine
            kinase receptor-related protein RYK
  JOURNAL   Mamm Genome 6 (4), 255-256 (1995)
   PUBMED   7613029
REFERENCE   7  (bases 1 to 3049)
  AUTHORS   Lee,S.T., Strunk,K.M. and Spritz,R.A.
  TITLE     A survey of protein tyrosine kinase mRNAs expressed in normal human
            melanocytes
  JOURNAL   Oncogene 8 (12), 3403-3410 (1993)
   PUBMED   8247543
REFERENCE   8  (bases 1 to 3049)
  AUTHORS   Tamagnone,L., Partanen,J., Armstrong,E., Lasota,J., Ohgami,K.,
            Tazunoki,T., LaForgia,S., Huebner,K. and Alitalo,K.
  TITLE     The human ryk cDNA sequence predicts a protein containing two
            putative transmembrane segments and a tyrosine kinase catalytic
            domain
  JOURNAL   Oncogene 8 (7), 2009-2014 (1993)
   PUBMED   8390040
REFERENCE   9  (bases 1 to 3049)
  AUTHORS   Stacker,S.A., Hovens,C.M., Vitali,A., Pritchard,M.A., Baker,E.,
            Sutherland,G.R. and Wilks,A.F.
  TITLE     Molecular cloning and chromosomal localisation of the human
            homologue of a receptor related to tyrosine kinases (RYK)
  JOURNAL   Oncogene 8 (5), 1347-1356 (1993)
   PUBMED   8386829
REFERENCE   10 (bases 1 to 3049)
  AUTHORS   Partanen,J., Makela,T.P., Alitalo,R., Lehvaslaiho,H. and Alitalo,K.
  TITLE     Putative tyrosine kinases expressed in K-562 human leukemia cells
  JOURNAL   Proc Natl Acad Sci U S A 87 (22), 8913-8917 (1990)
   PUBMED   2247464
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC096967.18, X69970.1,
            CN309980.1, BC021700.2, AB209405.1 and AC108742.6.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Feb 27, 2020 this sequence version replaced NM_002958.3.
            
            Summary: The protein encoded by this gene is an atypical member of
            the family of growth factor receptor protein tyrosine kinases,
            differing from other members at a number of conserved residues in
            the activation and nucleotide binding domains. This gene product
            belongs to a subfamily whose members do not appear to be regulated
            by phosphorylation in the activation segment. It has been suggested
            that mediation of biological activity by recruitment of a
            signaling-competent auxiliary protein may occur through an as yet
            uncharacterized mechanism. The encoded protein has a leucine-rich
            extracellular domain with a WIF-type Wnt binding region, a single
            transmembrane domain, and an intracellular tyrosine kinase domain.
            This protein is involved in stimulating Wnt signaling pathways such
            as the regulation of axon pathfinding. Alternative splicing results
            in multiple transcript variants encoding distinct isoforms.
            [provided by RefSeq, Feb 2012].
            
            Transcript Variant: This variant (2) uses an alternate in-frame
            splice site in the coding region, compared to variant 1, resulting
            in a shorter protein (isoform 2).
            
            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 :: X69970.1, SRR14038191.4088742.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000623711.4/ ENSP00000485095.1
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-115               AC096967.18        51484-51598         c
            116-279             X69970.1           1-164
            280-669             CN309980.1         9-398
            670-1159            X69970.1           555-1044
            1160-2442           BC021700.2         320-1602
            2443-3048           AB209405.1         4664-5269
            3049-3049           AC108742.6         9252-9252
FEATURES             Location/Qualifiers
     source          1..3049
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q22.2"
     gene            1..3049
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /note="receptor like tyrosine kinase"
                     /db_xref="GeneID:6259"
                     /db_xref="HGNC:HGNC:10481"
                     /db_xref="MIM:600524"
     exon            1..437
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     CDS             206..2029
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /EC_number="2.7.10.1"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; hydroxyaryl-protein kinase; JTK5A protein
                     tyrosine kinase"
                     /codon_start=1
                     /product="tyrosine-protein kinase RYK isoform 2 precursor"
                     /protein_id="NP_002949.2"
                     /db_xref="CCDS:CCDS77820.1"
                     /db_xref="GeneID:6259"
                     /db_xref="HGNC:HGNC:10481"
                     /db_xref="MIM:600524"
                     /translation="MRGAARLGRPGRSCLPGARGLRAPPPPPLLLLLALLPLLPAPGA
                     AAAPAPRPPELQSASAGPSVSLYLSEDEVRRLIGLDAELYYVRNDLISHYALSFSLLV
                     PSETNFLHFTWHAKSKVEYKLGFQVDNVLAMDMPQVNISVQGEVPRTLSVFRVELSCT
                     GKVDSEVMILMQLNLTVNSSKNFTVLNFKRRKMCYKKLEEVKTSALDKNTSRTIYDPV
                     HAAPTTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIELDDSISASSSSQGLSQP
                     STQTTQYLRADTPNNATPITSYPTLRIEKNDLRSVTLLEAKGKVKDIAISRERITLKD
                     VLQEGTFGRIFHGILIDEKDPNKEKQAFVKTVKDQASEIQVTMMLTESCKLRGLHHRN
                     LLPITHVCIEEGEKPMVILPYMNWGNLKLFLRQCKLVEANNPQAISQQDLVHMAIQIA
                     CGMSYLARREVIHKDLAARNCVIDDTLQVKITDNALSRDLFPMDYHCLGDNENRPVRW
                     MALESLVNNEFSSASDVWAFGVTLWELMTLGQTPYVDIDPFEMAAYLKDGYRIAQPIN
                     CPDELFAVMACCWALDPEERPKFQQLVQCLTEFHAALGAYV"
     exon            438..559
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            560..659
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            660..794
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            795..848
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            849..993
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            994..1094
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            1095..1220
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            1221..1307
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            1308..1377
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            1378..1510
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            1511..1620
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            1621..1780
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            1781..1917
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     exon            1918..3049
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3027..3032
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /note="hexamer: ATTAAA"
     polyA_site      3049
                     /gene="RYK"
                     /gene_synonym="D3S3195; JTK5; JTK5A; RYK1"
                     /note="major polyA site"
ORIGIN      
        1 agcccccaac tccggacgat gcagcgagga ggcggcggcg gcggcgcgct ccggaggtct
       61 gaagccactg ctggctgcca cgggccggcg gtgcgatgag ctgggcagcc gcccccggct
      121 cggggctgtg agcggctcgg ggccgggggt gggcggcggt gcggcgggcg gccgacgctc
      181 ctcttcggcg gcggcggcgg cggccatgcg tggggcggcg cggctggggc ggccgggccg
      241 gagttgcctc ccgggggccc gcggcctgag ggccccgccg ccgccgccgc tgctgcttct
      301 gcttgcgctg ttgccgctgc tgcccgcgcc tggcgctgcc gccgcccccg ccccgcggcc
      361 cccggagctg cagtcggctt ccgcggggcc cagcgtgagt ctctacctga gcgaggacga
      421 ggtgcgccgg ctgatcggtc ttgatgcaga actttattat gtgagaaatg accttattag
      481 tcactacgct ctatccttta gtctgttagt acccagtgag acaaatttcc tgcacttcac
      541 ctggcatgcg aagtccaagg ttgaatataa gctgggattc caagtggaca atgttttggc
      601 aatggatatg ccccaggtca acatttctgt tcagggggaa gttccacgca ctttatcagt
      661 gtttcgggta gagctttcct gtactggcaa agtagattct gaagttatga tactaatgca
      721 gctcaacttg acagtaaatt cttcaaaaaa ttttaccgtc ttaaatttta aacgaaggaa
      781 aatgtgctac aaaaaacttg aagaagtaaa aacttcagcc ttggacaaaa acactagcag
      841 aactatttat gatcctgtac atgcagctcc aaccacttct acgcgtgtgt tttatattag
      901 tgtaggggtt tgttgtgcag taatatttct cgtagcaata atattagctg ttttgcacct
      961 tcatagtatg aaaaggattg aactggatga cagcattagt gccagcagta gttcccaagg
     1021 gctgtctcag ccatccaccc agacgactca gtatctgaga gcagacacgc ccaacaatgc
     1081 aactcctatc accagttatc ctaccttgcg gatagagaag aacgacttga gaagtgtcac
     1141 tcttttggag gccaaaggca aggtgaagga tatagcaata tccagagaga ggataactct
     1201 aaaagatgta ctccaagaag gtacttttgg gcgtattttc catgggattt taatagatga
     1261 aaaagatcca aataaagaaa aacaagcatt tgtcaaaaca gttaaagatc aagcttctga
     1321 aattcaggtg acaatgatgc tcactgaaag ttgtaagctg cgaggtcttc atcacagaaa
     1381 tcttcttcct attactcatg tgtgtataga agaaggagaa aagcccatgg tgatattgcc
     1441 ttacatgaat tgggggaatc ttaaattgtt tttacgacag tgcaagttag tagaggccaa
     1501 taatccacag gcaatttctc agcaagacct ggtacacatg gctattcaga ttgcctgtgg
     1561 aatgagctac ctggccagaa gggaagtcat ccacaaagac ctggctgcca ggaactgtgt
     1621 cattgatgac acacttcaag ttaagatcac agacaatgcc ctctccagag acttgttccc
     1681 catggactat cactgtctgg gggacaatga aaacaggcca gttcgttgga tggctcttga
     1741 aagtctggtt aataacgagt tctctagcgc tagtgatgtg tgggcctttg gagtgacgct
     1801 gtgggaactc atgactctgg gccagactcc ctacgtggac attgacccct tcgagatggc
     1861 cgcatacctg aaagatggtt accgaatagc ccagccaatc aactgtcctg atgaattatt
     1921 tgctgtgatg gcctgttgct gggccttaga tccagaggag aggcccaagt ttcagcagct
     1981 ggtacagtgc ctaacagagt ttcatgcagc cctgggggcc tacgtctgac tcctctccaa
     2041 tcccacacca tcaggaagaa ggtgcctgtc ggggctcact tgaagcctgt cagggatgct
     2101 ttgtatctaa cacaacgcca acagaagcac atttgtcttc cagaacaccg tgccttagaa
     2161 atgctttaga atctgaactt tttaagacag acttaataat gtggcatatt ttctagatat
     2221 cacttttatt aggttgaact gaaagggttt ttgtaaattt tttggccaaa attttttaaa
     2281 acatacttac tttggactag gggtacattc ttacaaaata aataaacagt ttttaaaatt
     2341 gtttagacac agatatttgg aattagctat cttagtgcca actgcttttt atttttttac
     2401 ttcatcaagg tgatgtaagt gactcacctt taaagttttt ttagtgttat tttttatcac
     2461 tactctggga aatggtttgt cttcaagatg caatactttt cttagtaaag gaaaaacagc
     2521 ataaaaagat acctggtctg ccttgtacaa gaaaaggcaa tattagagga agaaaattta
     2581 aagaaaagct agaggaaaaa aaaatttttt taaaaatact tattagaagc aaactgccct
     2641 tgcatggaaa actgtttatt tttttcagtg aaaaggaatt ctgctttcgt gtttttggga
     2701 aagcaggaac tgagttcatt acatctttaa tttggcagaa attagccttt ctgtgaacca
     2761 gatgtggttt ggggcagatc tgtagtaaac aatggtgatt ttatttattt ttactctctg
     2821 gaaaaggaga taatacaatt ccagaaagtg aactcatatt tctaaggtta agattccctt
     2881 ttattgcacc tagaatagtg ctatgcacag agcgggtgct tgagttgttg tcgttttttg
     2941 tttgtttttt aaatgtaaac tggtaaattt tgtgcttatc ttcaaggctg gcttaagtat
     3001 aaaattgttt tttaaacact tgaaaaatta aaggatttgt tttatatta
//
