LOCUS       NM_001126328            3978 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens ligand of numb-protein X 1 (LNX1), transcript variant
            1, mRNA.
ACCESSION   NM_001126328
VERSION     NM_001126328.3
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 3978)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   2  (bases 1 to 3978)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   3  (bases 1 to 3978)
  AUTHORS   Fragoza,R., Das,J., Wierbowski,S.D., Liang,J., Tran,T.N., Liang,S.,
            Beltran,J.F., Rivera-Erick,C.A., Ye,K., Wang,T.Y., Yao,L., Mort,M.,
            Stenson,P.D., Cooper,D.N., Wei,X., Keinan,A., Schimenti,J.C.,
            Clark,A.G. and Yu,H.
  TITLE     Extensive disruption of protein interactions by genetic variants
            across the allele frequency spectrum in human populations
  JOURNAL   Nat Commun 10 (1), 4141 (2019)
   PUBMED   31515488
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3978)
  AUTHORS   Chen,S., Fragoza,R., Klei,L., Liu,Y., Wang,J., Roeder,K., Devlin,B.
            and Yu,H.
  TITLE     An interactome perturbation framework prioritizes damaging missense
            mutations for developmental disorders
  JOURNAL   Nat Genet 50 (7), 1032-1040 (2018)
   PUBMED   29892012
REFERENCE   5  (bases 1 to 3978)
  AUTHORS   Nayak,D. and Sivaraman,J.
  TITLE     Structure of LNX1:Ubc13 Ubiquitin Complex Reveals the Role of
            Additional Motifs for the E3 Ligase Activity of LNX1
  JOURNAL   J Mol Biol 430 (8), 1173-1188 (2018)
   PUBMED   29496391
  REMARK    GeneRIF: Study reveals how the LNX1 RING domain is structurally and
            mechanistically dependent on other motifs for its E3 ligase
            activity, and describes how dimeric LNX1 recruits ubiquitin
            (Ub)-loaded Ubc13 for Ub transfer via E3 ligase-mediated catalysis.
REFERENCE   6  (bases 1 to 3978)
  AUTHORS   Armbruester,V., Sauter,M., Roemer,K., Best,B., Hahn,S., Nty,A.,
            Schmid,A., Philipp,S., Mueller,A. and Mueller-Lantzsch,N.
  TITLE     Np9 protein of human endogenous retrovirus K interacts with ligand
            of numb protein X
  JOURNAL   J Virol 78 (19), 10310-10319 (2004)
   PUBMED   15367597
  REMARK    GeneRIF: identifed ligand of Numb protein X as an Np9-interacting
            partner; findings point to the possibility that Np9 affects
            tumorigenesis through the LNX/Numb/Notch pathway
REFERENCE   7  (bases 1 to 3978)
  AUTHORS   Katoh,M. and Katoh,M.
  TITLE     Identification and characterization of PDZRN3 and PDZRN4 genes in
            silico
  JOURNAL   Int J Mol Med 13 (4), 607-613 (2004)
   PUBMED   15010864
REFERENCE   8  (bases 1 to 3978)
  AUTHORS   Nie,J., McGill,M.A., Dermer,M., Dho,S.E., Wolting,C.D. and
            McGlade,C.J.
  TITLE     LNX functions as a RING type E3 ubiquitin ligase that targets the
            cell fate determinant Numb for ubiquitin-dependent degradation
  JOURNAL   EMBO J 21 (1-2), 93-102 (2002)
   PUBMED   11782429
REFERENCE   9  (bases 1 to 3978)
  AUTHORS   Xie,Y., Zhao,W., Wang,W., Zhao,S., Tang,R., Ying,K., Zhou,Z. and
            Mao,Y.
  TITLE     Identification of a human LNX protein containing multiple PDZ
            domains
  JOURNAL   Biochem Genet 39 (3-4), 117-126 (2001)
   PUBMED   11521506
REFERENCE   10 (bases 1 to 3978)
  AUTHORS   Dho,S.E., Jacob,S., Wolting,C.D., French,M.B., Rohrschneider,L.R.
            and McGlade,C.J.
  TITLE     The mammalian numb phosphotyrosine-binding domain. Characterization
            of binding specificity and identification of a novel PDZ
            domain-containing numb binding protein, LNX
  JOURNAL   J Biol Chem 273 (15), 9179-9187 (1998)
   PUBMED   9535908
  REMARK    GeneRIF: The tyrosine phosphorylation of the LDNPAY sequence motif
            in mouse LNX could generate a binding site for the
            phosphorylation-dependent binding of other PTB domain-containing
            proteins.
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB159390.1, BC022983.1,
            BC034737.1 and AC058822.6.
            
            On May 17, 2019 this sequence version replaced NM_001126328.2.
            
            Summary: This gene encodes a membrane-bound protein that is
            involved in signal transduction and protein interactions. The
            encoded product is an E3 ubiquitin-protein ligase, which mediates
            ubiquitination and subsequent proteasomal degradation of proteins
            containing phosphotyrosine binding (PTB) domains. This protein may
            play an important role in tumorogenesis. Alternatively spliced
            transcript variants encoding distinct isoforms have been described.
            A pseudogene, which is located on chromosome 17, has been
            identified for this gene. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (a, also known as
            LNXp80).
            
            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 :: BC022983.1, AK056823.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000263925.8/ ENSP00000263925.7
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-24                DB159390.1         101-124
            25-2819             BC022983.1         1-2795
            2820-3009           BC034737.1         2571-2760
            3010-3978           AC058822.6         73811-74779         c
FEATURES             Location/Qualifiers
     source          1..3978
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="4"
                     /map="4q12"
     gene            1..3978
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /note="ligand of numb-protein X 1"
                     /db_xref="GeneID:84708"
                     /db_xref="HGNC:HGNC:6657"
                     /db_xref="MIM:609732"
     exon            1..99
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            100..565
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     CDS             186..2372
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /EC_number="2.3.2.27"
                     /note="isoform a is encoded by transcript variant 1; PDZ
                     domain-containing ring finger protein 2;
                     multi-PDZ-domain-containing protein, E3 ubiquitin-protein
                     ligase LNX; numb-binding protein 1; ligand of numb-protein
                     X 1, E3 ubiquitin protein ligase; RING-type E3 ubiquitin
                     transferase LNX"
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase LNX isoform a"
                     /protein_id="NP_001119800.1"
                     /db_xref="CCDS:CCDS47057.1"
                     /db_xref="GeneID:84708"
                     /db_xref="HGNC:HGNC:6657"
                     /db_xref="MIM:609732"
                     /translation="MNQPESANDPEPLCAVCGQAHSLEENHFYSYPEEVDDDLICHIC
                     LQALLDPLDTPCGHTYCTLCLTNFLVEKDFCPMDRKPLVLQHCKKSSILVNKLLNKLL
                     VTCPFREHCTQVLQRCDLEHHFQTSCKGASHYGLTKDRKRRSQDGCPDGCASLTATAP
                     SPEVSAAATISLMTDEPGLDNPAYVSSAEDGQPAISPVDSGRSNRTRARPFERSTIRS
                     RSFKKINRALSVLRRTKSGSAVANHADQGRENSENTTAPEVFPRLYHLIPDGEITSIK
                     INRVDPSESLSIRLVGGSETPLVHIIIQHIYRDGVIARDGRLLPGDIILKVNGMDISN
                     VPHNYAVRLLRQPCQVLWLTVMREQKFRSRNNGQAPDAYRPRDDSFHVILNKSSPEEQ
                     LGIKLVRKVDEPGVFIFNVLDGGVAYRHGQLEENDRVLAINGHDLRYGSPESAAHLIQ
                     ASERRVHLVVSRQVRQRSPDIFQEAGWNSNGSWSPGPGERSNTPKPLHPTITCHEKVV
                     NIQKDPGESLGMTVAGGASHREWDLPIYVISVEPGGVISRDGRIKTGDILLNVDGVEL
                     TEVSRSEAVALLKRTSSSIVLKALEVKEYEPQEDCSSPAALDSNHNMAPPSDWSPSWV
                     MWLELPRCLYNCKDIVLRRNTAGSLGFCIVGGYEEYNGNKPFFIKSIVEGTPAYNDGR
                     IRCGDILLAVNGRSTSGMIHACLARLLKELKGRITLTIVSWPGTFL"
     exon            566..807
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            808..960
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            961..1163
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1164..1535
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1536..1670
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1671..1848
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1849..2077
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            2078..2236
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     exon            2237..3978
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2624..2629
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /note="hexamer: AATAAA"
     polyA_site      2649
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /note="major polyA site"
     regulatory      2802..2807
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /note="hexamer: AATAAA"
     polyA_site      2823
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /note="major polyA site"
     regulatory      2985..2990
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
                     /note="hexamer: TATAAA"
     polyA_site      3009
                     /gene="LNX1"
                     /gene_synonym="LNX; MPDZ; PDZRN2"
ORIGIN      
        1 acaactccgg cggcccaagg agctgctcgg ttcacccaca aggaatgaga gctgcctgcc
       61 tgctgctgct tggagagccc cagacagtcg cttgaagagg tgtgtggatg tctcctagat
      121 cttgacttgc tcctgaggaa atattgtgtg actgagtttc ctgttatact gctctccaat
      181 ccatcatgaa ccagccagag tctgccaacg atcctgaacc cctgtgtgca gtgtgtggcc
      241 aagcccactc cttggaggaa aaccacttct acagctatcc agaggaagtg gatgatgacc
      301 tcatctgcca catctgcctg caggctttgc tggaccccct ggacactccg tgtggacaca
      361 cctactgcac cctctgcctc accaacttcc tggtggagaa ggacttctgt cccatggacc
      421 gcaagcctct ggttctgcag cactgcaaga agtccagcat cctggtcaac aaactcctca
      481 acaagctact ggtgacctgc ccattcaggg agcactgcac ccaggtgttg cagcgctgtg
      541 acctcgagca tcactttcaa accagctgta aaggtgcctc ccactacggc ctgaccaaag
      601 ataggaagag gcgctcacaa gatggctgtc cagacggctg tgcgagcctc acagccacgg
      661 ctccctcccc agaggtttct gcagctgcca ccatctcctt aatgacagac gagcctggcc
      721 tagacaaccc tgcctacgtg tcctcggcag aggacgggca gccagcaatc agcccagtgg
      781 actctggccg gagcaaccga actagggcac ggccctttga gagatccact attagaagca
      841 gatcatttaa aaaaataaat cgagctttga gtgttcttcg aaggacaaag agcgggagtg
      901 cagttgccaa ccatgccgac cagggcaggg aaaattctga aaacaccact gcccctgaag
      961 tctttccaag gttgtaccac ctgattccag atggtgaaat taccagcatc aagatcaatc
     1021 gagtagatcc cagtgaaagc ctctctatta ggctggtggg aggtagcgaa accccactgg
     1081 tccatatcat tatccaacac atttatcgtg atggggtgat cgccagagac ggccggctac
     1141 tgccaggaga catcattcta aaggtcaacg ggatggacat cagcaatgtc cctcacaact
     1201 acgctgtgcg tctcctgcgg cagccctgcc aggtgctgtg gctgactgtg atgcgtgaac
     1261 agaagttccg cagcaggaac aatggacagg ccccggatgc ctacagaccc cgagatgaca
     1321 gctttcatgt gattctcaac aaaagtagcc ccgaggagca gcttggaata aaactggtgc
     1381 gcaaggtgga tgagcctggg gttttcatct tcaatgtgct ggatggcggt gtggcatatc
     1441 gacatggtca gcttgaggag aatgaccgtg tgttagccat caatggacat gatcttcgat
     1501 atggcagccc agaaagtgcg gctcatctga ttcaggccag tgaaagacgt gttcacctcg
     1561 tcgtgtcccg ccaggttcgg cagcggagcc ctgacatctt tcaggaagcc ggctggaaca
     1621 gcaatggcag ctggtcccca gggccagggg agaggagcaa cactcccaag cccctccatc
     1681 ctacaattac ttgtcatgag aaggtggtaa atatccaaaa agaccccggt gaatctctcg
     1741 gcatgaccgt cgcaggggga gcatcacata gagaatggga tttgcctatc tatgtcatca
     1801 gtgttgagcc cggaggagtc ataagcagag atggaagaat aaaaacaggt gacattttgt
     1861 tgaatgtgga tggggtcgaa ctgacagagg tcagccggag tgaggcagtg gcattattga
     1921 aaagaacatc atcctcgata gtactcaaag ctttggaagt caaagagtat gagccccagg
     1981 aagactgcag cagcccagca gccctggact ccaaccacaa catggcccca cccagtgact
     2041 ggtccccatc ctgggtcatg tggctggaat taccacggtg cttgtataac tgtaaagata
     2101 ttgtattacg aagaaacaca gctggaagtc tgggcttctg cattgtagga ggttatgaag
     2161 aatacaatgg aaacaaacct tttttcatca aatccattgt tgaaggaaca ccagcataca
     2221 atgatggaag aattagatgt ggtgatattc ttcttgctgt caatggtaga agtacatcag
     2281 gaatgataca tgcttgcttg gcaagactgc tgaaagaact taaaggaaga attactctaa
     2341 ctattgtttc ttggcctggc acttttttat agaatcaatg atgggtcaga ggaaaacaga
     2401 aaaatcacaa ataggctaag aagttgaaac actatattta tcttgtcagt ttttatattt
     2461 aaagaaagaa tacattgtaa aaatgtcagg aaaagtatga tcatctaatg aaagccagtt
     2521 acacctcaga aaatatgatt ccaaaaaaat taaaactact agtttttttt cagtgtggag
     2581 gatttctcat tactctacaa cattgtttat attttttcta ttcaataaaa agccctaaaa
     2641 caactaaaat gatttgtata ccccactgaa ttcaagctga tttaaattta aaatttggta
     2701 tatgctgaag tctgccaagg gtacattatg gccattttta atttacagct aaaatatttt
     2761 ttaaaatgca ttgctgagaa acgttgcttt catcaaacaa gaataaatat ttttcagaag
     2821 ttatagttgt cttttagtat gtgatactaa ttaagattac ttttgtatta tcactattta
     2881 aaagatccta gtaatttatt ctttcaaata ccatgttatt tgttaccatc accgatgaat
     2941 acctcctagg cttatcccta aaaatgctcg ctcagagaat taattataaa cttgttttgt
     3001 ttttagtaag aaatggctaa agctcttttt ttccacaatc gttagtaact gtataaaaac
     3061 tcatgctgct ccaccagtgg gccttggaaa atgcatcaag aaggccaaac cagcttgacc
     3121 ctggctcaca gacatggtca tgaggcgatt taaatttgtg ccacaatgaa gagtgtgtgt
     3181 acacatgcct cctagaaact acactatggg taattaatta atttatttca tagaggccac
     3241 ccagatgcct tataggtttt attaatttgg atatgaaagt gtaccccatt tggtttcacc
     3301 aggaacccaa atttagaata ttgaaaagcc atcaaaaagt tgtgatatca aaaatgtatg
     3361 agtctcttaa tatactaagc aagagtgtca cagcagtaat gataaagact agttttaatc
     3421 tcaagcctta gaggggccct ttgttgcctt ttgtgatgca gcctcttaag agagtggtgt
     3481 ttgattaaca aaaaaactgt ggcccaagtg gaacccttga ccttttctca gataatctgt
     3541 gtatgtacac agctaacaca gctctttaga ttccctgtta agtgactcat tcacattcct
     3601 ttcttggata taaagtcatt gctgtctttt tatttttgaa atagtacaag acaaagattt
     3661 ttaacttaac atgaaaaatt cactctttta ttttggaaaa aaagttaact tttcatacta
     3721 acaaacagaa caagatttaa ggtaaatttc ttaaacatta tccagaaaaa taacaagatt
     3781 tatagtatct acttctggta ctaatataca caaaaggcca aaaccatgcc tattctgcag
     3841 gtgtagcttc ggtgctctcc tgttcagggg caggctcact gcccgcttct tttccttctt
     3901 tgcttctttt agattttttg tgtttgtgtc tcctgtgact atctccttct tcactttcat
     3961 ggcgacgtct actattac
//
