LOCUS       NM_003687               2257 bp    mRNA    linear   PRI 06-JUN-2024
DEFINITION  Homo sapiens PDZ and LIM domain 4 (PDLIM4), transcript variant 1,
            mRNA.
ACCESSION   NM_003687
VERSION     NM_003687.4
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 2257)
  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   2  (bases 1 to 2257)
  AUTHORS   Jia,Y., Shi,H., Cao,Y., Feng,W., Li,M. and Li,X.
  TITLE     PDZ and LIM domain protein 4 suppresses the growth and invasion of
            ovarian cancer cells via inactivation of STAT3 signaling
  JOURNAL   Life Sci 233, 116715 (2019)
   PUBMED   31376371
  REMARK    GeneRIF: Low expression of PDLIM4 is associated with growth and
            invasion of ovarian cancer.
REFERENCE   3  (bases 1 to 2257)
  AUTHORS   Chen,J., Hong,Z., Zhao,C., Bi,Q. and Qiu,B.
  TITLE     Associations between polymorphisms of the PDLIM4 gene and
            susceptibility to osteoporotic fracture in an elderly population of
            Han Chinese
  JOURNAL   Biosci Rep 39 (1) (2019)
   PUBMED   30578378
  REMARK    GeneRIF: Our study provides supportive evidence for the
            contribution of PDLIM4 gene polymorphisms to the susceptibility to
            osteoporotic fracture and suggests that rs270611 and rs3900945 are
            genetic risk factors, while rs366512 might be a genetic protective
            factor against osteoporotic fracture in elderly Han individuals.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2257)
  AUTHORS   Yang,X., Coulombe-Huntington,J., Kang,S., Sheynkman,G.M., Hao,T.,
            Richardson,A., Sun,S., Yang,F., Shen,Y.A., Murray,R.R., Spirohn,K.,
            Begg,B.E., Duran-Frigola,M., MacWilliams,A., Pevzner,S.J.,
            Zhong,Q., Wanamaker,S.A., Tam,S., Ghamsari,L., Sahni,N., Yi,S.,
            Rodriguez,M.D., Balcha,D., Tan,G., Costanzo,M., Andrews,B.,
            Boone,C., Zhou,X.J., Salehi-Ashtiani,K., Charloteaux,B., Chen,A.A.,
            Calderwood,M.A., Aloy,P., Roth,F.P., Hill,D.E., Iakoucheva,L.M.,
            Xia,Y. and Vidal,M.
  TITLE     Widespread Expansion of Protein Interaction Capabilities by
            Alternative Splicing
  JOURNAL   Cell 164 (4), 805-817 (2016)
   PUBMED   26871637
REFERENCE   5  (bases 1 to 2257)
  AUTHORS   Ernst,A., Appleton,B.A., Ivarsson,Y., Zhang,Y., Gfeller,D.,
            Wiesmann,C. and Sidhu,S.S.
  TITLE     A structural portrait of the PDZ domain family
  JOURNAL   J Mol Biol 426 (21), 3509-3519 (2014)
   PUBMED   25158098
REFERENCE   6  (bases 1 to 2257)
  AUTHORS   Vallenius,T., Scharm,B., Vesikansa,A., Luukko,K., Schafer,R. and
            Makela,T.P.
  TITLE     The PDZ-LIM protein RIL modulates actin stress fiber turnover and
            enhances the association of alpha-actinin with F-actin
  JOURNAL   Exp Cell Res 293 (1), 117-128 (2004)
   PUBMED   14729062
  REMARK    GeneRIF: Ril modulates actin stress fiber turnover and enhances the
            association with actinin and actins.
REFERENCE   7  (bases 1 to 2257)
  AUTHORS   Omasu,F., Ezura,Y., Kajita,M., Ishida,R., Kodaira,M., Yoshida,H.,
            Suzuki,T., Hosoi,T., Inoue,S., Shiraki,M., Orimo,H. and Emi,M.
  TITLE     Association of genetic variation of the RIL gene, encoding a
            PDZ-LIM domain protein and localized in 5q31.1, with low bone
            mineral density in adult Japanese women
  JOURNAL   J Hum Genet 48 (7), 342-345 (2003)
   PUBMED   12908099
  REMARK    GeneRIF: RIL and its variant sequences may be an important
            determinant of osteoporosis
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 2257)
  AUTHORS   Walma,T., Spronk,C.A., Tessari,M., Aelen,J., Schepens,J.,
            Hendriks,W. and Vuister,G.W.
  TITLE     Structure, dynamics and binding characteristics of the second PDZ
            domain of PTP-BL
  JOURNAL   J Mol Biol 316 (5), 1101-1110 (2002)
   PUBMED   11884147
REFERENCE   9  (bases 1 to 2257)
  AUTHORS   Cuppen,E., van Ham,M., Wansink,D.G., de Leeuw,A., Wieringa,B. and
            Hendriks,W.
  TITLE     The zyxin-related protein TRIP6 interacts with PDZ motifs in the
            adaptor protein RIL and the protein tyrosine phosphatase PTP-BL
  JOURNAL   Eur J Cell Biol 79 (4), 283-293 (2000)
   PUBMED   10826496
REFERENCE   10 (bases 1 to 2257)
  AUTHORS   Bashirova,A.A., Markelov,M.L., Shlykova,T.V., Levshenkova,E.V.,
            Alibaeva,R.A. and Frolova,E.I.
  TITLE     The human RIL gene: mapping to human chromosome 5q31.1, genomic
            organization and alternative transcripts
  JOURNAL   Gene 210 (2), 239-245 (1998)
   PUBMED   9573374
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DN997097.1, BC016765.1,
            BF689609.1, AF153882.1, BF690514.1 and AW590987.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_003687.3.
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (1).
            
            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 :: AF153882.1, SRR1660807.108578.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968189
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000253754.8/ ENSP00000253754.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-391               DN997097.1         58-448
            392-1130            BC016765.1         432-1170
            1131-1595           BF689609.1         7-471
            1596-1718           AF153882.1         1597-1719
            1719-2185           BF690514.1         35-501              c
            2186-2257           AW590987.1         13-84               c
FEATURES             Location/Qualifiers
     source          1..2257
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.1"
     gene            1..2257
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /note="PDZ and LIM domain 4"
                     /db_xref="GeneID:8572"
                     /db_xref="HGNC:HGNC:16501"
                     /db_xref="MIM:603422"
     exon            1..132
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /inference="alignment:Splign:2.1.0"
     CDS             40..1032
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /note="isoform 1 is encoded by transcript variant 1; LIM
                     domain protein; enigma homolog; PDZ and LIM domain protein
                     4; reversion-induced LIM protein; LIM protein RIL"
                     /codon_start=1
                     /product="PDZ and LIM domain protein 4 isoform 1"
                     /protein_id="NP_003678.2"
                     /db_xref="CCDS:CCDS4152.1"
                     /db_xref="GeneID:8572"
                     /db_xref="HGNC:HGNC:16501"
                     /db_xref="MIM:603422"
                     /translation="MPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALC
                     PGDLIQAINGESTELMTHLEAQNRIKGCHDHLTLSVSRPEGRSWPSAPDDSKAQAHRI
                     HIDPEIQDGSPTTSRRPSGTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMS
                     TLHVSPPPSADPARGLPRSRDCRVDLGSEVYRMLREPAEPVAAEPKQSGSFRYLQGML
                     EAGEGGDWPGPGGPRNLKPTASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHP
                     ECFMCSDCGLNLKQRGYFFLDERLYCESHAKARVKPPEGYDVVAVYPNAKVELV"
     exon            133..284
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /inference="alignment:Splign:2.1.0"
     exon            285..366
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /inference="alignment:Splign:2.1.0"
     exon            367..545
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /inference="alignment:Splign:2.1.0"
     exon            546..709
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /inference="alignment:Splign:2.1.0"
     exon            710..827
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /inference="alignment:Splign:2.1.0"
     exon            828..2257
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1109..1114
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /note="hexamer: AATAAA"
     polyA_site      1135
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /note="major polyA site"
     regulatory      2230..2235
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
                     /note="hexamer: AGTAAA"
     polyA_site      2257
                     /gene="PDLIM4"
                     /gene_synonym="RIL"
ORIGIN      
        1 agagtccggc tcaggctccg gctgcggctc cagcccgcga tgccccattc cgtgaccctg
       61 cgcgggcctt cgccctgggg cttccgcctg gtgggcggcc gggacttcag cgcgcccctc
      121 accatctcac gggtccatgc tggcagcaag gctgcattgg ctgccctgtg cccaggagac
      181 ctgatccagg ccatcaatgg tgagagcaca gagctcatga cacacctgga ggcacagaac
      241 cgcatcaagg gctgccacga tcacctcaca ctgtctgtga gcaggcctga gggtaggagc
      301 tggcccagtg cccctgatga cagcaaggct caggcacaca ggatccacat cgatcctgag
      361 atccaggacg gcagcccaac aaccagcagg cggccctcag gcaccgggac tgggccagaa
      421 gatggcagac caagcctggg atctccatat ggacaacccc ctcgctttcc agtccctcac
      481 aatggcagca gcgaggccac cctgccagcc cagatgagca ccctgcatgt gtctccaccc
      541 cccagcgctg acccagccag aggcctcccg cggagccggg actgcagagt cgacctgggc
      601 tccgaggtgt acaggatgct gcgggagcca gccgagcccg tggccgcgga gcccaagcag
      661 tcaggctcct tccgctactt gcagggcatg ctagaggccg gcgagggcgg ggattggccc
      721 gggcctggcg gcccccggaa cctcaagccc acggccagca agctgggcgc tccgctgagc
      781 ggcctgcagg ggctgcccga gtgcacgcgc tgcggccacg gcatcgtggg caccatcgtc
      841 aaggcacggg acaagctcta ccatcccgag tgcttcatgt gcagtgactg cggcctgaac
      901 ctcaagcagc gtggttactt ctttctggac gagcggctct actgtgagag ccacgccaag
      961 gcgcgcgtga agccgcccga gggctacgac gtggtggcgg tgtaccccaa tgccaaggtg
     1021 gaactcgtct gagctgggac cctgctccca cgcctgcttc ttaaggtccc tgctcggccg
     1081 gtgtaaatat gtttcaccct gtccctctaa taaagctcct ctgctccacc ttgaacctgt
     1141 cacctggcct gccaccctcc tgcgcaggcc atgcatggct cccgagtaca gtagtatctg
     1201 cttaggtgcc aggcatgtcc taggctctgg gtgcagtagt gagcaggacg ggtaccatgc
     1261 tgccctgaag ggggccacag cctgggtgga aggcagacct gaatcacaac gggccagctc
     1321 tagtaatacg aaggtgaggt ctgggatgct gcgtgcggcg cgacgacagg aggtatgacc
     1381 tgggtggggt cagggaaagt cttagctgag aactaagaga tgagggaggc acaaactctg
     1441 cacgggggaa ctgtgtgtgc aaaggtgagc tgggggcgag aaaggcctct gtggccgtca
     1501 tcggcactag cgggttgggg gtggtggtgg ggtgctggca gcctcaggag cgatcgctcc
     1561 cctggagagg gtgattgagt gtggagatca ccggggccgc cgcgggccgt ctgcacttct
     1621 gttccaggtt tttctggcat tttctgttcc aggtttcttc cacccacgag cactttattc
     1681 tcctccgaga cccccttttc ttccccttcc tctctccccc accagggggc gcgcttaaat
     1741 ttccagacag agaccagaag gaaggtttag aaagaaaaga acacttgccc agggcagctt
     1801 tgccctccaa gaggctccct cctgtctcta agtcaattcc acccctcctc gaagtcccgg
     1861 cttccacccc tctcctcaga gtcccggcgt ttacctcgtg gtgtgtttgc cttgggcctt
     1921 tcatgccccg gctgcacaca tcgtctgtga attgtggctg ttcactcccg aggatgtgtc
     1981 ctagactccg ggtcgcgtgg atctaccctc tagtttactt gctcgggaga agaaactgac
     2041 tcgttttatt tagtgcctat ttagcgagcc cagagtaacg tacatttgtg ctgttttcaa
     2101 ttttgtgcta tcgcaaatca caaaaaaact gttatcaatt cacattcatc atcagcacga
     2161 gacccatttc cttgtgctcc tgccagctca ggatattatg tttctttttt catttttgcc
     2221 agtctgttaa gtaaaatgtc atatgcgttt gttttaa
//
