LOCUS       NM_007286               5359 bp    mRNA    linear   PRI 02-APR-2024
DEFINITION  Homo sapiens synaptopodin (SYNPO), transcript variant 1, mRNA.
ACCESSION   NM_007286
VERSION     NM_007286.6
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 5359)
  AUTHORS   Wang,R.X., Lee,J.S., Campbell,E.L. and Colgan,S.P.
  TITLE     Microbiota-derived butyrate dynamically regulates intestinal
            homeostasis through regulation of actin-associated protein
            synaptopodin
  JOURNAL   Proc Natl Acad Sci U S A 117 (21), 11648-11657 (2020)
   PUBMED   32398370
  REMARK    GeneRIF: Microbiota-derived butyrate dynamically regulates
            intestinal homeostasis through regulation of actin-associated
            protein synaptopodin.
REFERENCE   2  (bases 1 to 5359)
  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 5359)
  AUTHORS   Kwok,E., Rodriguez,D.J., Kremerskothen,J. and Nyarko,A.
  TITLE     Intrinsic disorder and amino acid specificity modulate binding of
            the WW2 domain in kidney and brain protein (KIBRA) to synaptopodin
  JOURNAL   J Biol Chem 294 (46), 17383-17394 (2019)
   PUBMED   31597702
  REMARK    GeneRIF: We show that recombinant human KIBRA WW2 domain is
            primarily disordered, binds SYNPO with relatively weak affinity and
            remains largely disordered in the complex.
REFERENCE   4  (bases 1 to 5359)
  AUTHORS   Dorval,G., Kuzmuk,V., Gribouval,O., Welsh,G.I., Bierzynska,A.,
            Schmitt,A., Miserey-Lenkei,S., Koziell,A., Haq,S., Benmerah,A.,
            Mollet,G., Boyer,O., Saleem,M.A. and Antignac,C.
  TITLE     TBC1D8B Loss-of-Function Mutations Lead to X-Linked Nephrotic
            Syndrome via Defective Trafficking Pathways
  JOURNAL   Am J Hum Genet 104 (2), 348-355 (2019)
   PUBMED   30661770
REFERENCE   5  (bases 1 to 5359)
  AUTHORS   Fasci,D., van Ingen,H., Scheltema,R.A. and Heck,A.J.R.
  TITLE     Histone Interaction Landscapes Visualized by Crosslinking Mass
            Spectrometry in Intact Cell Nuclei
  JOURNAL   Mol Cell Proteomics 17 (10), 2018-2033 (2018)
   PUBMED   30021884
REFERENCE   6  (bases 1 to 5359)
  AUTHORS   Kremerskothen,J., Plaas,C., Kindler,S., Frotscher,M. and
            Barnekow,A.
  TITLE     Synaptopodin, a molecule involved in the formation of the dendritic
            spine apparatus, is a dual actin/alpha-actinin binding protein
  JOURNAL   J Neurochem 92 (3), 597-606 (2005)
   PUBMED   15659229
  REMARK    GeneRIF: Our data suggest dendritic spine accumulation of SYNPO
            critically depends on interaction with postsynaptic alpha-actinin
            and that SYNPO may regulate spine morphology, motility and function
            via its distinct modes of association with the actin cytoskeleton.
REFERENCE   7  (bases 1 to 5359)
  AUTHORS   Patrie,K.M., Drescher,A.J., Welihinda,A., Mundel,P. and Margolis,B.
  TITLE     Interaction of two actin-binding proteins, synaptopodin and
            alpha-actinin-4, with the tight junction protein MAGI-1
  JOURNAL   J Biol Chem 277 (33), 30183-30190 (2002)
   PUBMED   12042308
  REMARK    GeneRIF: interaction with tight junction protein MAGI-1
REFERENCE   8  (bases 1 to 5359)
  AUTHORS   Simpson,J.C., Wellenreuther,R., Poustka,A., Pepperkok,R. and
            Wiemann,S.
  TITLE     Systematic subcellular localization of novel proteins identified by
            large-scale cDNA sequencing
  JOURNAL   EMBO Rep 1 (3), 287-292 (2000)
   PUBMED   11256614
REFERENCE   9  (bases 1 to 5359)
  AUTHORS   Mundel,P., Heid,H.W., Mundel,T.M., Kruger,M., Reiser,J. and Kriz,W.
  TITLE     Synaptopodin: an actin-associated protein in telencephalic
            dendrites and renal podocytes
  JOURNAL   J Cell Biol 139 (1), 193-204 (1997)
   PUBMED   9314539
REFERENCE   10 (bases 1 to 5359)
  AUTHORS   Lanfranchi,G., Muraro,T., Caldara,F., Pacchioni,B., Pallavicini,A.,
            Pandolfo,D., Toppo,S., Trevisan,S., Scarso,S. and Valle,G.
  TITLE     Identification of 4370 expressed sequence tags from a
            3'-end-specific cDNA library of human skeletal muscle by DNA
            sequencing and filter hybridization
  JOURNAL   Genome Res 6 (1), 35-42 (1996)
   PUBMED   8681137
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DA333058.1 and AB028952.1.
            
            On Nov 23, 2018 this sequence version replaced NM_007286.5.
            
            Summary: Synaptopodin is an actin-associated protein that may play
            a role in actin-based cell shape and motility. The name
            synaptopodin derives from the protein's associations with
            postsynaptic densities and dendritic spines and with renal
            podocytes (Mundel et al., 1997 [PubMed 9314539]).[supplied by OMIM,
            Mar 2008].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes isoform A, also referred to as 'Synpo-long'.
            
            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 :: AB028952.1, AF499136.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000307662.5/ ENSP00000302139.4
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-31                DA333058.1         17-47
            32-3629             AB028952.1         1-3598
            3630-5359           AB028952.1         3603-5332
FEATURES             Location/Qualifiers
     source          1..5359
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q33.1"
     gene            1..5359
                     /gene="SYNPO"
                     /gene_synonym="SYNPO1"
                     /note="synaptopodin"
                     /db_xref="GeneID:11346"
                     /db_xref="HGNC:HGNC:30672"
                     /db_xref="MIM:608155"
     exon            1..195
                     /gene="SYNPO"
                     /gene_synonym="SYNPO1"
                     /inference="alignment:Splign:2.1.0"
     exon            196..2555
                     /gene="SYNPO"
                     /gene_synonym="SYNPO1"
                     /inference="alignment:Splign:2.1.0"
     CDS             528..3239
                     /gene="SYNPO"
                     /gene_synonym="SYNPO1"
                     /note="isoform A is encoded by transcript variant 1"
                     /codon_start=1
                     /product="synaptopodin isoform A"
                     /protein_id="NP_009217.3"
                     /db_xref="CCDS:CCDS4308.1"
                     /db_xref="GeneID:11346"
                     /db_xref="HGNC:HGNC:30672"
                     /db_xref="MIM:608155"
                     /translation="MEGYSEEASLLRHLEKVASEEEEVPLVVYLKENAALLTANGLHL
                     SQNREAQQSSPAPPPAEVHSPAADVNQNLASPSATLTTPTSNSSHNPPATDVNQNPPA
                     TVVPQSLPLSSIQQNSSEAQLPSNGTGPASKPSTLCADGQPQAPAEEVRCSTLLIDKV
                     STPATTTSTFSREATLIPSSRPPASDFMSSSLLIDIQPNTLVVSADQEMSGRAAATTP
                     TKVYSEVHFTLAKPPSVVNRTARPFGIQAPGGTSQMERSPMLERRHFGEKAPAPQPPS
                     LPDRSPRPQRHIMSRSPMVERRMMGQRSPASERRPLGNFTAPPTYTETLSTAPLASWV
                     RSPPSYSVLYPSSDPKSSHLKGQAVPASKTGILEESMARRGSRKSMFTFVEKPKVTPN
                     PDLLDLVQTADEKRRQRDQGEVGVEEEPFALGAEASNFQQEPAPRDRASPAAAEEVVP
                     EWASCLKSPRIQAKPKPKPNQNLSEASGKGAELYARRQSRMEKYVIESSSHTPELARC
                     PSPTMSLPSSWKYPTNAPGAFRVASRSPARTPPASLYHGYLPENGVLRPEPTKQPPYQ
                     LRPSLFVLSPIKEPAKVSPRAASPAKPSSLDLVPNLPKGALPPSPALPRPSRSSPGLY
                     TSPGQDSLQPTAVSPPYGGDISPVSPSRAWSPRAKQAPRPSFSTRNAGIEAQDRRESL
                     PTSPPWTPGASRPPSSLDGWVSPGPWEPGRGSSMSSPPPLPPPPPMSPSWSERSVSPL
                     RPETEARPPSRQLQALLARNIINAARRKSASPRSAGAENPRPFSPPRAPPPPPPPPPP
                     PPRMRSPQPARPGSAAVPGAAFAPIPRSPLPAGPSSCTSPRSPLPAPPRPFLYRRSPT
                     DSDVSLDSEDSGAKSPGILGYNICPRGWNGSLRLKRGSLPAEASCTT"
     exon            2556..5359
                     /gene="SYNPO"
                     /gene_synonym="SYNPO1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      5341..5346
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SYNPO"
                     /gene_synonym="SYNPO1"
                     /note="hexamer: AATAAA"
     polyA_site      5359
                     /gene="SYNPO"
                     /gene_synonym="SYNPO1"
                     /note="major polyA site"
ORIGIN      
        1 gataaagagc tgggctgagt catctgtgga ggagaaaagt cacatccagc tccttcatgt
       61 tgctgccgat gtgggatttt cctggcttcg tcagccaagc aattggctgc ctttgccgga
      121 ggctttgaga accaaggctt gaaggccggc aggagcatcc agggggaagc ttggcttcag
      181 ggaggaccta gcagacgttg ggccggagca ctagcctcac ggagaaggat ctgaaagaag
      241 ccaaggcgcg gagccagcag attgcagccc agctgaccac ccctcccagc tccaattccc
      301 gtggcgtcca gctcttcaac aggcgccggc agagggtgaa cgagttcacc ttggagagcc
      361 acggccagag gggacagaag cccagccagg agtccctcag agtgctccct tcaagcctcc
      421 caggccatgc accggggctc agcctgagtt ccacctcgct gccggagcca ggccctccac
      481 ggcaccccag tccccagagc cccgacagag gggtccctgg ccacagcatg gaggggtact
      541 cagaggaggc tagcttgctg cggcacctgg agaaggtggc cagtgaggag gaagaggtac
      601 cactggtggt ttatctaaag gagaatgcag cactgctgac agccaatggg ctgcacctgt
      661 cccaaaaccg agaggcccag cagtcctcac cggccccacc tccagctgag gtccacagcc
      721 cagctgcaga tgtcaaccaa aaccttgcct cgcccagtgc cacgctcacc acaccaactt
      781 ctaacagcag ccacaatccg ccagccaccg atgtcaatca gaacccaccg gcaactgttg
      841 tcccacagag cctgccactt tctagcatcc aacagaattc ctcagaggcc caactcccat
      901 ctaatggcac agggcctgct tccaaaccca gcaccctgtg tgctgatggg caaccccagg
      961 caccggctga ggaggtgaga tgcagcacac tcctaattga caaggtatca actccagcta
     1021 ccaccaccag caccttctcc agagaagcta cgctcatccc cagctccagg cccccagcct
     1081 cagatttcat gtccagctcc ctgctcattg acatccagcc caacacccta gtggtgtcag
     1141 cagatcaaga gatgtctggg cgagcagctg ccaccacgcc caccaaggtc tacagtgagg
     1201 tccacttcac actggccaag cccccatcag tggtcaacag gacggccagg ccttttggga
     1261 tccaggcgcc agggggcacc agccagatgg agaggagccc catgctagag agacgacatt
     1321 ttggggagaa ggccccggct ccccagcccc ccagtttgcc agacaggagc ccccggccac
     1381 agagacacat aatgtcccgc agccccatgg tggaaaggag gatgatgggg cagcgaagcc
     1441 cggcctcaga gagacgcccc ttggggaact tcactgcacc ccccacctac actgagacct
     1501 tgtccacagc ccctctggct tcctgggtga ggtctcctcc ctcatattct gtcctgtatc
     1561 ccagctccga ccccaagtct tctcatctga agggccaggc ggttcctgcc agcaagacgg
     1621 gcattctgga ggagtcgatg gcccgccggg gcagccgcaa atccatgttt actttcgtgg
     1681 agaagcccaa ggtgaccccg aatccagact tgctggatct ggtacagaca gcggatgaga
     1741 agcggcggca gagggaccag ggggaggtag gcgtggagga ggagcccttc gcactggggg
     1801 ccgaggcctc caacttccag caggagccag cacctcgtga cagggccagc cccgcggcgg
     1861 cggaggaggt ggtaccagag tgggcctcct gcctcaagtc accccgcatc caggccaagc
     1921 cgaagcccaa acccaaccag aacctctccg aggcctctgg gaagggagct gagctctacg
     1981 cccgccgcca gtcacggatg gagaaatatg tcatcgagtc ttcaagccac acgccagagc
     2041 tggcccgctg cccatcacct accatgtccc tgccttcctc ctggaaatac cccactaacg
     2101 cccccggggc cttccgagtg gcatcccgaa gcccagcccg gaccccgcct gcctccctct
     2161 accatggcta cctgcctgag aacggggtcc tgcgcccaga gcccaccaag cagccgccat
     2221 accagctgcg cccctcgctc tttgtcctct cacctatcaa ggagcctgcc aaggtctcac
     2281 caagagctgc ctcgcccgcc aagcccagct ccttggacct ggtgcccaac ctgcccaagg
     2341 gggctctccc tccatctcct gccctgcctc ggccctcgcg ctcctcaccg ggcctctaca
     2401 cctcccccgg ccaggacagc ctgcagccca ctgccgtgag ccctccttac ggcggtgaca
     2461 tctcccccgt gtctccctcc agggcgtggt ctccccgagc caagcaggcc cccaggccct
     2521 ccttctctac ccggaacgcc gggatcgagg ctcaggaccg ccgggagagc ctgcccacct
     2581 ccccaccctg gacgccgggc gcgtcccggc cccccagcag cctagacggc tgggtgagcc
     2641 cgggcccgtg ggagccaggt cgcgggagca gcatgagcag ccccccgccg ctgccgccgc
     2701 caccgcccat gtctccctcg tggagcgagc gctcggtgtc cccgctgcga cctgagaccg
     2761 aggcgcggcc ccccagccgc cagctgcagg cgcttctggc gcgaaacatc atcaatgcgg
     2821 cccggcgcaa gagcgcctcc ccgcggtcgg cgggcgccga gaacccgcgg cccttctccc
     2881 cgccgagggc gccaccgccc ccgcccccgc ccccgccccc gcccccgcgc atgcgctcgc
     2941 cacagcccgc ccgccccggc tcggctgctg tgccgggggc agccttcgcg cccatcccgc
     3001 ggagcccgtt gcccgccggt ccttcgtcct gcaccagtcc ccggagcccg ctgcccgcgc
     3061 ctcccaggcc cttcctctac cgccgctcgc ccacggactc cgacgtgtcc ctcgactccg
     3121 aggactccgg ggctaagtct ccaggcatcc tgggctacaa tatctgtccc cgcgggtgga
     3181 atggcagcct tcggctcaag cgtggcagcc tccccgccga ggcctcctgc accacctaga
     3241 gccccacccc cgaccccacc ccgggagggc agagccagaa gaaggctcat tagacctggg
     3301 ggacccaaag ggtctggcct ctttgggcag ccccagagat gaggggtcag cagaggagag
     3361 ctctggggtt ggggatgggt tagggacgca agcttgagtt ctagcccttg ctctcattca
     3421 gctgttgtgt gaccctgggt aagacccttc cttgtttgac cctcagcttt cccatctgtt
     3481 taatggtggc tttggccaag gcaatccaca aacgtcaaaa ttccccttcc catcagtaca
     3541 cacaccgatg cacacacact ctctctttct ctctctctct ctctcacaca cacacacaca
     3601 cacacacaca cacacacaca cacacacact agttagtgcc ttggatgagg cggggcagtg
     3661 tgtatatgga cccctggact tgctaccttc agggttccat actcgtccct cccctcctgg
     3721 ctctgctgtc tggagtctgg caagcggggt gtgttcagaa ggtcctaggc ctgtgtcgca
     3781 tgtccaggca ctggcctgac catccggctc cctggcacca agtcccaggc aggagcagct
     3841 gttttccatc ccttcccaga caagctctat ttttatcaca atgaccttta gagaggtctc
     3901 ccaggccagc tcaaggtgtc ccactatccc ctctggaggg aagaggcagg aaaattctcc
     3961 ccgggtccct gtcatgctac tttctccatc ccagttcaga ctgtccagga catcttatct
     4021 gcagccataa gagaattata aggcagtgat ttcccttagg cccaggactt gggcctccag
     4081 ctcatctgtt ccttctgggc ccattcatgg caggttctgg gctcaaagct gaactgggga
     4141 gagaagagat acagagctac catgtgactt tacctgattg ccctcagttt ggggttgctt
     4201 attgggaaag agagagacaa agagttactt gttacgggaa atatgaaaag catggccagg
     4261 atgcatagag gagattctag caggggacag gattggctca gatgacccct gagggctctt
     4321 ccagtcttga aatgcattcc atgatattag gaagtcgggg gtgggtggtg gtggtgggct
     4381 agttgggctt gaatttaggg gccgatgagc ttgggtacgt gagcagggtg ttaagttagg
     4441 gtctgcctgt atttctggtc cccttggaaa tgtccccttc ttcagtgtca gacctcagtc
     4501 ccagtgtcca tatcgtgccc agaaaagtag acattatcct gccccatccc ttccccagtg
     4561 cactctgacc tagctagtgc ctggtgccca gtgacctggg ggagcctggc tgcaggccct
     4621 cactggttcc ctaaaccttg gtggctgtga ttcaggtccc caggggggac tcagggagga
     4681 atatggctga gttctgtagt ttccagagtt ggctggtaga gccttctaga ggttcagaat
     4741 attagcttca ggatcagctg ggggtatgga attggctgag gatcaaacgt atgtaggtga
     4801 aaggatacca ggatgttgct aaaggtgagg gacagtttgg gtttgggact taccggggtg
     4861 atgttagatc tggaaccccc aagtgaggct ggagggagtt aaggtcagta tggaagatag
     4921 ggttgggaca gggtgctttg gaatgaaaga gtgaccttag agggctcctt gggcctcagg
     4981 aatgctcctg ctgctgtgaa gatgagaagg tgctcttact cagttaatga tgagtgacta
     5041 tatttaccaa agcccctacc tgctgctggg tcccttgtag cacaggagac tggggctaag
     5101 ggcccctccc agggaaggga caccatcagg cctctggctg aggcagtagc atagaggatc
     5161 catttctacc tgcatttccc agaggactag caggaggcag ccttgagaaa ccggcagttc
     5221 ccaagccagc gcctggctgt tctctcattg tcactgccct ctccccaacc tctcctctaa
     5281 cccactagag attgcctgtg tcctgcctct tgcctcttgt agaatgcagc tctggccctc
     5341 aataaatgct tcctgcatt
//
