LOCUS       NM_001242935            2596 bp    mRNA    linear   PRI 13-OCT-2024
DEFINITION  Homo sapiens synuclein alpha interacting protein (SNCAIP),
            transcript variant 1A, mRNA.
ACCESSION   NM_001242935
VERSION     NM_001242935.3
KEYWORDS    RefSeq.
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 2596)
  AUTHORS   Varenyk,Y., Theodorakis,P.E., Pham,D.Q.H., Li,M.S. and Krupa,P.
  TITLE     Exploring Structural Insights of Abeta42 and alpha-Synuclein
            Monomers and Heterodimer: A Comparative Study Using Implicit and
            Explicit Solvent Simulations
  JOURNAL   J Phys Chem B 128 (19), 4655-4669 (2024)
   PUBMED   38700150
  REMARK    GeneRIF: Exploring Structural Insights of Abeta42 and
            alpha-Synuclein Monomers and Heterodimer: A Comparative Study Using
            Implicit and Explicit Solvent Simulations.
REFERENCE   2  (bases 1 to 2596)
  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   3  (bases 1 to 2596)
  AUTHORS   Shishido,T., Nagano,Y., Araki,M., Kurashige,T., Obayashi,H.,
            Nakamura,T., Takahashi,T., Matsumoto,M. and Maruyama,H.
  TITLE     Synphilin-1 has neuroprotective effects on MPP+-induced Parkinson's
            disease model cells by inhibiting ROS production and apoptosis
  JOURNAL   Neurosci Lett 690, 145-150 (2019)
   PUBMED   30316984
  REMARK    GeneRIF: results indicated that synphilin-1 may play
            neuroprotective roles in Parkinson Disease pathogenesis by
            inhibiting ROS production and apoptosis.
REFERENCE   4  (bases 1 to 2596)
  AUTHORS   Brudek,T., Winge,K., Rasmussen,N.B., Bahl,J.M., Tanassi,J.,
            Agander,T.K., Hyde,T.M. and Pakkenberg,B.
  TITLE     Altered alpha-synuclein, parkin, and synphilin isoform levels in
            multiple system atrophy brains
  JOURNAL   J Neurochem 136 (1), 172-185 (2016)
   PUBMED   26465922
  REMARK    GeneRIF: Differential expression of synphilin-1 isoforms (and
            alpha-synuclein and parkin) was found in multiple system atrophy
            brains compared to control brain.
REFERENCE   5  (bases 1 to 2596)
  AUTHORS   Eyal,A., Szargel,R., Avraham,E., Liani,E., Haskin,J., Rott,R. and
            Engelender,S.
  TITLE     Synphilin-1A: an aggregation-prone isoform of synphilin-1 that
            causes neuronal death and is present in aggregates from
            alpha-synucleinopathy patients
  JOURNAL   Proc Natl Acad Sci U S A 103 (15), 5917-5922 (2006)
   PUBMED   16595633
  REMARK    GeneRIF: Synphilin-1A may contribute to neuronal degeneration in
            alpha-synuclein mutations and provides insights into the role of
            inclusion bodies in neurodegenerative disorders.
REFERENCE   6  (bases 1 to 2596)
  AUTHORS   Bandopadhyay,R., de Silva,R., Khan,N., Graham,E., Vaughan,J.,
            Engelender,S., Ross,C., Morris,H., Morris,C., Wood,N.W., Daniel,S.
            and Lees,A.
  TITLE     No pathogenic mutations in the synphilin-1 gene in Parkinson's
            disease
  JOURNAL   Neurosci Lett 307 (2), 125-127 (2001)
   PUBMED   11427316
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 2596)
  AUTHORS   Kawamata,H., McLean,P.J., Sharma,N. and Hyman,B.T.
  TITLE     Interaction of alpha-synuclein and synphilin-1: effect of
            Parkinson's disease-associated mutations
  JOURNAL   J Neurochem 77 (3), 929-934 (2001)
   PUBMED   11331421
REFERENCE   8  (bases 1 to 2596)
  AUTHORS   Engelender,S., Wanner,T., Kleiderlein,J.J., Wakabayashi,K.,
            Tsuji,S., Takahashi,H., Ashworth,R., Margolis,R.L. and Ross,C.A.
  TITLE     Organization of the human synphilin-1 gene, a candidate for
            Parkinson's disease
  JOURNAL   Mamm Genome 11 (9), 763-766 (2000)
   PUBMED   10967135
REFERENCE   9  (bases 1 to 2596)
  AUTHORS   Engelender,S., Kaminsky,Z., Guo,X., Sharp,A.H., Amaravi,R.K.,
            Kleiderlein,J.J., Margolis,R.L., Troncoso,J.C., Lanahan,A.A.,
            Worley,P.F., Dawson,V.L., Dawson,T.M. and Ross,C.A.
  TITLE     Synphilin-1 associates with alpha-synuclein and promotes the
            formation of cytosolic inclusions
  JOURNAL   Nat Genet 22 (1), 110-114 (1999)
   PUBMED   10319874
REFERENCE   10 (bases 1 to 2596)
  AUTHORS   Cook Shukla,L., Schulze,J., Farlow,J., Pankratz,N.D., Wojcieszek,J.
            and Foroud,T.
  TITLE     Parkinson Disease Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301402
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DQ227317.1, BC040552.1 and
            N21998.1.
            
            On Aug 14, 2020 this sequence version replaced NM_001242935.2.
            
            Summary: This gene encodes a protein containing several
            protein-protein interaction domains, including ankyrin-like
            repeats, a coiled-coil domain, and an ATP/GTP-binding motif. The
            encoded protein interacts with alpha-synuclein in neuronal tissue
            and may play a role in the formation of cytoplasmic inclusions and
            neurodegeneration. A mutation in this gene has been associated with
            Parkinson's disease. Alternative splicing results in multiple
            transcript variants. [provided by RefSeq, Apr 2015].
            
            Transcript Variant: This variant (1A) differs in the 5' UTR, lacks
            an alternate exon in the 5' coding region that results in
            translation initiation from a downstream start codon in a different
            reading frame, and lacks two alternate exons in the central coding
            region, compared to variant 2. The encoded isoform (1A) has a
            distinct N-terminus and is shorter than 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 :: DQ227317.1, BC094759.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2148093
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            CDS uses downstream in-frame AUG :: experimental evidence
                                                (PMID:16595633)
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2186              DQ227317.1         113-2298
            2187-2432           BC040552.1         4714-4959
            2433-2596           N21998.1           3-166               c
FEATURES             Location/Qualifiers
     source          1..2596
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q23.2"
     gene            1..2596
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="synuclein alpha interacting protein"
                     /db_xref="GeneID:9627"
                     /db_xref="HGNC:HGNC:11139"
                     /db_xref="MIM:603779"
     exon            1..48
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            49..151
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     CDS             141..1952
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="isoform 1A is encoded by transcript variant 1A;
                     synphilin-1"
                     /codon_start=1
                     /product="synphilin-1 isoform 1A"
                     /protein_id="NP_001229864.1"
                     /db_xref="GeneID:9627"
                     /db_xref="HGNC:HGNC:11139"
                     /db_xref="MIM:603779"
                     /translation="MTYLIQSHHSRRSQNCAEDVIRKTKTDQNGQLECVRWMVSETEA
                     IAELSCSKDFPSLIHYAGCYGQEKILLWLLQFMQEQGISLDEVDQDGNSAVHVASQHG
                     YLGCIQTLVEYGANVTMQNHAGEKPSQSAERQGHTLCSRYLVVVETCMSLASQVVKLT
                     KQLKEQTVERVTLQNQLQQFLEAQKSEGKSLPSSPSSPSSPASRKSQWKSPDADDDSV
                     AKSKPGVQEGIQVLGSLSASSRARPKAKDEDSDKILRQLLGKEISENVCTQEKLSLEF
                     QDAQASSRNSKKIPLEKRELKLARLRQLMQRSLSESDTDSNNSEDPKTTPVRKADRPR
                     PQPIVESVESMDSAESLHLMIKKHTLASGGRRFPFSIKASKSLDGHSPSPTSESSEPD
                     LESQYPGSGSIPPNQPSGDPQQPSPDSTAAQKVATSPKSALKSPSSKRRTSQNLKLRV
                     TFEEPVVQMEQPSLELNGEKDKDKGRTLQRTSTSNESGDQLKRPFGAFRSIMETLSGN
                     QNNNNNYQAANQLKTSTLPLTSLGRKTDAKGNPASSASKGKNKAEMYSSCINLSSNML
                     IEEHLCNDTRHNDINRKMKKSYSIKHIAEPESKELFL"
     exon            152..224
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            225..338
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            339..464
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            465..634
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            635..727
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            728..1796
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1797..1867
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1868..2596
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2411..2416
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="hexamer: AATAAA"
     polyA_site      2432
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="major polyA site"
     polyA_site      2465
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
     regulatory      2569..2574
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="hexamer: AATAAA"
     polyA_site      2596
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
ORIGIN      
        1 agtcagtccc ttcgcgctcc tgagccgccg gcgcgccggg cgccccggga atttataagt
       61 atttgaccgt actcaaaatg tgcaaggaag aataatggaa gcccctgaat accttgattt
      121 ggatgaaatt gactttagtg atgacatatc ttattcagtc acatcactca agacgatccc
      181 agaactgtgc cgaagatgtg atacgcaaaa cgaagacaga tcagaatggt cagttggagt
      241 gcgtacgctg gatggtgagc gaaacagaag ccattgcaga actgagttgt tctaaggatt
      301 ttccaagcct tattcattac gcaggttgct atggccagga aaagattctt ctgtggcttc
      361 ttcagtttat gcaagaacag ggcatctcgt tggatgaagt agaccaggat ggcaacagtg
      421 ccgttcacgt agcctcacag catggctacc ttggatgcat acagaccttg gttgaatatg
      481 gagcaaatgt caccatgcag aaccacgctg gggaaaagcc ctcccagagc gccgagcggc
      541 aggggcacac cctgtgctcc aggtacctgg tggtggtgga gacctgcatg tcgctggcct
      601 ctcaagtggt gaagttaacc aagcagctaa aggaacaaac agtagaacgt gtcacgctgc
      661 agaaccaact ccaacaattt ctagaagccc agaaatcaga gggcaagtca ctcccttctt
      721 cacccagttc accatcctca cctgcctcca gaaagtccca gtggaaatct ccagatgcag
      781 atgatgattc tgtagccaaa agcaagccag gagtccaaga ggggattcag gttcttggaa
      841 gcctgtcagc ctccagccgg gctagaccca aagcaaaaga tgaagattct gataaaatct
      901 tacgccagtt attgggaaag gaaatctcag aaaatgtctg cacccaggaa aaactgtcct
      961 tggaattcca ggatgctcag gcttcctcta gaaattctaa aaagatccca ctggagaaga
     1021 gggaactgaa gttagccagg ctgagacagc tgatgcagag gtcactgagt gagtctgaca
     1081 cagactccaa caactctgag gaccccaaga ctaccccagt gaggaaggct gaccgaccaa
     1141 ggccgcagcc cattgtagaa agcgtagaga gtatggacag cgcagaaagc ctgcacctga
     1201 tgattaagaa acacaccttg gcatcagggg gacgcaggtt tcctttcagc atcaaggcct
     1261 ccaaatccct ggatggccac agcccatctc ccacctcaga gagcagcgaa ccagacttag
     1321 aatcccagta tccaggctca gggagtattc ctccaaacca gccctctggt gaccctcagc
     1381 agcccagccc tgacagtact gctgcccaga aagttgccac aagtcccaag agtgccctca
     1441 agtctccatc ttccaagcgt aggacatctc agaacttaaa actgagagtt acctttgagg
     1501 agcctgtggt gcagatggag cagcctagcc ttgaactgaa tggagaaaaa gacaaagata
     1561 agggcaggac tctccagcgg acctccacaa gtaacgaatc gggggatcaa ctgaaaaggc
     1621 cttttggagc ctttcgatct atcatggaga cactaagtgg caaccaaaac aataataata
     1681 actaccaggc agccaaccag ctgaaaacct ctacattgcc cttgacctca cttgggagga
     1741 agacagatgc caagggaaac cctgccagct ccgctagcaa aggaaagaat aaggcagaaa
     1801 tgtacagcag ctgcatcaat ctttcctcta acatgctgat tgaagagcat ctgtgtaacg
     1861 acacacggca taatgacatc aatagaaaaa tgaagaaatc ctacagcata aagcacattg
     1921 ctgagccaga gtcaaaagaa ctcttcttgt aaatcacttt ttaaattttc tctcactgat
     1981 gccctttgga aattattgga aatttctgga ctatcctctt tggaaagaga accatgaaaa
     2041 caatgcctca ccagcagaag aacagaatat caggatgcct taaatttata gtagtagact
     2101 gtaaaagatt cattttgggg tgatatctgt atatataact tgttttttta aaagatgccg
     2161 tttaaaagca tgattgggaa aatgtatgtt ttttaagagt agattgattc accctaccca
     2221 caggacattc accaagccac tgataccatt ttatatttca tcaattgcat gagtatttgc
     2281 taatgttgat tgaacctccc tttccccata atgtgggcag atttggctca gctccttcat
     2341 gagatcaggt cagtggtatt gtttctgtca agagtgtttt ttctgtcatt tctacttttt
     2401 gtataaagga aataaaacaa tgttaacagc cacctataag cttggggcac ctactttcta
     2461 acaaatctgt gatgttctga tttctaaggg actttgcaag tattttgatt gctgatattt
     2521 gatttcagga acaaactgct cagtttagca gttttcccat aggcgtcaaa taaaacattc
     2581 tatatttcat taagta
//
