LOCUS       NM_005460               3577 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens synuclein alpha interacting protein (SNCAIP),
            transcript variant 1, mRNA.
ACCESSION   NM_005460
VERSION     NM_005460.4
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 3577)
  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 3577)
  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 3577)
  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 3577)
  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 3577)
  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 3577)
  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 3577)
  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 3577)
  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 3577)
  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 3577)
  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 AI702863.1, AF076929.1,
            BC040552.1 and N21998.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_005460.3.
            
            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 (1, also known as variant a)
            differs in the 5' UTR, lacks an alternate in-frame exon in the 5'
            coding region, and lacks an exon that results in a frameshift in
            the 3' coding region, compared to variant 2. The encoded isoform
            (1) has a distinct C-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 :: AF076929.1, SRR1803616.66361.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000261368.13/ ENSP00000261368.8
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1                 AI702863.1         169-169
            2-224               AF076929.1         1-223
            225-656             BC040552.1         1700-2131
            657-3167            AF076929.1         656-3166
            3168-3413           BC040552.1         4714-4959
            3414-3577           N21998.1           3-166               c
FEATURES             Location/Qualifiers
     source          1..3577
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q23.2"
     gene            1..3577
                     /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             95..2854
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="isoform 1 is encoded by transcript variant 1;
                     synphilin-1"
                     /codon_start=1
                     /product="synphilin-1 isoform 1"
                     /protein_id="NP_005451.2"
                     /db_xref="CCDS:CCDS4131.1"
                     /db_xref="GeneID:9627"
                     /db_xref="HGNC:HGNC:11139"
                     /db_xref="MIM:603779"
                     /translation="MEAPEYLDLDEIDFSDDISYSVTSLKTIPELCRRCDTQNEDRSV
                     SSSSWNCGISTLITNTQKPTGIADVYSKFRPVKRVSPLKHQPETLENNESDDQKNQKV
                     VEYQKGGESDLGPQPQELGPGDGVGGPPGKSSEPSTSLGELEHYDLDMDEILDVPYIK
                     SSQQLASFTKVTSEKRILGLCTTINGLSGKACSTGSSESSSSNMAPFCVLSPVKSPHL
                     RKASAVIHDQHKLSTEETEISPPLVKCGSAYEPENQSKDFLNKTFSDPHGRKVEKTTP
                     DCQLRAFHLQSSAAESKPEEQVSGLNRTSSQGPEERSEYLKKVKSILNIVKEGQISLL
                     PHLAADNLDKIHDENGNNLLHIAASQGHAECLQHLTSLMGEDCLNERNTEKLTPAGLA
                     IKNGQLECVRWMVSETEAIAELSCSKDFPSLIHYAGCYGQEKILLWLLQFMQEQGISL
                     DEVDQDGNSAVHVASQHGYLGCIQTLVEYGANVTMQNHAGEKPSQSAERQGHTLCSRY
                     LVVVETCMSLASQVVKLTKQLKEQTVERVTLQNQLQQFLEAQKSEGKSLPSSPSSPSS
                     PASRKSQWKSPDADDDSVAKSKPGVQEGIQVLGSLSASSRARPKAKDEDSDKILRQLL
                     GKEISENVCTQEKLSLEFQDAQASSRNSKKIPLEKRELKLARLRQLMQRSLSESDTDS
                     NNSEDPKTTPVRKADRPRPQPIVESVESMDSAESLHLMIKKHTLASGGRRFPFSIKAS
                     KSLDGHSPSPTSESSEPDLESQYPGSGSIPPNQPSGDPQQPSPDSTAAQKVATSPKSA
                     LKSPSSKRRTSQNLKLRVTFEEPVVQMEQPSLELNGEKDKDKGRTLQRTSTSNESGDQ
                     LKRPFGAFRSIMETLSGNQNNNNNYQAANQLKTSTLPLTSLGRKTDAKGNPASSASKG
                     KNKAA"
     exon            152..224
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            225..1096
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1097..1276
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1277..1390
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1391..1516
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1517..1686
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1687..1779
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1780..2848
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     exon            2849..3577
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3392..3397
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="hexamer: AATAAA"
     polyA_site      3413
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="major polyA site"
     polyA_site      3446
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
     regulatory      3550..3555
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNCAIP"
                     /gene_synonym="Sph1; SYPH1"
                     /note="hexamer: AATAAA"
     polyA_site      3577
                     /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 tcagtttcta gctctagctg
      241 gaattgtggc atctcaactc ttattacaaa cacgcaaaag cccacaggaa tcgctgatgt
      301 gtacagtaag ttccgcccag tgaagcgggt ttcgccactg aaacatcagc cagagactct
      361 ggagaacaat gaaagtgatg accaaaagaa ccagaaagtg gttgagtacc agaaaggggg
      421 tgagtctgac ctgggccccc agcctcagga gcttggccct ggagatggag tgggcggccc
      481 accaggtaag agctctgagc ccagcacatc gctgggtgaa ctggagcact acgacctcga
      541 catggatgag attctggatg tgccttatat taaatccagt cagcagcttg cctcttttac
      601 caaggtgact tcagaaaaaa gaattttggg cttatgcaca accatcaatg gcctttctgg
      661 caaagcctgc tctacaggaa gttctgagag ctcatcatcc aacatggcac cattttgtgt
      721 tctttctccc gtgaaaagcc ctcacttgag aaaagcatca gctgtcatcc acgaccagca
      781 caagctgtcc actgaagaaa ccgagatctc acctcctctg gttaaatgtg gctctgcata
      841 tgagcctgaa aaccagagta aagacttcct aaacaagaca tttagtgatc ctcatggtcg
      901 aaaagttgag aagacaacac cagactgcca gctcagggcc ttccacctac aatcctcagc
      961 agcagaatcc aaaccagaag agcaggtcag tggcctaaac cggaccagct cccaaggccc
     1021 agaagaaagg agtgagtatc tgaaaaaagt gaaaagcatc ttgaacattg ttaaagaagg
     1081 acagatctct ctcctgccac acctagctgc agacaatcta gacaaaattc acgacgaaaa
     1141 tggaaacaat ctattacata ttgcggcgtc acagggacac gcagagtgtc tacagcacct
     1201 cacttctttg atgggagaag actgcctcaa tgagcgcaac actgagaagt tgactccagc
     1261 aggcctggcc attaagaatg gtcagttgga gtgcgtacgc tggatggtga gcgaaacaga
     1321 agccattgca gaactgagtt gttctaagga ttttccaagc cttattcatt acgcaggttg
     1381 ctatggccag gaaaagattc ttctgtggct tcttcagttt atgcaagaac agggcatctc
     1441 gttggatgaa gtagaccagg atggcaacag tgccgttcac gtagcctcac agcatggcta
     1501 ccttggatgc atacagacct tggttgaata tggagcaaat gtcaccatgc agaaccacgc
     1561 tggggaaaag ccctcccaga gcgccgagcg gcaggggcac accctgtgct ccaggtacct
     1621 ggtggtggtg gagacctgca tgtcgctggc ctctcaagtg gtgaagttaa ccaagcagct
     1681 aaaggaacaa acagtagaac gtgtcacgct gcagaaccaa ctccaacaat ttctagaagc
     1741 ccagaaatca gagggcaagt cactcccttc ttcacccagt tcaccatcct cacctgcctc
     1801 cagaaagtcc cagtggaaat ctccagatgc agatgatgat tctgtagcca aaagcaagcc
     1861 aggagtccaa gaggggattc aggttcttgg aagcctgtca gcctccagcc gggctagacc
     1921 caaagcaaaa gatgaagatt ctgataaaat cttacgccag ttattgggaa aggaaatctc
     1981 agaaaatgtc tgcacccagg aaaaactgtc cttggaattc caggatgctc aggcttcctc
     2041 tagaaattct aaaaagatcc cactggagaa gagggaactg aagttagcca ggctgagaca
     2101 gctgatgcag aggtcactga gtgagtctga cacagactcc aacaactctg aggaccccaa
     2161 gactacccca gtgaggaagg ctgaccgacc aaggccgcag cccattgtag aaagcgtaga
     2221 gagtatggac agcgcagaaa gcctgcacct gatgattaag aaacacacct tggcatcagg
     2281 gggacgcagg tttcctttca gcatcaaggc ctccaaatcc ctggatggcc acagcccatc
     2341 tcccacctca gagagcagcg aaccagactt agaatcccag tatccaggct cagggagtat
     2401 tcctccaaac cagccctctg gtgaccctca gcagcccagc cctgacagta ctgctgccca
     2461 gaaagttgcc acaagtccca agagtgccct caagtctcca tcttccaagc gtaggacatc
     2521 tcagaactta aaactgagag ttacctttga ggagcctgtg gtgcagatgg agcagcctag
     2581 ccttgaactg aatggagaaa aagacaaaga taagggcagg actctccagc ggacctccac
     2641 aagtaacgaa tcgggggatc aactgaaaag gccttttgga gcctttcgat ctatcatgga
     2701 gacactaagt ggcaaccaaa acaataataa taactaccag gcagccaacc agctgaaaac
     2761 ctctacattg cccttgacct cacttgggag gaagacagat gccaagggaa accctgccag
     2821 ctccgctagc aaaggaaaga ataaggcagc ataatgacat caatagaaaa atgaagaaat
     2881 cctacagcat aaagcacatt gctgagccag agtcaaaaga actcttcttg taaatcactt
     2941 tttaaatttt ctctcactga tgccctttgg aaattattgg aaatttctgg actatcctct
     3001 ttggaaagag aaccatgaaa acaatgcctc accagcagaa gaacagaata tcaggatgcc
     3061 ttaaatttat agtagtagac tgtaaaagat tcattttggg gtgatatctg tatatataac
     3121 ttgttttttt aaaagatgcc gtttaaaagc atgattggga aaatgtatgt tttttaagag
     3181 tagattgatt caccctaccc acaggacatt caccaagcca ctgataccat tttatatttc
     3241 atcaattgca tgagtatttg ctaatgttga ttgaacctcc ctttccccat aatgtgggca
     3301 gatttggctc agctccttca tgagatcagg tcagtggtat tgtttctgtc aagagtgttt
     3361 tttctgtcat ttctactttt tgtataaagg aaataaaaca atgttaacag ccacctataa
     3421 gcttggggca cctactttct aacaaatctg tgatgttctg atttctaagg gactttgcaa
     3481 gtattttgat tgctgatatt tgatttcagg aacaaactgc tcagtttagc agttttccca
     3541 taggcgtcaa ataaaacatt ctatatttca ttaagta
//
