LOCUS       NM_028277               4844 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus shisa family member 9 (Shisa9), transcript variant 1,
            mRNA.
ACCESSION   NM_028277 XM_908737 XM_980313
VERSION     NM_028277.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 4844)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 4844)
  AUTHORS   Zheng,Y., Wang,L., Liu,Q., Xian,H., Zhang,C., Cai,S., Yang,S.,
            Jin,S. and Cui,J.
  TITLE     Modulation of virus-induced neuroinflammation by the autophagy
            receptor SHISA9 in mice
  JOURNAL   Nat Microbiol 8 (5), 958-972 (2023)
   PUBMED   37081201
  REMARK    GeneRIF: Modulation of virus-induced neuroinflammation by the
            autophagy receptor SHISA9 in mice.
REFERENCE   3  (bases 1 to 4844)
  AUTHORS   Hetsch,F., Wang,D., Chen,X., Zhang,J., Aslam,M., Kegel,M.,
            Tonner,H., Grus,F. and von Engelhardt,J.
  TITLE     CKAMP44 controls synaptic function and strength of relay neurons
            during early development of the dorsal lateral geniculate nucleus
  JOURNAL   J Physiol 600 (15), 3549-3565 (2022)
   PUBMED   35770953
  REMARK    GeneRIF: CKAMP44 controls synaptic function and strength of relay
            neurons during early development of the dorsal lateral geniculate
            nucleus.
REFERENCE   4  (bases 1 to 4844)
  AUTHORS   Chen,X., Aslam,M., Gollisch,T., Allen,K. and von Engelhardt,J.
  TITLE     CKAMP44 modulates integration of visual inputs in the lateral
            geniculate nucleus
  JOURNAL   Nat Commun 9 (1), 261 (2018)
   PUBMED   29343769
  REMARK    GeneRIF: Data indicate the importance of CKAMP44 for modulating
            synaptic short-term depression and visual input integration.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 4844)
  AUTHORS   Yang,B., Dormann,C., Vogt,M.A., Sprengel,R., Gass,P. and Inta,D.
  TITLE     Facilitated c-Fos Induction in Mice Deficient for the AMPA
            Receptor-Associated Protein Ckamp44
  JOURNAL   Cell Mol Neurobiol 36 (7), 1215-1218 (2016)
   PUBMED   26645823
  REMARK    GeneRIF: Ckamp44 expression is strongest in dentate gyrus granule
            cells and less abundant in the rest of the brain
REFERENCE   6  (bases 1 to 4844)
  AUTHORS   Khodosevich,K., Jacobi,E., Farrow,P., Schulmann,A., Rusu,A.,
            Zhang,L., Sprengel,R., Monyer,H. and von Engelhardt,J.
  TITLE     Coexpressed auxiliary subunits exhibit distinct modulatory profiles
            on AMPA receptor function
  JOURNAL   Neuron 83 (3), 601-615 (2014)
   PUBMED   25066086
  REMARK    GeneRIF: coexpression of both auxiliary subunits,CKAMP44 and TARP
            gamma-8 is necessary for the efficient targeting of AMPARs to the
            cell surface of dentate gyrus granule cells
REFERENCE   7  (bases 1 to 4844)
  AUTHORS   Karataeva,A.R., Klaassen,R.V., Stroder,J., Ruiperez-Alonso,M.,
            Hjorth,J.J., van Nierop,P., Spijker,S., Mansvelder,H.D. and
            Smit,A.B.
  TITLE     C-terminal interactors of the AMPA receptor auxiliary subunit
            Shisa9
  JOURNAL   PLoS One 9 (2), e87360 (2014)
   PUBMED   24498314
  REMARK    GeneRIF: Data show interaction partners of AMPA receptor auxiliary
            subunit Shisa9, and that the C-terminal interactions of Shisa9
            through its PDZ domain interaction motif are important for AMPA
            receptor synaptic and network functions.
            Publication Status: Online-Only
REFERENCE   8  (bases 1 to 4844)
  AUTHORS   Schwenk,J., Harmel,N., Brechet,A., Zolles,G., Berkefeld,H.,
            Muller,C.S., Bildl,W., Baehrens,D., Huber,B., Kulik,A., Klocker,N.,
            Schulte,U. and Fakler,B.
  TITLE     High-resolution proteomics unravel architecture and molecular
            diversity of native AMPA receptor complexes
  JOURNAL   Neuron 74 (4), 621-633 (2012)
   PUBMED   22632720
REFERENCE   9  (bases 1 to 4844)
  AUTHORS   von Engelhardt,J., Mack,V., Sprengel,R., Kavenstock,N., Li,K.W.,
            Stern-Bach,Y., Smit,A.B., Seeburg,P.H. and Monyer,H.
  TITLE     CKAMP44: a brain-specific protein attenuating short-term synaptic
            plasticity in the dentate gyrus
  JOURNAL   Science 327 (5972), 1518-1522 (2010)
   PUBMED   20185686
  REMARK    GeneRIF: CKAMP44 identified as a brain-specific type I
            transmembrane protein that associates with AMPA receptors in
            synaptic spines; findings show that CKAMP44 modulates short-term
            plasticity at specific excitatory synapses
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC154289.1, AK049860.1 and AC129020.4.
            
            On Mar 24, 2010 this sequence version replaced NM_028277.1.
            
            Transcript Variant: This variant (1, also known as CKAMP44a)
            represents the longer transcript and encodes the longer isoform
            (1). Isoform 1 contains an in-frame start site 41 codons upstream
            from the currently annotated site, but signal sequence
            considerations and orthology data support use of the downstream
            AUG.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK049860.1, SRR1660821.124526.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131, SAMN01164132
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            CDS uses downstream in-frame AUG :: downstream AUG is associated
                                                with N-terminal localization
                                                signal
            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
            1-475               AC154289.1         155953-156427       c
            476-3172            AK049860.1         2-2698
            3173-4844           AC129020.4         45860-47531         c
FEATURES             Location/Qualifiers
     source          1..4844
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="16"
                     /map="16 6.89 cM"
     gene            1..4844
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /note="shisa family member 9"
                     /db_xref="GeneID:72555"
                     /db_xref="MGI:MGI:1919805"
     exon            1..1031
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /inference="alignment:Splign:2.1.0"
     CDS             469..1743
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; protein shisa-9; cystine-knot AMPAR modulating
                     protein of 44 kDa; shisa homolog 9"
                     /codon_start=1
                     /product="protein shisa-9 isoform 1 precursor"
                     /protein_id="NP_082553.2"
                     /db_xref="CCDS:CCDS49766.1"
                     /db_xref="GeneID:72555"
                     /db_xref="MGI:MGI:1919805"
                     /translation="MRRVLRLLLGCFLTELCARMCRAQERSGHGQLAQLGGVLLLTGG
                     NRSGAASGEAGEGVGGSDAPPTRAPTPDSCRGYFDVMGQWDPPFNCSSGDFIFCCGTC
                     GFRFCCTFKKRRLNQSTCTNYDTPLWLNTGKPPARKDDPLHDPTKDKTNLIVYIICGV
                     VAVMVLVGIFTKLGLEKAHRPQREHMSRALADVMRPQGHCNTDHMERDLNIVVHVQHY
                     ENMDSRTPINNLHTTQMNNAVPTSPLLQQMGHPHSYPNLGQISNPYEQQPPGKELNKY
                     ASLKAVGNSDGDWAVATLKSPKADKVNDDFYAKRRHLAELAVKGNLPLHPVRVEDEPR
                     AFSPEHGPAQQNGQKSRTNKMPPHPLAYNSTANFKTWDPSDQSLRRQAYGNKGKLGIA
                     ESGSCDPLGTRTQHFPPTQPYFITNSKTEVTV"
     exon            1032..1159
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /inference="alignment:Splign:2.1.0"
     exon            1160..1315
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /inference="alignment:Splign:2.1.0"
     exon            1316..1363
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /inference="alignment:Splign:2.1.0"
     exon            1364..4844
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4824..4829
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /note="hexamer: AATAAA"
     polyA_site      4843
                     /gene="Shisa9"
                     /gene_synonym="2700045P11Rik; Ckamp44"
                     /note="major polyA site"
ORIGIN      
        1 attccacaag tgtcgcttct ctctctctct ccagcgcact tggcgtgcta gagaggtgaa
       61 gagcatcctg cgagcgagcg gacgtgggga gccgagtccc gggtggcggg tggaagggag
      121 ttacggacac agcgactctc tcctgttttc cacccccgcc tcccccggtg gccagcagga
      181 cctgcacccc gcgctggccc ccgctcctgc tccgtccccg cccggccccg gcgcgctcct
      241 ccccggccgg cccccttcct cggcgcgcgt cgcgctggag gcgaacgcag tctgagccga
      301 gcgcagtggc cgccgaccac cgagcgcccc gcgccgcctc cctgcatgtg cggccagcgg
      361 cggcccgcag cccccgccag cagcctcggc agcttcggcc gcgcgtccag aggcggcggt
      421 agcggctcca gcggcggccg agcgctccag cccgggttgg gagacacgat gcgccgagtc
      481 cttcggctgc ttctcggctg cttcctcacc gagctgtgtg cccgcatgtg ccgggcgcag
      541 gagcgatctg ggcacgggca gctagcgcaa ctgggcggcg tactgctgct cacagggggc
      601 aaccgctccg gagccgcctc cggagaggcc ggcgagggcg tcgggggctc ggacgcaccg
      661 ccgactcgag cgcccacgcc agactcctgt cggggctact tcgatgtcat gggccagtgg
      721 gacccgccgt tcaactgcag ctcgggcgac ttcatcttct gctgcgggac ttgtggcttc
      781 cggttctgct gcacgtttaa gaagcggcga ctgaaccaga gcacctgtac caactacgac
      841 acgccactct ggcttaacac gggcaagccc ccagcgcgta aggatgaccc cttgcacgac
      901 cccaccaagg acaagaccaa ccttatcgtc tacatcatct gcggggtggt ggctgtcatg
      961 gtgctggtgg gcatcttcac caagctgggg ctggagaaag cgcaccggcc ccaaagggaa
     1021 cacatgtcca gagcccttgc ggatgtcatg aggccacagg gccactgcaa cactgaccac
     1081 atggagagag accttaacat cgtggtccac gtgcagcatt atgagaacat ggactcaaga
     1141 acccccataa ataatctcca taccactcag atgaacaacg cagtgcccac ttctcctctg
     1201 ctccagcaga tgggacaccc acattcatac cccaacctgg gtcagatttc taatccatat
     1261 gaacagcagc ctccaggcaa agagctcaac aagtacgcct ccttaaaggc agtaggaaat
     1321 tctgatggtg actgggcagt ggcaacgctt aagtcaccaa aagctgacaa ggtcaatgat
     1381 gacttctacg ccaaaagaag gcacctggca gagctggctg tcaagggaaa tctccctttg
     1441 caccctgtaa gagtggaaga tgagcctcgc gccttcagcc cagagcacgg gcctgcacag
     1501 cagaatggac agaagtctcg caccaacaag atgcccccac atcccctggc ctacaactct
     1561 actgccaact ttaagacctg ggaccccagt gaccagtctc tccggcggca ggcttatggc
     1621 aacaagggca agcttggcat agctgagtca ggctcttgtg accccttggg gactcgcacc
     1681 cagcacttcc cacccacaca gccatatttc atcactaaca gcaaaacaga agtgactgtc
     1741 tgagctttta cttcagggag caccctggag accacactca actgaaagag gcaaaaaata
     1801 tcatcccact tacaccttcc tggtcctgta caccccactc ccaacccctc agcagacaca
     1861 cactccgggt gttctacagg aaccaaccac agacctactc ataaggagtc atgcttttcc
     1921 tgggtcatgc ctactatgct cccgcaggca gctgagcgag accgaagcat ggacattcag
     1981 caatatagag gggaaacttt cagcttcagg cccaaattgt gggggctcat ttccttttcc
     2041 cccaagagaa aactgaaatc cattttaaca gatatataag tagcacaatt tagacaaact
     2101 gcccatggag cgcattgggt ccccctgttc tgtctttcct ggtagaagaa aaaggatggg
     2161 cacacgaaga ggagtgtgcc agagtgcttg ggaaggaatt tgctcatgtc acaagcattt
     2221 ccttgtccca agaagtgatg caaacacaga atagtgaaaa gtgtgaggta gtaatggacc
     2281 ctgagtgtca cactgatgga acattgcata ccattgaagc tgaaagcaaa aagctcacaa
     2341 agtaagtctt ctctaagccc ttggtcaatg atggaaaggg gagaacattc taaagaactc
     2401 cctggaagac catgatgttg gcagtgatag gtttttatga tggccaaggg gtccagagaa
     2461 taataaagaa gaacttctaa agtgacacat taaatgaaca cacaaaatat tagttttgcc
     2521 cgggacttag agaacctgca gttggagagt taacagcagg tgagaggcac agaggagcct
     2581 tcacttcccg ggtcatctcc aagaactgga acaaagacaa aaaccatcct ctatgaacag
     2641 tctgtcccca ccactctttc cctttcagcg tgccgctgcc actgctgcca aacttcaact
     2701 gctttggagt gaaaaatgtc ataagtgtgg gtggtgcctt cagtgtgtcg ctgttgttca
     2761 agtgatggtc tcgtttccca agtgcatcct ctgttccttt aaccttcctg cctcctgttt
     2821 tcctgcagta gtgatgttgt ctttcctttg taggtgagcc cagacaatta acaccctttg
     2881 aaggagctgc tacaatgtca gaggtaccta agaatacccc agttcccacc ctcccaccag
     2941 attacctcca ggggcaccct catgccatcc tttcttacct ggactctccc aaagttgcgt
     3001 taaagattgg ttccatcagc cacagccatt ggatcccaac aaggaaggtc cccctgaaag
     3061 tcttttgttt agtggaaggg cagacaggtg catggagagg caagagagtt ttgtttagaa
     3121 agaagagtct gcaactatcc cctggaactc tgagctaatt tacaggaatc ttctaaaacc
     3181 tcacagcttc tttggtgtaa aaatctagtg aaatagaatt ggagcatccc atgtggtgat
     3241 gttctgctgc ctgggctctc ggcatcacag catcagcata ccagatagtt tccatgttcc
     3301 aagcaagtag gaagaatttg gcaatatctt tgatctttcc agggctgtgt cccatctgaa
     3361 gcatggggaa tctgacttaa gtaaagcctt ttcagttttt taaaaacagt actctgttct
     3421 tatttacaaa agaaattctg caaagtccaa actttataag attctaaaaa agaagaggtg
     3481 cagaggctaa cacagaggtc ggagtaaatg ttgagagccc tgcactctcg atagagcagt
     3541 atgagctact ggcttgcaca tctctctttg acatgagtta attatgtcct cgccacacat
     3601 cagcatccgg ggattatcat cacagtattt ggtatctgaa tgcatttgct tttaagccat
     3661 gttattttaa aagggaagca ttttgtattt atcacatata gaacactagc atccattgcc
     3721 atgaacagac aataaacatt atgggaaaca tattggcctc aaagacaaaa ctctagtgga
     3781 catctggcct gctctcttgt ttctcaaaaa gaccttagtc tagttaaaga tactggtaca
     3841 caatagagag tttgtccttg gaataatcca gtgaagggga aagcagatga aaaaaaaaga
     3901 aaacctccct tttttaagtt ggtgttagat cgtgccctct atccatatgc tacctccatg
     3961 acatacaatt tgcatgcact agtgacatac agtcctactt caagaagtac ttacctgaaa
     4021 cgttcttttc aggtcaagtt ctgcaatctt ttccttcctt ccagctcaat ttcccctctc
     4081 cactcccttc acttcccctt catctaactc taacttaaaa gtctttcttg atctttagtc
     4141 tatttcttac tcatccttct ttttgaagat gacttcatcc aagtagacgt ggctccttgg
     4201 tctgcaattg taattttgac ttccaagaca gagtctggcc actagcaggt agcatatact
     4261 tcccaagtaa ttcggtcata gacagctcgc acagtgcttg ctcgttgctt cctgtttgac
     4321 tttgggagat gaactgtgga gtgacaatca gtagagaata tctgtttatt ctttgccttc
     4381 ctcttgggaa ggcagataaa ccttacaata ttgaaagaga acatgaccta tacaataatt
     4441 gaagagaaag agtaagatta taaaactgtt ttcttctcct tccatgtgat ccccaatttc
     4501 taactctatg ggaccagatc ctggcttccc tcaccttcct ggagtcttaa cctccatccg
     4561 ccttgggctc tgcctggaat tcccatctaa cctcccccag attttttttt ttgtgtgtgt
     4621 gtataaatgg agcatatttt atgtgcaaat attttagtaa ccgtatgttc tgcaagtaaa
     4681 cctgtgttaa cacttgtcac actgcagagt ttatgataca ataacacttc ctacaatgaa
     4741 gaaaaaaaca tttgtttgtt ttctaagaat gtttatttgt aaacatatgt attcactata
     4801 ttaatatgaa tttcttacct ggcaataaac tgattatatg tgat
//
