LOCUS       NM_001081343            3151 bp    mRNA    linear   ROD 09-FEB-2025
DEFINITION  Mus musculus C9orf72, member of C9orf72-SMCR8 complex (C9orf72),
            transcript variant 1, mRNA.
ACCESSION   NM_001081343 XM_896098
VERSION     NM_001081343.2
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 3151)
  AUTHORS   Meng,Q., Chen,J., Liang,Y., Zhang,X., Ding,J., Fang,Y. and Hu,G.
  TITLE     miR-142-3p alleviates neuronal apoptosis in Parkinson's disease via
            negatively regulating C9orf72
  JOURNAL   Neurosci Lett 836, 137887 (2024)
   PUBMED   38942112
  REMARK    GeneRIF: miR-142-3p alleviates neuronal apoptosis in Parkinson's
            disease via negatively regulating C9orf72.
REFERENCE   2  (bases 1 to 3151)
  AUTHORS   Nelson,A.T., Cicardi,M.E., Markandaiah,S.S., Han,J.Y., Philp,N.J.,
            Welebob,E., Haeusler,A.R., Pasinelli,P., Manfredi,G., Kawamata,H.
            and Trotti,D.
  TITLE     Glucose hypometabolism prompts RAN translation and exacerbates
            C9orf72-related ALS/FTD phenotypes
  JOURNAL   EMBO Rep 25 (5), 2479-2510 (2024)
   PUBMED   38684907
  REMARK    GeneRIF: Glucose hypometabolism prompts RAN translation and
            exacerbates C9orf72-related ALS/FTD phenotypes.
REFERENCE   3  (bases 1 to 3151)
  AUTHORS   Ounissi,M., Latouche,M. and Racoceanu,D.
  TITLE     PhagoStat a scalable and interpretable end to end framework for
            efficient quantification of cell phagocytosis in neurodegenerative
            disease studies
  JOURNAL   Sci Rep 14 (1), 6482 (2024)
   PUBMED   38499658
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3151)
  AUTHORS   Limone,F., Couto,A., Wang,J.Y., Zhang,Y., McCourt,B., Huang,C.,
            Minkin,A., Jani,M., McNeer,S., Keaney,J., Gillet,G., Gonzalez,R.L.,
            Goodman,W.A., Kadiu,I., Eggan,K. and Burberry,A.
  TITLE     Myeloid and lymphoid expression of C9orf72 regulates IL-17A
            signaling in mice
  JOURNAL   Sci Transl Med 16 (732), eadg7895 (2024)
   PUBMED   38295187
  REMARK    GeneRIF: Myeloid and lymphoid expression of C9orf72 regulates
            IL-17A signaling in mice.
REFERENCE   5  (bases 1 to 3151)
  AUTHORS   Tang,D., Zheng,K., Zhu,J., Jin,X., Bao,H., Jiang,L., Li,H.,
            Wang,Y., Lu,Y., Liu,J., Liu,H., Tang,C., Feng,S., Dong,X., Xu,L.,
            Yin,Y., Dang,S., Wei,X., Ren,H., Dong,B., Dai,L., Cheng,W., Wan,M.,
            Li,Z., Chen,J., Li,H., Kong,E., Wang,K., Lu,K. and Qi,S.
  TITLE     ALS-linked C9orf72-SMCR8 complex is a negative regulator of primary
            ciliogenesis
  JOURNAL   Proc Natl Acad Sci U S A 120 (50), e2220496120 (2023)
   PUBMED   38064514
  REMARK    GeneRIF: ALS-linked C9orf72-SMCR8 complex is a negative regulator
            of primary ciliogenesis.
REFERENCE   6  (bases 1 to 3151)
  AUTHORS   Chew,J., Gendron,T.F., Prudencio,M., Sasaguri,H., Zhang,Y.J.,
            Castanedes-Casey,M., Lee,C.W., Jansen-West,K., Kurti,A.,
            Murray,M.E., Bieniek,K.F., Bauer,P.O., Whitelaw,E.C., Rousseau,L.,
            Stankowski,J.N., Stetler,C., Daughrity,L.M., Perkerson,E.A.,
            Desaro,P., Johnston,A., Overstreet,K., Edbauer,D., Rademakers,R.,
            Boylan,K.B., Dickson,D.W., Fryer,J.D. and Petrucelli,L.
  TITLE     Neurodegeneration. C9ORF72 repeat expansions in mice cause TDP-43
            pathology, neuronal loss, and behavioral deficits
  JOURNAL   Science 348 (6239), 1151-1154 (2015)
   PUBMED   25977373
REFERENCE   7  (bases 1 to 3151)
  AUTHORS   Farg,M.A., Sundaramoorthy,V., Sultana,J.M., Yang,S., Atkinson,R.A.,
            Levina,V., Halloran,M.A., Gleeson,P.A., Blair,I.P., Soo,K.Y.,
            King,A.E. and Atkin,J.D.
  TITLE     C9ORF72, implicated in amytrophic lateral sclerosis and
            frontotemporal dementia, regulates endosomal trafficking
  JOURNAL   Hum Mol Genet 23 (13), 3579-3595 (2014)
   PUBMED   24549040
  REMARK    Erratum:[Hum Mol Genet. 2017 Oct 15;26(20):4093-4094. doi:
            10.1093/hmg/ddx309.. PMID: 28973528]
REFERENCE   8  (bases 1 to 3151)
  AUTHORS   Suzuki,N., Maroof,A.M., Merkle,F.T., Koszka,K., Intoh,A.,
            Armstrong,I., Moccia,R., Davis-Dusenbery,B.N. and Eggan,K.
  TITLE     The mouse C9ORF72 ortholog is enriched in neurons known to
            degenerate in ALS and FTD
  JOURNAL   Nat Neurosci 16 (12), 1725-1727 (2013)
   PUBMED   24185425
REFERENCE   9  (bases 1 to 3151)
  AUTHORS   Lagier-Tourenne,C., Baughn,M., Rigo,F., Sun,S., Liu,P., Li,H.R.,
            Jiang,J., Watt,A.T., Chun,S., Katz,M., Qiu,J., Sun,Y., Ling,S.C.,
            Zhu,Q., Polymenidou,M., Drenner,K., Artates,J.W.,
            McAlonis-Downes,M., Markmiller,S., Hutt,K.R., Pizzo,D.P., Cady,J.,
            Harms,M.B., Baloh,R.H., Vandenberg,S.R., Yeo,G.W., Fu,X.D.,
            Bennett,C.F., Cleveland,D.W. and Ravits,J.
  TITLE     Targeted degradation of sense and antisense C9orf72 RNA foci as
            therapy for ALS and frontotemporal degeneration
  JOURNAL   Proc Natl Acad Sci U S A 110 (47), E4530-E4539 (2013)
   PUBMED   24170860
REFERENCE   10 (bases 1 to 3151)
  AUTHORS   Panda,S.K., Wefers,B., Ortiz,O., Floss,T., Schmid,B., Haass,C.,
            Wurst,W. and Kuhn,R.
  TITLE     Highly efficient targeted mutagenesis in mice using TALENs
  JOURNAL   Genetics 195 (3), 703-713 (2013)
   PUBMED   23979585
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL831776.3.
            
            On May 4, 2018 this sequence version replaced NM_001081343.1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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 :: AK154817.1, AK167354.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849381, SAMN01164138
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            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
            1-49                AL831776.3         51609-51657         c
            50-552              AL831776.3         44235-44737         c
            553-612             AL831776.3         43034-43093         c
            613-708             AL831776.3         39370-39465         c
            709-773             AL831776.3         38830-38894         c
            774-846             AL831776.3         37113-37185         c
            847-963             AL831776.3         31589-31705         c
            964-1199            AL831776.3         22794-23029         c
            1200-1257           AL831776.3         19958-20015         c
            1258-1367           AL831776.3         19006-19115         c
            1368-3151           AL831776.3         17106-18889         c
FEATURES             Location/Qualifiers
     source          1..3151
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="4"
                     /map="4 17.13 cM"
     gene            1..3151
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /note="C9orf72, member of C9orf72-SMCR8 complex"
                     /db_xref="GeneID:73205"
                     /db_xref="MGI:MGI:1920455"
     exon            1..49
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            50..552
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     CDS             109..1554
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /note="isoform 1 is encoded by transcript variant 1;
                     protein C9orf72 homolog; guanine nucleotide exchange
                     C9orf72 homolog; guanine nucleotide exchange factor
                     C9orf72 homolog"
                     /codon_start=1
                     /product="guanine nucleotide exchange factor C9orf72
                     homolog isoform 1"
                     /protein_id="NP_001074812.1"
                     /db_xref="CCDS:CCDS38708.1"
                     /db_xref="GeneID:73205"
                     /db_xref="MGI:MGI:1920455"
                     /translation="MSTICPPPSPAVAKTEIALSGESPLLAATFAYWDNILGPRVRHI
                     WAPKTDQVLLSDGEITFLANHTLNGEILRNAESGAIDVKFFVLSEKGVIIVSLIFDGN
                     WNGDRSTYGLSIILPQTELSFYLPLHRVCVDRLTHIIRKGRIWMHKERQENVQKIVLE
                     GTERMEDQGQSIIPMLTGEVIPVMELLASMKSHSVPEDIDIADTVLNDDDIGDSCHEG
                     FLLNAISSHLQTCGCSVVVGSSAEKVNKIVRTLCLFLTPAERKCSRLCEAESSFKYES
                     GLFVQGLLKDATGSFVLPFRQVMYAPYPTTHIDVDVNTVKQMPPCHEHIYNQRRYMRS
                     ELTAFWRATSEEDMAQDTIIYTDESFTPDLNIFQDVLHRDTLVKAFLDQVFHLKPGLS
                     LRSTFLAQFLLILHRKALTLIKYIEDDTQKGKKPFKSLRNLKIDLDLTAEGDLNIIMA
                     LAEKIKPGLHSFIFGRPFYTSVQERDVLMTF"
     exon            553..612
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            613..708
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            709..773
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            774..846
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            847..963
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            964..1199
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            1200..1257
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            1258..1367
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     exon            1368..3151
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3129..3134
                     /regulatory_class="polyA_signal_sequence"
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /note="hexamer: AATAAA"
     polyA_site      3151
                     /gene="C9orf72"
                     /gene_synonym="3110043O21Rik; Dennd9"
                     /note="major polyA site"
ORIGIN      
        1 gcggttgcgg tccctgcgcc ggcggtgaag gcgcagcagc ggcgagtggc tattgcaagc
       61 gttcggataa tgtgagacct ggaatgcagt gagacctggg atgcagggat gtcgactatc
      121 tgccccccac catctcctgc tgttgccaag acagagattg ctttaagtgg tgaatcaccc
      181 ttgttggcgg ctacctttgc ttactgggat aatattcttg gtcctagagt aaggcatatt
      241 tgggctccaa agacagacca agtgcttctc agtgatggag aaataacttt tcttgccaac
      301 cacactctaa atggagaaat tcttcgaaat gcagagagtg gggctataga tgtaaaattt
      361 tttgtcttat ctgaaaaagg ggtaattatt gtttcattaa tcttcgacgg aaactggaat
      421 ggagatcgga gcacttatgg actatcaatt atactgccgc agacagagct gagcttctac
      481 ctcccacttc acagagtgtg tgttgacagg ctaacacaca ttattcgaaa aggaagaata
      541 tggatgcata aggaaagaca agaaaatgtc cagaaaattg tcttggaagg cacagagagg
      601 atggaagatc agggtcagag tatcattccc atgcttactg gggaagtcat tcctgtaatg
      661 gagctgcttg catctatgaa atcccacagt gttcctgaag acattgatat agctgataca
      721 gtgctcaatg atgatgacat tggtgacagc tgtcacgaag gctttcttct caatgccatc
      781 agctcacacc tgcagacctg tggctgttcc gttgtagttg gcagcagtgc agagaaagta
      841 aataagatag taagaacgct gtgccttttt ctgacaccag cagagaggaa atgctccagg
      901 ctgtgtgaag cagaatcgtc ctttaagtac gaatcgggac tctttgtgca aggcttgcta
      961 aaggatgcaa caggcagttt tgtcctaccc ttccggcaag ttatgtatgc cccgtacccc
     1021 accacgcaca ttgatgtgga tgtcaacact gtcaagcaga tgccaccgtg tcatgaacat
     1081 atttataatc aacgcagata catgaggtca gagctgacag ccttctggag ggcaacttca
     1141 gaagaggaca tggcgcagga caccatcatc tacacagatg agagcttcac tcctgatttg
     1201 aatattttcc aagatgtctt acacagagac actctagtga aagccttcct ggatcaggtc
     1261 ttccatttga agcctggcct gtctctcagg agtactttcc ttgcacagtt cctcctcatt
     1321 cttcacagaa aagccttgac actaatcaag tacatcgagg atgatacgca gaaggggaaa
     1381 aagcccttta agtctcttcg gaacctgaag atagatcttg atttaacagc agagggcgat
     1441 cttaacataa taatggctct agctgagaaa attaagccag gcctacactc tttcatcttt
     1501 gggagacctt tctacactag tgtacaagaa cgtgatgttc taatgacctt ttgaccgtgt
     1561 ggtttgctgt gtctgtctct tcacagtcac acctgctgtt acagtgtctc agcagtgtgt
     1621 gggcacatcc ttcctcccga gtcctgctgc aggacagggt acactacact tgtcagtaga
     1681 agtctgtacc tgatgtcagg tgcatcgtta cagtgaatga ctcttcctag aatagatgta
     1741 ctcttttagg gccttatgtt tacaattatc ctaagtacta ttgctgtctt ttaaagatat
     1801 gaatgatgga atatacactt gaccataact gctgattggt tttttgtttt gttttgtttg
     1861 ttttcttgga aacttatgat tcctggttta catgtaccac actgaaaccc tcgttagctt
     1921 tacagataaa gtgtgagttg acttcctgcc cctctgtgtt ctgtggtatg tccgattact
     1981 tctgccacag ctaaacatta gagcatttaa agtttgcagt tcctcagaaa ggaacttagt
     2041 ctgactacag attagttctt gagagaagac actgataggg cagagctgta ggtgaaatca
     2101 gttgttagcc cttcctttat agacgtagtc cttcagattc ggtctgtaca gaaatgccga
     2161 ggggtcatgc atgggccctg agtatcgtga cctgtgacaa gttttttgtt ggtttattgt
     2221 agttctgtca aagaaagtgg catttgtttt tataattgtt gccaactttt aaggttaatt
     2281 ttcattattt ttgagccgaa ttaaaatgcg cacctcctgt gcctttccca atcttggaaa
     2341 atataatttc ttggcagagg gtcagatttc agggcccagt cactttcatc tgaccaccct
     2401 ttgcacggct gccgtgtgcc tggcttagat tagaagtcct tgttaagtat gtcagagtac
     2461 attcgctgat aagatctttg aagagcaggg aagcgtcttg cctctttcct ttggtttctg
     2521 cctgtactct ggtgtttccc gtgtcacctg catcatagga acagcagaga aatctgaccc
     2581 agtgctattt ttctaggtgc tactatggca aactcaagtg gtctgtttct gttcctgtaa
     2641 cgttcgacta tctcgctagc tgtgaagtac tgattagtgg agttctgtgc aacagcagtg
     2701 taggagtata cacaaacaca aatatgtgtt tctatttaaa actgtggact tagcataaaa
     2761 agggagaata tatttatttt ttacaaaagg gataaaaatg ggccccgttc ctcacccacc
     2821 agatttagcg agaaaaagct ttctattctg aaaggtcacg gtggctttgg cattacaaat
     2881 cagaacaaca cacactgacc atgatggctt gtgaactaac tgcaaggcac tccgtcatgg
     2941 taagcgagta ggtcccacct cctagtgtgc cgctcattgc tttacacagt agaatcttat
     3001 ttgagtgcta attgttgtct ttgctgcttt actgtgttgt tatagaaaat gtaagctgta
     3061 cagtgaataa gttattgaag catgtgtaaa cactgttata tatcttttct cctagatggg
     3121 gaattttgaa taaaatacct ttgaaattct g
//
