LOCUS       NM_001013362            4891 bp    mRNA    linear   ROD 02-MAY-2024
DEFINITION  Mus musculus neuronal pentraxin chromo domain (Npcd), transcript
            variant 2, mRNA.
ACCESSION   NM_001013362
VERSION     NM_001013362.2
KEYWORDS    RefSeq.
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 4891)
  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 4891)
  AUTHORS   Tseng,L.A. and Bixby,J.L.
  TITLE     Interaction of an intracellular pentraxin with a BTB-Kelch protein
            is associated with ubiquitylation, aggregation and neuronal
            apoptosis
  JOURNAL   Mol Cell Neurosci 47 (4), 254-264 (2011)
   PUBMED   21549840
REFERENCE   3  (bases 1 to 4891)
  AUTHORS   Chen,B. and Bixby,J.L.
  TITLE     A novel substrate of receptor tyrosine phosphatase PTPRO is
            required for nerve growth factor-induced process outgrowth
  JOURNAL   J Neurosci 25 (4), 880-888 (2005)
   PUBMED   15673668
  REMARK    GeneRIF: We confirm that NPCD isoforms interact with the catalytic
            phosphatase domain of PTPRO and also that NPCD is likely to be
            relevant to axon growth and/or guidance.
REFERENCE   4  (bases 1 to 4891)
  AUTHORS   Chen,B. and Bixby,J.L.
  TITLE     Neuronal pentraxin with chromo domain (NPCD) is a novel class of
            protein expressed in multiple neuronal domains
  JOURNAL   J Comp Neurol 481 (4), 391-402 (2005)
   PUBMED   15593341
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC113595.11, AY394489.1, AC118227.12, CD578976.1 and BC060093.1.
            
            On Aug 29, 2006 this sequence version replaced NM_001013362.1.
            
            Summary: This gene encodes multiple cytoplasmic proteins composed
            of a neuronal pentraxin domain linked to a chromo domain. These
            isoforms are expressed in numerous regions of the central nervous
            system, where they are present in distinct subcellular arrangements
            in different brain regions. This gene may play a role in neuronal
            differentiation. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (2) represents the longer
            transcript and encodes the longer isoform (2).
            
            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 :: AY394489.1, SRR7345562.1636447.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849379, SAMN01164133
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            readthrough transcript :: includes exons from GeneID 73340, 494448
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-96                AC113595.11        49139-49234         c
            97-683              AY394489.1         2-588
            684-685             AC118227.12        182669-182670       c
            686-1413            CD578976.1         1-728
            1414-2487           AC118227.12        176956-178029       c
            2488-4891           BC060093.1         1-2404
FEATURES             Location/Qualifiers
     source          1..4891
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="15"
                     /map="15 37.85 cM"
     gene            1..4891
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /note="neuronal pentraxin chromo domain"
                     /db_xref="GeneID:504193"
                     /db_xref="MGI:MGI:3845555"
     exon            1..191
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     CDS             123..1532
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /note="isoform 2 is encoded by transcript variant 2;
                     neuronal pentraxin with chromo domain; Cbx6-Nptxr
                     readthrough transcripts"
                     /codon_start=1
                     /product="neuronal pentraxin with chromo domain isoform 2"
                     /protein_id="NP_001013380.2"
                     /db_xref="GeneID:504193"
                     /db_xref="MGI:MGI:3845555"
                     /translation="MELSAVGERVFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEP
                     EENILDSRLIAAFEQKERERELYGPKKRGPKPKTFLLKARAQAEALRISDVHFSVKPS
                     ASASSPKLHSSAAVHRLKKDIRRCHRMSRRPLPRPDPQGGSPGLRPPISPFSETVRII
                     NRKVKPREPKRNRIILNLKQELPARGNISSAPAPAMPTALHSKMDELEGQLLAKVLAL
                     EKERAALSHGSHQQRQEVEKELNALQGRVAELEHGSSAYSPPDAFKVSIPIRNNYMYA
                     RVRKALPELYAFTACMWLRSRSGGSGQGTPFSYSVPGQANEIVLLEAGLEPMELLIND
                     KVAQLPLSLKDSNWHHICISWTTRDGLWSAYQDGELRGSGENLAAWHPIKPHGILILG
                     QEQDTLGGRFDATQAFVGDIAQFNLWDHALTPAQVLGMANCTGPLMGNVLPWEDKLVE
                     AFGGAKKAAFDVCKGRAKA"
     exon            192..235
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     exon            236..301
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     exon            302..368
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     exon            369..659
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     exon            660..879
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     exon            880..1127
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     exon            1128..1307
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     exon            1308..4873
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4852..4857
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /note="hexamer: AATAAA"
     polyA_site      4873
                     /gene="Npcd"
                     /gene_synonym="Cbx6-Nptxr"
                     /note="major polyA site"
ORIGIN      
        1 gagcgcgcgc cccgccgagc gcccgcccgc cgggggcctg agcgctgggg cgcgtgcgcg
       61 agcggtgcag caccggccgc gggagcaggg agtattatgg gctgtgggtg ccgctgagca
      121 agatggagct gtctgcagta ggcgagcggg tcttcgcggc cgaatccatc attaaacgcc
      181 ggatccgcaa gggacgcatc gagtacctgg tgaaatggaa agggtgggcg atcaagtaca
      241 gcacttggga gccagaggag aacattctgg attcgaggct catcgcagcc ttcgagcaga
      301 aggaaaggga acgtgagctg tatgggccca agaagagggg acctaaaccc aaaactttcc
      361 tcctaaaggc ccgggcccag gcggaggccc tccgcatcag tgatgtgcat ttctctgtca
      421 agccgagcgc cagcgcctcc tcgcccaagc tgcactccag cgctgcggtg caccggctca
      481 agaaagacat ccgccgctgc caccgtatgt ctcgccgtcc cctgccacga ccagacccac
      541 aagggggtag ccctggccta cgcccaccca tctcgccctt ttctgagacc gtgcgcatca
      601 tcaaccgtaa ggtgaagccc cgggagccca agcggaaccg catcatcctg aacctgaagc
      661 aggagctccc agcccgtggg aacatctcct cggcgccagc tccagccatg cccaccgccc
      721 tgcactccaa gatggacgaa ctagaaggcc agctgctggc caaggtgctg gcgctggaga
      781 aggagcgagc cgccctcagt cacgggagcc accagcaacg acaggaagtg gagaaggagc
      841 tgaatgccct gcagggtcgc gtggccgagc tggagcacgg gtcctcggcc tacagtcccc
      901 ctgatgcctt caaggtcagc atccccatcc gcaacaacta catgtacgcc cgcgtgcgca
      961 aggcgctgcc ggaactctac gccttcactg cctgcatgtg gctgcgctcc aggtcaggtg
     1021 gctccggcca gggcaccccc ttctcctact cggtgcccgg gcaggccaat gagatcgtgc
     1081 ttctggaggc cggccttgag ccaatggagc tgctgatcaa cgacaaggtg gcccagctgc
     1141 ccctgagcct gaaagacagc aactggcacc atatctgcat ctcctggact acaagggatg
     1201 ggctgtggtc tgcataccag gacggagaac tgcggggttc tggcgagaac ctagcagcct
     1261 ggcaccccat caagccacac ggcatcctta tcctgggcca agagcaggat accttgggag
     1321 gccgatttga cgccacacag gccttcgttg gtgacattgc acagttcaac ctgtgggacc
     1381 acgctctgac accggcccag gtgctgggca tggccaactg caccgggcca ctgatgggca
     1441 atgtcctccc ctgggaagat aagctggtag aggcctttgg aggtgcgaag aaggccgcct
     1501 ttgatgtgtg caaggggagg gcaaaggcat gaggggccac cttgttcagg gcccctccat
     1561 tgcctgtcag tttcaggact ttgaaggggc aatccctcct cagcctgtct acacgccggc
     1621 cttcccttct accccactcc tggctatacc tcccacttct cctcatgggc acccactgct
     1681 ccagagtgcc ctgccctgga tgggtgtccc ctcagccacc tggataggga ccagtatctc
     1741 acatcaatgt aggggttgag gcagtcccgc ctcctggcaa tgtattggct tggtctctcc
     1801 catcatatac actgtcctgc cgatcacatc ggaccccact aattccaagg acatccccta
     1861 aggagtcgtg ggtagaggta gcctttgacc ctcaaatccc ctatgctcca ggcctacctc
     1921 gggctgcaga agggatgcca gagatgtata aagatcagac gctccttctc tatcttcctg
     1981 ggttactcac aggggctgcg gggtcatcgc tcccactgcc cctgccttgc cctccctcct
     2041 ctcaccagtt tctctgtgtg ttgtggtttg aatgttggtt tcatgtcggt tcaagcctca
     2101 cctcagtttc caggatgttc cttccccagc ccctacccta acagctaggg accaaaaccc
     2161 tggaggccaa agggctgtaa tcaccccctg tacccactgg caactttgcc caccagcagg
     2221 gttgtccacc ccaccccctc catgcctgag acaggacctg ctgggtcact ctagcctgtc
     2281 ctgagaacat ctaaaacaga ggcacaatga atgaggggat gcttcccagg cagagcctgg
     2341 tggcttagcc accatatcac ctctttctgc atggccctgg aaaggatgga ggatgctggg
     2401 atggaaagca gaacactgag agagagagag agagagagag agagagagag agagagagag
     2461 agagaacccc taggttctta tgacttgctg tgtggctttc agtaagaacc taccctctct
     2521 gggcctcgct ttctcctagt ccctaccaac ttccccaaga gcacagaaga atgtcagagc
     2581 tgagaaaaac catccattgt aagctcttgc tggtgagaga tggaaaagag cacagagagg
     2641 gccattaact tgtctaggat caaacagcac aacatagcag gcccaggccc tctgagtccc
     2701 tccaaagtgc tcttccctgt gaaccacact gcctgtcctt gagccctgct tatacctgtg
     2761 cagggaggca cttgagagga cacgtgcttt cacacagggt accaaaatat cttctgggga
     2821 caccccaaca ccttgacagc ctgaggaggt gagaggaaaa gcccagacag acagagttcc
     2881 aacagacagc agaggatgca aggccctgtt ggtcctctcc catggattgg aacagtagca
     2941 ggttgggtga atcactgggc accggtgcct cttgccctac cccacccacc acttttgtcc
     3001 gtctgtgctc tccatggcca ctcagcccga gacgtgacgc aggagaggct gcagcccatg
     3061 tcagggaagc atggccgaga ctcgcctctg ggctgcagat ctgcatttcc attttgagag
     3121 caactacacg gcacagcacc ccccatcccc atcccctgga gagagctgca gaggcttcac
     3181 ccagaacctg ctgagatccc ggttgcccag taacaaccaa tgacatcagc cccagtgcta
     3241 ggtcaagtgt cttttgtgag gacaccggtt gttgctgggt gacagctgga ttcagaactt
     3301 agacctgggg gactctaagc tgcactgggc tcctgctatt gttctagaag aggcctttgc
     3361 tattgattta gaggaggcct tgggaagaca gcatcttagg aaggatgtag cagaaactgc
     3421 ctgctcactg gagcccacca gacacaccat ccccatcctt ttgctttgtc tcagtggtga
     3481 tgagaaacag cacctcagtc acatttccat gccaggtcac cctggttaaa ctgccacctc
     3541 cccaccccaa ccccacccag gaggggaaaa aacagaggca cctggtcaag gctctgtgta
     3601 tggattactg gggaaggggc tgcctctcta tttcccaagt ccccacctgc tctcatctat
     3661 tgtgctgtga acattctctg agcatgtgga gcccccactc aatcttctgc tgtctcccca
     3721 agcacatcca acaagacagc tgcggccctg agttgcccct gggtctgaca aagatggaac
     3781 taggctggtt aggtagtctt aggcctggag acagcacgga gcacggtatc cgcaccatct
     3841 ggtttatcct cacagcacaa agcgagactg ttcttagccc tgtggtgcac aagagaagga
     3901 tgagaggtaa agtaacttgc ccagtgttga ttggccagcc gggaacagcg cgatttccat
     3961 ttggaggcag gttagatgcc taaaggtcca cgccacctcc ttcagagtgc agaaggagca
     4021 gaggtggggg tgtggggcgt gaagccaggg agggaggggt ctctcaccta tgcccagcct
     4081 cagcctcagc ctgagctgca gtctaagggc aagaaaggag tatctttaga ggtcgtcaga
     4141 aaaggcaggg tggaagtggt tcttgctcgg cccctgttct gggcacgacc tatgtcaggt
     4201 tctctaagct gttttctgcc agatctccta tctgtgaggc atggagtggc cactcccatg
     4261 tcccaagggt catcttacca cagttacatg tgaatgggga ccacagactg aagtatgagg
     4321 atctgttggg ggttgggggg ggtgtaactc aacccttggc ttgtagatga gggagctgag
     4381 gtctggccag gaagctcaaa tgaccctgga agttcccttg actgtccttc tcttctccag
     4441 gacccggtgg tcactccctt cccttgcaaa ctgaattcct atctactagt cccagcacct
     4501 ttggcctgag agaaaactgg agaaggttct cctcccaaat tagggactag tatcctcctt
     4561 accccttaac tccagctgcc tgccacccct gatcccgcct tccacccacc ctattccctg
     4621 cccctgctgg atggagaaca gactccttcc ctggctgagc cgccagcagc gagcatgtga
     4681 agtcatctgg ttggacactt tggaacgagg accctccact gccctcctcc cccaccttgc
     4741 cctattttgt acataagtaa cacgagatgc tctgtatgtg tgagtgcgtg tgtgatctgt
     4801 gccatggctt ttgttaccat ttcttgtttt tttgtaaatt tgaatgttca aaataaaacg
     4861 tggtttactc ggaaaaaaaa aaaaaaaaaa a
//
