LOCUS       NM_019649               4147 bp    mRNA    linear   ROD 09-FEB-2025
DEFINITION  Mus musculus cleft lip and palate associated transmembrane protein
            1 (Clptm1), mRNA.
ACCESSION   NM_019649
VERSION     NM_019649.2
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 4147)
  AUTHORS   Ge,Y. and Craig,A.M.
  TITLE     Haploinsufficiency of GABAA Receptor-Associated Clptm1 Enhances
            Phasic and Tonic Inhibitory Neurotransmission, Suppresses
            Excitatory Synaptic Plasticity, and Impairs Memory
  JOURNAL   J Neurosci 44 (32), e0521242024 (2024)
   PUBMED   38942471
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4147)
  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   3  (bases 1 to 4147)
  AUTHORS   Ge,Y., Kang,Y., Cassidy,R.M., Moon,K.M., Lewis,R., Wong,R.O.L.,
            Foster,L.J. and Craig,A.M.
  TITLE     Clptm1 Limits Forward Trafficking of GABAA Receptors to Scale
            Inhibitory Synaptic Strength
  JOURNAL   Neuron 97 (3), 596-610 (2018)
   PUBMED   29395912
  REMARK    GeneRIF: Study shows that in complement to other GABAAR-associated
            proteins that promote receptor surface expression, Clptm1 limits
            GABAAR forward trafficking and regulates inhibitory homeostatic
            plasticity.
REFERENCE   4  (bases 1 to 4147)
  AUTHORS   Taniwaki,T., Haruna,K., Nakamura,H., Sekimoto,T., Oike,Y.,
            Imaizumi,T., Saito,F., Muta,M., Soejima,Y., Utoh,A., Nakagata,N.,
            Araki,M., Yamamura,K. and Araki,K.
  TITLE     Characterization of an exchangeable gene trap using pU-17 carrying
            a stop codon-beta geo cassette
  JOURNAL   Dev Growth Differ 47 (3), 163-172 (2005)
   PUBMED   15840001
REFERENCE   5  (bases 1 to 4147)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
REFERENCE   6  (bases 1 to 4147)
  AUTHORS   Araki,K., Imaizumi,T., Sekimoto,T., Yoshinobu,K., Yoshimuta,J.,
            Akizuki,M., Miura,K., Araki,M. and Yamamura,K.
  TITLE     Exchangeable gene trap using the Cre/mutated lox system
  JOURNAL   Cell Mol Biol (Noisy-le-grand) 45 (5), 737-750 (1999)
   PUBMED   10512203
REFERENCE   7  (bases 1 to 4147)
  AUTHORS   Miyazawa,H., Takeuchi,T. and Yamamoto,H.
  TITLE     Structure and promoter region of the surface membrane protein HS9
            gene expressed on the thymic epithelial cells
  JOURNAL   Biochim Biophys Acta 1444 (3), 407-411 (1999)
   PUBMED   10095063
REFERENCE   8  (bases 1 to 4147)
  AUTHORS   Yoshiura,K., Machida,J., Daack-Hirsch,S., Patil,S.R.,
            Ashworth,L.K., Hecht,J.T. and Murray,J.C.
  TITLE     Characterization of a novel gene disrupted by a balanced
            chromosomal translocation t(2;19)(q11.2;q13.3) in a family with
            cleft lip and palate
  JOURNAL   Genomics 54 (2), 231-240 (1998)
   PUBMED   9828125
REFERENCE   9  (bases 1 to 4147)
  AUTHORS   Takeuchi,T., Kuro-o,M., Miyazawa,H., Ohtsuki,Y. and Yamamoto,H.
  TITLE     Transgenic expression of a novel thymic epithelial cell antigen
            stimulates abberant development of thymocytes
  JOURNAL   J Immunol 159 (2), 726-733 (1997)
   PUBMED   9218588
REFERENCE   10 (bases 1 to 4147)
  AUTHORS   Takeuchi,T., Tamamoto,T., Tamura,H. and Yamamoto,H.
  TITLE     Characterization of a 50 kDa surface membrane protein on thymic
            stromal cells as an important factor for early T cell development
  JOURNAL   Int Immunol 7 (4), 583-590 (1995)
   PUBMED   7547685
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BY288640.1, AK152410.1, AK165742.1 and AI844337.1.
            
            On May 27, 2006 this sequence version replaced NM_019649.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660811.126799.1,
                                           SRR1660817.280970.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849380, SAMN01164131
                                           [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
            1-11                BY288640.1         5-15
            12-1461             AK152410.1         2-1451
            1462-4125           AK165742.1         2156-4819
            4126-4147           AI844337.1         1-22                c
FEATURES             Location/Qualifiers
     source          1..4147
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="7"
                     /map="7 9.93 cM"
     gene            1..4147
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /note="cleft lip and palate associated transmembrane
                     protein 1"
                     /db_xref="GeneID:56457"
                     /db_xref="MGI:MGI:1927155"
     exon            1..97
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     CDS             26..2020
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /note="thymic epithelial cell surface antigen; cleft lip
                     and palate transmembrane protein 1 homolog"
                     /codon_start=1
                     /product="putative lipid scramblase CLPTM1"
                     /protein_id="NP_062623.2"
                     /db_xref="CCDS:CCDS39800.1"
                     /db_xref="GeneID:56457"
                     /db_xref="MGI:MGI:1927155"
                     /translation="MAAAQEADGAGSAVVAAGGGSSGQVTSNGSIGRDTPAETQPQNP
                     PPQPAPNAWQVIKGVLFRIFIIWAISSWFRRGPSPQDQSGPGGAPRVASRNLFPKDTL
                     MNLHVYISEHEHFTDFNATSALFWEQHDLVYGDWTSGENSDGCYEHFAELDIPQSVQQ
                     NGSIYIHVYFTKSGFHPDPRQKALYRRLATVHMSRMINKYKRRRFQKTKNLLTGETEA
                     DPEMIKRAEDYGPVEVISHWHPNITINIVDDHTPWVKGSVPPPLDQYVKFDAVSGDYY
                     PIIYFNDYWNLQKDYYPINESLASLPLRVSFCPLSLWRWQLYAAQSTKSPWNFLGDEL
                     YEQSDEEQDSVKVALLETSPYLLALTIIVSIVHSVFEFLAFKNDIQFWNSRQSLEGLS
                     VRSVFFGVFQSFVVLLYILDNETNFVVQVSVFIGVLIDLWKITKVMDVRLDREHRVAG
                     IFPCPTFKDKSTYIESSTKVYDDMAFRYLSWILFPLLGCYAVYSLLYLEHKGWYSWVL
                     SMLYGFLLTFGFITMTPQLFINYKLKSVAHLPWRMLTYKALNTFIDDLFAFVIKMPVM
                     YRIGCLRDDVVFFIYLYQRWIYRVDPTRVNEFGMSGEDVSAAASRAQASTAAGALTPA
                     PSTAVSGEDASTVPKATSGACTASQPQEAPPKPAEDKKKD"
     exon            98..210
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            211..334
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            335..493
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            494..611
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            612..697
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            698..818
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            819..1063
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            1064..1157
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            1158..1348
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            1349..1444
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            1445..1580
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            1581..1748
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     exon            1749..4131
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2437..2442
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /note="hexamer: AATAAA"
     polyA_site      2470
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /note="major polyA site"
     polyA_site      2607
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
     regulatory      4107..4112
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
                     /note="hexamer: AATAAA"
     polyA_site      4127
                     /gene="Clptm1"
                     /gene_synonym="HS9; N14"
ORIGIN      
        1 gggggcgggg acccggagca ggaagatggc ggcggcgcag gaggcggacg gggccggcag
       61 cgccgtggtg gcggccgggg gaggcagctc tggtcaggtg accagcaatg gcagcattgg
      121 gagggacacg ccagccgaga cccagcctca gaaccctcca ccccagccag cccccaacgc
      181 ctggcaggtc atcaaaggcg ttctgttcag gatcttcatc atctgggcca tcagcagctg
      241 gttccgccga gggccgtccc ctcaggacca gtcaggccct ggaggggccc cacgtgtcgc
      301 cagccgaaac ctattcccca aagacactct aatgaacctg cacgtgtaca tctcagagca
      361 cgagcacttc acagacttca acgccacctc ggcgctcttc tgggagcagc atgacctggt
      421 gtatggtgac tggaccagtg gagagaactc tgatggctgc tacgagcact ttgcagagct
      481 tgacatccca cagagtgtac agcagaatgg ctccatctat atccatgtct acttcactaa
      541 gagtggcttc catccagacc cccggcagaa ggccctgtac cgccggcttg ccactgtcca
      601 catgtcccgg atgatcaaca aatacaagcg taggcgattt cagaaaacca agaacctact
      661 gacaggagag acagaagctg acccagaaat gatcaagagg gctgaggact atggccctgt
      721 agaagtaatc tcgcactggc accccaacat caccatcaac atcgtggatg accacacacc
      781 atgggtgaag ggcagtgtgc cacccccact ggaccaatat gtgaagtttg atgccgtgag
      841 tggtgactac taccccatca tctatttcaa tgactactgg aacctgcaga aggattacta
      901 ccccattaat gagagtctgg ccagcctacc actgcgtgtc tctttctgcc cgctgtcact
      961 atggcgctgg caactctatg ctgcacagag taccaagtca ccctggaact tcttaggtga
     1021 cgagctgtat gagcaatcgg atgaggagca ggattcagtg aaggttgctc tgctggaaac
     1081 cagcccgtat cttctggcac tcaccatcat cgtctccatt gtccacagtg tctttgagtt
     1141 cctggctttc aaaaatgaca ttcagttctg gaacagtcgt cagtccttgg aggggctgtc
     1201 agtgcgctcc gtcttctttg gcgttttcca gtcctttgtg gttctccttt acatcctgga
     1261 caatgagacc aactttgtgg tacaggtcag cgtcttcatt ggggtcctca tcgacctctg
     1321 gaagattacc aaagtcatgg acgtccggct ggaccgggag catagagtgg caggaatctt
     1381 cccttgccca accttcaaag acaagtccac ctatattgaa tcttcaacca aagtatatga
     1441 tgatatggcg ttccggtacc tgtcatggat cctctttccc ttgctgggct gctatgccgt
     1501 ctacagcctt ctgtacctgg agcacaaggg ctggtactcc tgggtgctca gcatgctcta
     1561 cggtttcctg ctgacctttg gcttcatcac tatgacacca cagctcttca tcaactataa
     1621 gctcaagtct gtggcccatt tgccctggcg gatgctcacc tacaaggccc tcaacacttt
     1681 cattgatgac ttatttgcct ttgtcatcaa gatgcctgtc atgtaccgga tcggctgcct
     1741 gcgggatgat gtggttttct tcatctacct ctaccaacgg tggatctacc gcgtcgaccc
     1801 cacccgtgtg aacgagttcg gtatgagtgg agaggatgtc tcagcagcgg catccagggc
     1861 ccaggcatcc actgcagcag gggctctcac acctgcaccc agcacagctg tcagcggaga
     1921 ggatgcctcc acagtcccaa aggccacttc tggggcctgc actgccagcc agccccagga
     1981 agcccctcca aagccagcag aggacaagaa aaaggattag ccactgcagt cctccttatc
     2041 tgctcctggt gactgaccac caccacctcc cgggcccctc ccttaccctc tctgtcgccc
     2101 tcttcctgga cagatcaggc cggggcggca ggaggccccc agggccaggg cccggtgtgt
     2161 gagatggggc cgggcaggtt ggggctggct gtgtgtatgt ggaggcaccg tccatcgtct
     2221 tgtctatccg tctgttccta tgtgtttgca gacatctcgc cctgccagcc caacaccatc
     2281 gggaatcatg gtgaagccaa tatggcgccg agggtgggcc aggcggggaa ggggccaggg
     2341 ctcctctgtg ggacgcctgt ggtcctccat catcttgtcc ctcatccccc gaccaccctg
     2401 ctcccagacc gccacccttt aacacagtct ggatttaata aattcatatg ggtgtttaac
     2461 ttaagctcaa ccaccgcacc tcctctgcct tccttgtccg gaccatgcag ctggctcagg
     2521 tcttcaagag acctggaggt gatgacggag tggaatctgg ggttgttcag catttaacac
     2581 cctgggttaa ccctgtgctg cataaaacag tggtgttgta tgcctgtaag tcagagctaa
     2641 cttagatggc agaggcttgc aaggtggctc agtgggtgaa ggtacttgcc atgcaaccct
     2701 gataacctgg ctttgcactt ccattgtgct acaaggccac acaacctaag ttgatcacca
     2761 aaccacacag aggcaggagg gaagcaacta tagtgttatc tgacctccac acacacactg
     2821 tagcacacat acccaaacag gataactgcc ctgcaagagg tctcccaaaa cagttccatc
     2881 ttagactcct acaaggctgc tggctaaaag catctggtat ttgtggctag ctgtgtgcca
     2941 ccaggcagga cctgaaacac taaacaccac caagtctgcc tgtgaatcaa gaggctaccc
     3001 ccaagaagga caagccctat ttaacactcc tcaatggaga aaacagaatg gggcctgtat
     3061 gcacttatct gggccacagc agagtgagtc cttgggtgtc attgcagtgt ccctcaagag
     3121 cctaactgtc cataccagga gcagggcctg cttaccctct ctaggagaat gacagccatt
     3181 gggggtactc actacacctt cccagactgt aggatcagca gtgctgcaag gaggcactgg
     3241 cccaacccca ggttgcttca ggctccacct acttctccct gctgagtcaa gcagggatgg
     3301 tgcctcacag gtaggtatca tacccactct ccttgctggg ctccccttcc acctgctgac
     3361 ccagtgctct cagaagacag ctaatgtgat ccccaggggg ctgctgcatg tccccagcct
     3421 ttgtctcatg ctctgccaca gcctcacctc tagccccagt ctctcaagtc ctttctggga
     3481 cacaagtacc ttcaggatac aattggtggt gttcccaggc accccttacc gcctagtcct
     3541 gaggctctgc ccactggtac atcatggcaa ggagacttcc ttcactggac caagacctgt
     3601 gaaaacatga ctgtatccta gccactctgg tgccatttgc tttcacggac atctggacat
     3661 atccagtgcc cttattgggg tactggtgga tgggtctcta ttaacccttc gcaagtctgt
     3721 ctgggcaaac agcacaaaac agttctgtgt acacagtagg accagcattc catggcagtt
     3781 ctgaggagct cacaacttag cagaattcta ggtagtgttg ggcacagtgg ttattcccca
     3841 tccttgattt tgagaggtca atccagattt aaaaactttc agctagcctg ggctacaaaa
     3901 caagacttgg catagtggca cacacttgta atcctggcac ttgggaggtg gaggcagaag
     3961 ggtcaggaca tcaaagtcat cctcactgct ttgagttggg tctgaggggc tggagagatg
     4021 gctcctctgt tacaggctag gctcacaacc agaaatagaa gctgggtctg aggccagcct
     4081 gggctattta acaccttgtt tgaaagaata aaaaatggaa aacaccatgg aaaaaaaaaa
     4141 aaaaaaa
//
