LOCUS       NM_138296               1019 bp    mRNA    linear   PRI 20-FEB-2025
DEFINITION  Homo sapiens pre T cell antigen receptor alpha (PTCRA), transcript
            variant 2, mRNA.
ACCESSION   NM_138296
VERSION     NM_138296.3
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 1019)
  AUTHORS   Materna,M., Delmonte,O.M., Bosticardo,M., Momenilandi,M.,
            Conrey,P.E., Charmeteau-De Muylder,B., Bravetti,C., Bellworthy,R.,
            Cederholm,A., Staels,F., Ganoza,C.A., Darko,S., Sayed,S., Le
            Floc'h,C., Ogishi,M., Rinchai,D., Guenoun,A., Bolze,A., Khan,T.,
            Gervais,A., Kruger,R., Voller,M., Palterer,B.,
            Sadeghi-Shabestari,M., Langlois de Septenville,A., Schramm,C.A.,
            Shah,S., Tello-Cajiao,J.J., Pala,F., Amini,K., Campos,J.S.,
            Lima,N.S., Eriksson,D., Levy,R., Seeleuthner,Y., Jyonouchi,S.,
            Ata,M., Al Ali,F., Stittrich,A., Deswarte,C., Pereira,A.,
            Megret,J., Le Voyer,T., Bastard,P., Berteloot,L., Dussiot,M.,
            Vladikine,N., Cardenas,P.P., Jouanguy,E., Alqahtani,M., Hasan,A.,
            Thanaraj,T.A., Rosain,J., Al Qureshah,F., Sabato,V.,
            Alyanakian,M.A., Leruez-Ville,M., Rozenberg,F., Haddad,E.,
            Regueiro,J.R., Toribio,M.L., Kelsen,J.R., Salehi,M., Nasiri,S.,
            Torabizadeh,M., Rokni-Zadeh,H., Changi-Ashtiani,M., Vatandoost,N.,
            Moravej,H., Akrami,S.M., Mazloomrezaei,M., Cobat,A., Meyts,I.,
            Toyofuku,E., Nishimura,M., Moriya,K., Mizukami,T., Imai,K.,
            Abel,L., Malissen,B., Al-Mulla,F., Alkuraya,F.S., Parvaneh,N., von
            Bernuth,H., Beetz,C., Davi,F., Douek,D.C., Cheynier,R.,
            Langlais,D., Landegren,N., Marr,N., Morio,T., Shahrooei,M.,
            Schrijvers,R., Henrickson,S.E., Luche,H., Notarangelo,L.D.,
            Casanova,J.L. and Beziat,V.
  TITLE     The immunopathological landscape of human pre-TCRalpha deficiency:
            From rare to common variants
  JOURNAL   Science 383 (6686), eadh4059 (2024)
   PUBMED   38422122
REFERENCE   2  (bases 1 to 1019)
  AUTHORS   Heikkila,N., Sormunen,S., Mattila,J., Harkonen,T., Knip,M.,
            Ihantola,E.L., Kinnunen,T., Mattila,I.P., Saramaki,J. and
            Arstila,T.P.
  TITLE     Generation of self-reactive, shared T-cell receptor alpha chains in
            the human thymus
  JOURNAL   J Autoimmun 119, 102616 (2021)
   PUBMED   33652347
  REMARK    GeneRIF: Generation of self-reactive, shared T-cell receptor alpha
            chains in the human thymus.
REFERENCE   3  (bases 1 to 1019)
  AUTHORS   Guan,W., Steffen,B.T., Lemaitre,R.N., Wu,J.H.Y., Tanaka,T.,
            Manichaikul,A., Foy,M., Rich,S.S., Wang,L., Nettleton,J.A.,
            Tang,W., Gu,X., Bandinelli,S., King,I.B., McKnight,B., Psaty,B.M.,
            Siscovick,D., Djousse,L., Chen,Y.I., Ferrucci,L., Fornage,M.,
            Mozafarrian,D., Tsai,M.Y. and Steffen,L.M.
  TITLE     Genome-wide association study of plasma N6 polyunsaturated fatty
            acids within the cohorts for heart and aging research in genomic
            epidemiology consortium
  JOURNAL   Circ Cardiovasc Genet 7 (3), 321-331 (2014)
   PUBMED   24823311
REFERENCE   4  (bases 1 to 1019)
  AUTHORS   Fleig,L., Bergbold,N., Sahasrabudhe,P., Geiger,B., Kaltak,L. and
            Lemberg,M.K.
  TITLE     Ubiquitin-dependent intramembrane rhomboid protease promotes ERAD
            of membrane proteins
  JOURNAL   Mol Cell 47 (4), 558-569 (2012)
   PUBMED   22795130
REFERENCE   5  (bases 1 to 1019)
  AUTHORS   Menon,R., Pearce,B., Velez,D.R., Merialdi,M., Williams,S.M.,
            Fortunato,S.J. and Thorsen,P.
  TITLE     Racial disparity in pathophysiologic pathways of preterm birth
            based on genetic variants
  JOURNAL   Reprod Biol Endocrinol 7, 62 (2009)
   PUBMED   19527514
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1019)
  AUTHORS   Aifantis,I., Borowski,C., Gounari,F., Lacorazza,H.D.,
            Nikolich-Zugich,J. and von Boehmer,H.
  TITLE     A critical role for the cytoplasmic tail of pTalpha in T lymphocyte
            development
  JOURNAL   Nat Immunol 3 (5), 483-488 (2002)
   PUBMED   11927911
  REMARK    Erratum:[Nat Immunol 2002 Jun;3(6):591]
REFERENCE   7  (bases 1 to 1019)
  AUTHORS   Bellavia,D., Campese,A.F., Checquolo,S., Balestri,A., Biondi,A.,
            Cazzaniga,G., Lendahl,U., Fehling,H.J., Hayday,A.C., Frati,L., von
            Boehmer,H., Gulino,A. and Screpanti,I.
  TITLE     Combined expression of pTalpha and Notch3 in T cell leukemia
            identifies the requirement of preTCR for leukemogenesis
  JOURNAL   Proc Natl Acad Sci U S A 99 (6), 3788-3793 (2002)
   PUBMED   11891328
  REMARK    GeneRIF: Combined expression of pTalpha and Notch3 in T cell
            leukemia identifies the requirement of preTCR for leukemogenesis
REFERENCE   8  (bases 1 to 1019)
  AUTHORS   Saint-Ruf,C., Lechner,O., Feinberg,J. and von Boehmer,H.
  TITLE     Genomic structure of the human pre-T cell receptor alpha chain and
            expression of two mRNA isoforms
  JOURNAL   Eur J Immunol 28 (11), 3824-3831 (1998)
   PUBMED   9842925
REFERENCE   9  (bases 1 to 1019)
  AUTHORS   Ramiro,A.R., Trigueros,C., Marquez,C., San Millan,J.L. and
            Toribio,M.L.
  TITLE     Regulation of pre-T cell receptor (pT alpha-TCR beta) gene
            expression during human thymic development
  JOURNAL   J Exp Med 184 (2), 519-530 (1996)
   PUBMED   8760805
REFERENCE   10 (bases 1 to 1019)
  AUTHORS   Del Porto,P., Bruno,L., Mattei,M.G., von Boehmer,H. and
            Saint-Ruf,C.
  TITLE     Cloning and comparative analysis of the human pre-T-cell receptor
            alpha-chain gene
  JOURNAL   Proc Natl Acad Sci U S A 92 (26), 12105-12109 (1995)
   PUBMED   8618853
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC100771.1, U38996.1 and
            AW014894.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_138296.2.
            
            Summary: The protein encoded by this gene is a single-pass type I
            membrane protein that is found in immmature but not mature T-cells.
            Along with TCRB and CD3 complex, the encoded protein forms the
            pre-T-cell receptor complex, which regulates early T-cell
            development. Four transcript variants encoding different isoforms
            have been found for this gene.[provided by RefSeq, Jul 2011].
            
            Transcript Variant: This variant (2) uses an alternate in-frame
            splice junction at the 5' end of an exon compared to variant 1. The
            resulting isoform (2) lacks an alternate internal segment compared
            to isoform 1.
            
            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 :: U36759.1, BC100773.2 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA2142670
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000304672.6/ ENSP00000304447.2
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-985               BC100771.1         7-991
            986-1010            U38996.1           934-958
            1011-1019           AW014894.1         15-23               c
FEATURES             Location/Qualifiers
     source          1..1019
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p21.1"
     gene            1..1019
                     /gene="PTCRA"
                     /gene_synonym="IMD126; PT-ALPHA; PTA"
                     /note="pre T cell antigen receptor alpha"
                     /db_xref="GeneID:171558"
                     /db_xref="HGNC:HGNC:21290"
                     /db_xref="MIM:606817"
     exon            1..75
                     /gene="PTCRA"
                     /gene_synonym="IMD126; PT-ALPHA; PTA"
                     /inference="alignment:Splign:2.1.0"
     CDS             18..863
                     /gene="PTCRA"
                     /gene_synonym="IMD126; PT-ALPHA; PTA"
                     /note="isoform 2 precursor is encoded by transcript
                     variant 2; pre-T-cell receptor alpha chain; pT-alpha-TCR"
                     /codon_start=1
                     /product="pre T-cell antigen receptor alpha isoform 2
                     precursor"
                     /protein_id="NP_612153.2"
                     /db_xref="CCDS:CCDS4874.1"
                     /db_xref="GeneID:171558"
                     /db_xref="HGNC:HGNC:21290"
                     /db_xref="MIM:606817"
                     /translation="MAGTWLLLLLALGCPALPTGVGGTPFPSLAPPIMLLVDGKQQMV
                     VVCLVLDVAPPGLDSPIWFSAGNGSALDAFTYGPSPATDGTWTNLAHLSLPSEELASW
                     EPLVCHTGPGAEGHSRSTQPMHLSGEASTARTCPQEPLRGTPGGALWLGVLRLLLFKL
                     LLFDLLLTCSCLCDPAGPLPSPATTTRLRALGSHRLHPATETGGREATSSPRPQPRDR
                     RWGDTPPGRKPGSPVWGEGSYLSSYPTCPAQAWCSRSALRAPSSSLGAFFAGDLPPPL
                     QAGAA"
     exon            76..396
                     /gene="PTCRA"
                     /gene_synonym="IMD126; PT-ALPHA; PTA"
                     /inference="alignment:Splign:2.1.0"
     exon            397..441
                     /gene="PTCRA"
                     /gene_synonym="IMD126; PT-ALPHA; PTA"
                     /inference="alignment:Splign:2.1.0"
     exon            442..1019
                     /gene="PTCRA"
                     /gene_synonym="IMD126; PT-ALPHA; PTA"
                     /inference="alignment:Splign:2.1.0"
     regulatory      990..995
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PTCRA"
                     /gene_synonym="IMD126; PT-ALPHA; PTA"
                     /note="hexamer: ATTAAA"
     polyA_site      1019
                     /gene="PTCRA"
                     /gene_synonym="IMD126; PT-ALPHA; PTA"
                     /note="major polyA site"
ORIGIN      
        1 ctccttccga gtgggccatg gccggtacat ggctgctact tctcctggcc cttgggtgtc
       61 cagccctacc cacaggtgtg ggcggcacac cctttccttc tctggcccca ccaatcatgc
      121 tgctggtgga tggaaagcag cagatggtgg tggtctgcct ggtccttgat gttgcacccc
      181 ctggccttga cagccccatc tggttctcag ccggcaatgg cagtgcactg gatgccttca
      241 cctatggccc ttccccagca acggatggca cctggaccaa cttggcccat ctctccctgc
      301 cttctgagga gctggcatcc tgggagcctt tggtctgcca cactgggcct ggggctgagg
      361 gtcacagcag gagtacacag cccatgcatc tgtcaggaga ggcttctaca gccaggacct
      421 gcccccagga gcctctcagg gggacaccgg gtggggcgct gtggctgggg gtcctgcggc
      481 tgctgctctt caagctgctg ctgtttgacc tgctcctgac ctgcagctgc ctgtgcgacc
      541 ccgcgggccc gctgccttcc cccgcaacca ccacccgcct gcgagccctc ggctcccatc
      601 gactgcaccc ggccacggag actgggggac gagaggccac cagctcaccc agaccccagc
      661 ctcgggaccg ccgctggggt gacacccctc cgggtcggaa gcccgggagc ccagtatggg
      721 gggaagggtc ttacctcagc agttacccca cttgcccagc acaggcctgg tgctcaagat
      781 ctgccctcag ggctccttcc tccagtcttg gagcattttt tgcaggtgac ctgcctcctc
      841 ctctgcaggc tggagctgcc tgagggcagg gctctacctc ccctgcgtca cactgtgtga
      901 ggctgtgtct ctgccatcca aaagggggcc ccttgagaat ggtgatccac ccagttacag
      961 gggcatttag ggagcagatg actgagaaca ttaaaaaaga acttaaatga cacagcaaa
//
