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2024-03-30 00:42:46, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_001243169            1022 bp    mRNA    linear   PRI 12-MAY-2013
DEFINITION  Homo sapiens pre T-cell antigen receptor alpha (PTCRA), transcript
            variant 3, mRNA.
ACCESSION   NM_001243169
VERSION     NM_001243169.1  GI:341926170
KEYWORDS    RefSeq.
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 1022)
  AUTHORS   Velez,D.R., Fortunato,S., Thorsen,P., Lombardi,S.J., Williams,S.M.
            and Menon,R.
  TITLE     Spontaneous preterm birth in African Americans is associated with
            infection and inflammatory response gene variants
  JOURNAL   Am. J. Obstet. Gynecol. 200 (2), 209 (2009)
   PUBMED   19019335
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   2  (bases 1 to 1022)
  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   3  (bases 1 to 1022)
  AUTHORS   Velez,D.R., Fortunato,S.J., Thorsen,P., Lombardi,S.J.,
            Williams,S.M. and Menon,R.
  TITLE     Preterm birth in Caucasians is associated with coagulation and
            inflammation pathway gene variants
  JOURNAL   PLoS ONE 3 (9), E3283 (2008)
   PUBMED   18818748
  REMARK    GeneRIF: Observational study of gene-disease association and
            gene-gene interaction. (HuGE Navigator)
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1022)
  AUTHORS   Navarro,M.N., Nusspaumer,G., Fuentes,P., Gonzalez-Garcia,S.,
            Alcain,J. and Toribio,M.L.
  TITLE     Identification of CMS as a cytosolic adaptor of the human pTalpha
            chain involved in pre-TCR function
  JOURNAL   Blood 110 (13), 4331-4340 (2007)
   PUBMED   17823309
  REMARK    GeneRIF: identified a polyproline-arginine sequence in the pTalpha
            cytoplasmic tail that interacted in vitro with SH3 domains of the
            CIN85/CMS family of adaptors, and mediated the recruitment of
            multiprotein complexes involving all (CMS, CIN85, and CD2BP3)
            members
REFERENCE   5  (bases 1 to 1022)
  AUTHORS   Bas,A., Hammarstrom,S.G. and Hammarstrom,M.L.
  TITLE     Extrathymic TCR gene rearrangement in human small intestine:
            identification of new splice forms of recombination activating
            gene-1 mRNA with selective tissue expression
  JOURNAL   J. Immunol. 171 (7), 3359-3371 (2003)
   PUBMED   14500629
  REMARK    GeneRIF: High levels of pre-T cell receptor alpha-chain mRNA splice
            forms have been demonstrated in immature CD2+CD7+CD3- T cells of
            the jejunal mucosa, both intraepithelially and in lamina propria.
REFERENCE   6  (bases 1 to 1022)
  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 1022)
  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 1022)
  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 1022)
  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 1022)
  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 U36759.1, AF165312.1,
            BC153829.1 and AW014894.1.
            
            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 (3) uses alternate in-frame splice
            junctions at the 5' ends of two exons and contains an alternate
            in-frame exon compared to variant 1. The resulting isoform (3)
            contains an alternate internal segment but lacks two others
            compared to isoform 1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF165312.1 [ECO:0000332]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-81                U36759.1           1-81
            82-771              AF165312.1         1-690
            772-974             BC153829.1         789-991
            975-1022            AW014894.1         1-48                c
FEATURES             Location/Qualifiers
     source          1..1022
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p21.3"
     gene            1..1022
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /note="pre T-cell antigen receptor alpha"
                     /db_xref="GeneID:171558"
                     /db_xref="HGNC:21290"
                     /db_xref="MIM:606817"
     exon            1..139
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /inference="alignment:Splign:1.39.8"
     misc_feature    1..3
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /note="upstream in-frame stop codon"
     variation       25
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:374451302"
     variation       27
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:200306211"
     STS             32..902
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /db_xref="UniSTS:480837"
     STS             59..974
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /db_xref="UniSTS:484104"
     CDS             82..852
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /note="isoform 3 precursor is encoded by transcript
                     variant 3; pre-T-cell receptor alpha chain; pT-alpha-TCR"
                     /codon_start=1
                     /product="pre T-cell antigen receptor alpha isoform 3
                     precursor"
                     /protein_id="NP_001230098.1"
                     /db_xref="GI:341926171"
                     /db_xref="CCDS:CCDS59019.1"
                     /db_xref="GeneID:171558"
                     /db_xref="HGNC:21290"
                     /db_xref="MIM:606817"
                     /translation="
MAGTWLLLLLALGCPALPTGPVSFPSSPEAATTGPIWFSAGNGSALDAFTYGPSPATDGTWTNLAHLSLPSEELASWEPLVCHTGPGAEGHSRSTQPMHLSGEASTARTCPQEPLRGTPGGALWLGVLRLLLFKLLLFDLLLTCSCLCDPAGPLPSPATTTRLRALGSHRLHPATETGGREATSSPRPQPRDRRWGDTPPGRKPGSPVWGEGSYLSSYPTCPAQAWCSRSALRAPSSSLGAFFAGDLPPPLQAGAA
"
     sig_peptide     82..135
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /inference="COORDINATES: ab initio prediction:SignalP:4.0"
     variation       88
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:376557082"
     variation       93
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:138459529"
     variation       96
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:188435679"
     exon            140..182
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /inference="alignment:Splign:1.39.8"
     exon            183..385
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /inference="alignment:Splign:1.39.8"
     variation       183
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:372102699"
     variation       201
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:137970521"
     variation       233
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:141630791"
     variation       274
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:201708224"
     variation       301
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:147986652"
     variation       316
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:150508492"
     variation       322
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:9471966"
     variation       330
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201816889"
     variation       354
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:200182239"
     variation       377
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:141979329"
     exon            386..430
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /inference="alignment:Splign:1.39.8"
     exon            431..1008
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /inference="alignment:Splign:1.39.8"
     variation       533
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:376897338"
     variation       539
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:367893841"
     variation       540
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:184782115"
     variation       553
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:36111725"
     variation       565
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:187988655"
     variation       572
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:111782749"
     variation       580
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:373866603"
     variation       658
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:200928800"
     variation       659
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:369843415"
     variation       661
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:201876282"
     variation       680
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:373020262"
     variation       685
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:375988717"
     variation       686
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:146531157"
     variation       691
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:184524047"
     variation       695
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:200924110"
     variation       705
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:369095740"
     variation       708
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:112142292"
     variation       719
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:61745373"
     STS             730..911
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /standard_name="RH46834"
                     /db_xref="UniSTS:16710"
     variation       751
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="c"
                     /db_xref="dbSNP:371204759"
     variation       756
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:375457877"
     variation       760
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:115331994"
     variation       769
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:368573599"
     variation       772..773
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="c"
                     /replace="g"
                     /db_xref="dbSNP:1997554"
     variation       779
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:370217795"
     variation       841
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:372426467"
     variation       847
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:61743125"
     variation       854
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:368137542"
     variation       918
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace=""
                     /replace="c"
                     /db_xref="dbSNP:34259318"
     polyA_signal    979..984
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
     variation       992
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:41274882"
     polyA_site      1008
                     /gene="PTCRA"
                     /gene_synonym="PT-ALPHA; PTA"
ORIGIN      
tagaaggcagtcttgtgggtgcctcctcccccagccgcaactcaggtctgcagctgggtcctgcctccttccgagtgggccatggccggtacatggctgctacttctcctggcccttgggtgtccagccctacccacaggtcctgtttccttcccttcctcaccagaggctgccacaacaggccccatctggttctcagccggcaatggcagtgcactggatgccttcacctatggcccttccccagcaacggatggcacctggaccaacttggcccatctctccctgccttctgaggagctggcatcctgggagcctttggtctgccacactgggcctggggctgagggtcacagcaggagtacacagcccatgcatctgtcaggagaggcttctacagccaggacctgcccccaggagcctctcagggggacaccgggtggggcgctgtggctgggggtcctgcggctgctgctcttcaagctgctgctgtttgacctgctcctgacctgcagctgcctgtgcgaccccgcgggcccgctgccttcccccgcaaccaccacccgcctgcgagccctcggctcccatcgactgcacccggccacggagactgggggacgagaggccaccagctcacccagaccccagcctcgggaccgccgctggggtgacacccctccgggtcggaagcccgggagcccagtatggggggaagggtcttacctcagcagttaccccacttgcccagcacaggcctggtgctcaagatctgccctcagggctccttcctccagtcttggagcattttttgcaggtgacctgcctcctcctctgcaggctggagctgcctgagggcagggctctacctcccctgcgtcacactgtgtgaggctgtgtctctgccatccaaaagggggccccttgagaatggtgatccacccagttacaggggcatttagggagcagatgactgagaacattaaaaaagaacttaaatgacacagcaaaaaaaaaaaaaaaaa
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:171558 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
            GeneID:171558 -> Biological process: GO:0070244 [negative regulation of thymocyte apoptotic process] evidence: IEA
            GeneID:171558 -> Cellular component: GO:0016021 [integral to membrane] evidence: IEA

by @meso_cacase at DBCLS
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