LOCUS       NM_001366285            2230 bp    mRNA    linear   PRI 16-NOV-2024
DEFINITION  Homo sapiens T-box transcription factor T (TBXT), transcript
            variant 3, mRNA.
ACCESSION   NM_001366285 XM_011536080
VERSION     NM_001366285.2
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 2230)
  AUTHORS   Xia,B., Zhang,W., Zhao,G., Zhang,X., Bai,J., Brosh,R.,
            Wudzinska,A., Huang,E., Ashe,H., Ellis,G., Pour,M., Zhao,Y.,
            Coelho,C., Zhu,Y., Miller,A., Dasen,J.S., Maurano,M.T., Kim,S.Y.,
            Boeke,J.D. and Yanai,I.
  TITLE     On the genetic basis of tail-loss evolution in humans and apes
  JOURNAL   Nature 626 (8001), 1042-1048 (2024)
   PUBMED   38418917
  REMARK    GeneRIF: On the genetic basis of tail-loss evolution in humans and
            apes.
REFERENCE   2  (bases 1 to 2230)
  AUTHORS   Jalessi,M., Gholami,M.S., Razmara,E., Hassanzadeh,S.,
            Sadeghipour,A., Jahanbakhshi,A., Tabibkhooei,A., Bahrami,E. and
            Falah,M.
  TITLE     Association between TBXT rs2305089 polymorphism and chordoma in
            Iranian patients identified by a developed T-ARMS-PCR assay
  JOURNAL   J Clin Lab Anal 36 (1), e24150 (2022)
   PUBMED   34837714
  REMARK    GeneRIF: Association between TBXT rs2305089 polymorphism and
            chordoma in Iranian patients identified by a developed T-ARMS-PCR
            assay.
REFERENCE   3  (bases 1 to 2230)
  AUTHORS   Wen,X., Cimera,R., Aryeequaye,R., Abhinta,M., Athanasian,E.,
            Healey,J., Fabbri,N., Boland,P., Zhang,Y. and Hameed,M.
  TITLE     Recurrent loss of chromosome 22 and SMARCB1 deletion in extra-axial
            chordoma: A clinicopathological and molecular analysis
  JOURNAL   Genes Chromosomes Cancer 60 (12), 796-807 (2021)
   PUBMED   34392582
  REMARK    GeneRIF: Recurrent loss of chromosome 22 and SMARCB1 deletion in
            extra-axial chordoma: A clinicopathological and molecular analysis.
REFERENCE   4  (bases 1 to 2230)
  AUTHORS   Li,K., Wang,Q., Lu,Y., Pan,X., Liu,L., Cheng,S., Wu,B., Song,Z. and
            Gao,W.
  TITLE     Machine learning based tissue analysis reveals Brachyury has a
            diagnosis value in breast cancer
  JOURNAL   Biosci Rep 41 (4) (2021)
   PUBMED   33734319
  REMARK    GeneRIF: Machine learning based tissue analysis reveals Brachyury
            has a diagnosis value in breast cancer.
REFERENCE   5  (bases 1 to 2230)
  AUTHORS   Sheppard,H.E., Dall'Agnese,A., Park,W.D., Shamim,M.H., Dubrulle,J.,
            Johnson,H.L., Stossi,F., Cogswell,P., Sommer,J., Levy,J.,
            Sharifnia,T., Wawer,M.J., Nabet,B., Gray,N.S., Clemons,P.A.,
            Schreiber,S.L., Workman,P., Young,R.A. and Lin,C.Y.
  TITLE     Targeted brachyury degradation disrupts a highly specific
            autoregulatory program controlling chordoma cell identity
  JOURNAL   Cell Rep Med 2 (1), 100188 (2021)
   PUBMED   33521702
  REMARK    GeneRIF: Targeted brachyury degradation disrupts a highly specific
            autoregulatory program controlling chordoma cell identity.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2230)
  AUTHORS   Trembath,D., Sherbondy,A.L., Vandyke,D.C., Shaw,G.M., Todoroff,K.,
            Lammer,E.J., Finnell,R.H., Marker,S., Lerner,G. and Murray,J.C.
  TITLE     Analysis of select folate pathway genes, PAX3, and human T in a
            Midwestern neural tube defect population
  JOURNAL   Teratology 59 (5), 331-341 (1999)
   PUBMED   10332959
REFERENCE   7  (bases 1 to 2230)
  AUTHORS   Papapetrou,C., Drummond,F., Reardon,W., Winter,R., Spitz,L. and
            Edwards,Y.H.
  TITLE     A genetic study of the human T gene and its exclusion as a major
            candidate gene for sacral agenesis with anorectal atresia
  JOURNAL   J Med Genet 36 (3), 208-213 (1999)
   PUBMED   10204846
REFERENCE   8  (bases 1 to 2230)
  AUTHORS   Morrison,K., Papapetrou,C., Attwood,J., Hol,F., Lynch,S.A.,
            Sampath,A., Hamel,B., Burn,J., Sowden,J., Stott,D., Mariman,E. and
            Edwards,Y.H.
  TITLE     Genetic mapping of the human homologue (T) of mouse T(Brachyury)
            and a search for allele association between human T and spina
            bifida
  JOURNAL   Hum Mol Genet 5 (5), 669-674 (1996)
   PUBMED   8733136
REFERENCE   9  (bases 1 to 2230)
  AUTHORS   Edwards,Y.H., Putt,W., Lekoape,K.M., Stott,D., Fox,M.,
            Hopkinson,D.A. and Sowden,J.
  TITLE     The human homolog T of the mouse T(Brachyury) gene; gene structure,
            cDNA sequence, and assignment to chromosome 6q27
  JOURNAL   Genome Res 6 (3), 226-233 (1996)
   PUBMED   8963900
REFERENCE   10 (bases 1 to 2230)
  AUTHORS   Herrmann,B.G.
  TITLE     Action of the Brachyury gene in mouse embryogenesis
  JOURNAL   Ciba Found Symp 165, 78-86 (1992)
   PUBMED   1516477
  REMARK    Review article
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL627443.6.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Feb 5, 2020 this sequence version replaced NM_001366285.1.
            
            Summary: The protein encoded by this gene is an embryonic nuclear
            transcription factor that binds to a specific DNA element, the
            palindromic T-site. It binds through a region in its N-terminus,
            called the T-box, and effects transcription of genes required for
            mesoderm formation and differentiation. The protein is localized to
            notochord-derived cells. Variation in this gene was associated with
            susceptibility to neural tube defects and chordoma. A mutation in
            this gene was found in a family with sacral agenesis with vertebral
            anomalies. [provided by RefSeq, Sep 2018].
            
            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 :: BC039877.1, SRR11853561.25599.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000366876.7/ ENSP00000355841.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-466               AL627443.6         109627-110092       c
            467-731             AL627443.6         108833-109097       c
            732-866             AL627443.6         107947-108081       c
            867-928             AL627443.6         107041-107102       c
            929-990             AL627443.6         106846-106907       c
            991-1167            AL627443.6         104688-104864       c
            1168-1297           AL627443.6         103078-103207       c
            1298-2230           AL627443.6         99897-100829        c
FEATURES             Location/Qualifiers
     source          1..2230
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6q27"
     gene            1..2230
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /note="T-box transcription factor T"
                     /db_xref="GeneID:6862"
                     /db_xref="HGNC:HGNC:11515"
                     /db_xref="MIM:601397"
     exon            1..466
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /inference="alignment:Splign:2.1.0"
     CDS             261..1571
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /note="isoform 3 is encoded by transcript variant 3; T,
                     brachyury homolog; brachyury protein; protein T; T
                     brachyury transcription factor"
                     /codon_start=1
                     /product="T-box transcription factor T isoform 3"
                     /protein_id="NP_001353214.1"
                     /db_xref="CCDS:CCDS94030.1"
                     /db_xref="GeneID:6862"
                     /db_xref="HGNC:HGNC:11515"
                     /db_xref="MIM:601397"
                     /translation="MSSPGTESAGKSLQYRVDHLLSAVENELQAGSEKGDPTERELRV
                     GLEESELWLRFKELTNEMIVTKNGRRMFPVLKVNVSGLDPNAMYSFLLDFVAADNHRW
                     KYVNGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKAPVSFSKVKLTNKLNGGGQIML
                     NSLHKYEPRIHIVRVGGPQRMITSHCFPETQFIAVTAYQNEEITALKIKYNPFAKAFL
                     DAKERSDHKEMMEEPGDSQQPGYSQSGGWLLPGTSTLCPPANPHPQFGGALSLPSTHS
                     CDRYPTLRSHRSSPYPSPYAHRNNSPTYSDNSPACLSMLQSHDNWSSLGMPAHPSMLP
                     VSHNASPPTSSSQYPSLWSVSNGAVTPGSQAAAVSNGLGAQFFRGSPAHYTPLTHPVS
                     APSSSGSPLYEGAAAATDIVDSQYDAAAQGRLIASWTPVSPPSM"
     exon            467..731
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /inference="alignment:Splign:2.1.0"
     exon            732..866
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /inference="alignment:Splign:2.1.0"
     exon            867..928
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /inference="alignment:Splign:2.1.0"
     exon            929..990
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /inference="alignment:Splign:2.1.0"
     exon            991..1167
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /inference="alignment:Splign:2.1.0"
     exon            1168..1297
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /inference="alignment:Splign:2.1.0"
     exon            1298..2230
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2211..2216
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /note="hexamer: AATAAA"
     polyA_site      2230
                     /gene="TBXT"
                     /gene_synonym="SAVA; T; TFT"
                     /note="major polyA site"
ORIGIN      
        1 agagacctac actagtagag ccttggggag ttcaagtgga ataacttctc cccacccctc
       61 tgcccccgtc ccctcccccc aagtcttggt ccgcgccctc ctcccgggtc tgtgccggga
      121 cccgggaccc gggagccgtc gcaggtctcg gtccaagggg ccccttttct cggaagggcg
      181 gcggccaaga gcagggaagg tggatctcag gtagcgagtc tgggcttcgg ggacggcggg
      241 gaggggagcc ggacgggagg atgagctccc ctggcaccga gagcgcggga aagagcctgc
      301 agtaccgagt ggaccacctg ctgagcgccg tggagaatga gctgcaggcg ggcagcgaga
      361 agggcgaccc cacagagcgc gaactgcgcg tgggcctgga ggagagcgag ctgtggctgc
      421 gcttcaagga gctcaccaat gagatgatcg tgaccaagaa cggcaggagg atgtttccgg
      481 tgctgaaggt gaacgtgtct ggcctggacc ccaacgccat gtactccttc ctgctggact
      541 tcgtggcggc ggacaaccac cgctggaagt acgtgaacgg ggaatgggtg ccggggggca
      601 agccggagcc gcaggcgccc agctgcgtct acatccaccc cgactcgccc aacttcgggg
      661 cccactggat gaaggctccc gtctccttca gcaaagtcaa gctcaccaac aagctcaacg
      721 gagggggcca gatcatgctg aactccttgc ataagtatga gcctcgaatc cacatagtga
      781 gagttggggg tccacagcgc atgatcacca gccactgctt ccctgagacc cagttcatag
      841 cggtgactgc ttatcagaac gaggagatca cagctcttaa aattaagtac aatccatttg
      901 caaaagcttt ccttgatgca aaggaaagaa gtgatcacaa agagatgatg gaggaacccg
      961 gagacagcca gcaacctggg tactcccaat caggggggtg gcttcttcct ggaaccagca
     1021 ccctgtgtcc acctgcaaat cctcatcctc agtttggagg tgccctctcc ctcccctcca
     1081 cgcacagctg tgacaggtac ccaaccctga ggagccaccg gtcctcaccc taccccagcc
     1141 cctatgctca tcggaacaat tctccaacct attctgacaa ctcacctgca tgtttatcca
     1201 tgctgcaatc ccatgacaat tggtccagcc ttggaatgcc tgcccatccc agcatgctcc
     1261 ccgtgagcca caatgccagc ccacctacca gctccagtca gtaccccagc ctgtggtctg
     1321 tgagcaacgg cgccgtcacc ccgggctccc aggcagcagc cgtgtccaac gggctggggg
     1381 cccagttctt ccggggctcc cccgcgcact acacacccct cacccatccg gtctcggcgc
     1441 cctcttcctc gggatcccca ctgtacgaag gggcggccgc ggccacagac atcgtggaca
     1501 gccagtacga cgccgcagcc caaggccgcc tcatagcctc atggacacct gtgtcgccac
     1561 cttccatgtg aagcagcaag gcccaggtcc cgaaagatgc agtgactttt tgtcgtggca
     1621 gccagtggtg actggattga cctactaggt acccagtggc agtctcaggt taagaaggaa
     1681 atgcagcctc agtaacttcc ttttcaaagc agtggaggag cacacggcac ctttccccag
     1741 agccccagca tcccttgctc acacctgcag tagcggtgct gtcccaggtg gcttacagat
     1801 gaacccaact gtggagatga tgcagttggc ccaacctcac tgacggtgaa aaaatgtttg
     1861 ccagggtcca gaaacttttt ttggtttatt tctcatacag tgtattggca actttggcac
     1921 accagaattt gtaaactcca ccagtcctac tttagtgaga taaaaagcac actcttaatc
     1981 ttcttccttg ttgctttcaa gtagttagag ttgagctgtt aaggacagaa taaaatcata
     2041 gttgaggaca gcaggtttta gttgaattga aaatttgact gctctgcccc ctagaatgtg
     2101 tgtattttaa gcatatgtag ctaatctctt gtgttgttaa actataactg tttcatattt
     2161 ttcttttgac aaagtagcca aagacaatca gcagaaagca ttttctgcaa aataaacgca
     2221 atatgcaaaa
//
