LOCUS       NM_001017409             999 bp    mRNA    linear   ROD 02-JUN-2024
DEFINITION  Mus musculus thymus, brain and testes associated (Tbata),
            transcript variant 6, mRNA.
ACCESSION   NM_001017409
VERSION     NM_001017409.1
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 999)
  AUTHORS   Yammine,M., Saade,M., Chauvet,S. and Nguyen,C.
  TITLE     Spatial gene's (Tbata) implication in neurite outgrowth and
            dendrite patterning in hippocampal neurons
  JOURNAL   Mol Cell Neurosci 59, 1-9 (2014)
   PUBMED   24361585
  REMARK    GeneRIF: Spatial, through its transport by Kif17, is crucial for
            neuronal polarization.
REFERENCE   2  (bases 1 to 999)
  AUTHORS   Flomerfelt,F.A., El Kassar,N., Gurunathan,C., Chua,K.S.,
            League,S.C., Schmitz,S., Gershon,T.R., Kapoor,V., Yan,X.Y.,
            Schwartz,R.H. and Gress,R.E.
  TITLE     Tbata modulates thymic stromal cell proliferation and thymus
            function
  JOURNAL   J Exp Med 207 (11), 2521-2532 (2010)
   PUBMED   20937703
  REMARK    GeneRIF: Tbata modulates thymus function by regulating stromal cell
            proliferation via the Nedd8 pathway.
REFERENCE   3  (bases 1 to 999)
  AUTHORS   Saade,M., Irla,M., Yammine,M., Boulanger,N., Victorero,G.,
            Vincentelli,R., Penninger,J.M., Hollander,G.A., Chauvet,S. and
            Nguyen,C.
  TITLE     Spatial (Tbata) expression in mature medullary thymic epithelial
            cells
  JOURNAL   Eur J Immunol 40 (2), 530-538 (2010)
   PUBMED   19918778
  REMARK    GeneRIF: Data show that Spatial expression is independent of
            thymocyte-derived signals during thymus organogenesis.
REFERENCE   4  (bases 1 to 999)
  AUTHORS   Irla,M., Saade,M., Fernandez,C., Chasson,L., Victorero,G.,
            Dahmane,N., Chazal,G. and Nguyen,C.
  TITLE     Neuronal distribution of spatial in the developing cerebellum and
            hippocampus and its somatodendritic association with the kinesin
            motor KIF17
  JOURNAL   Exp Cell Res 313 (20), 4107-4119 (2007)
   PUBMED   17961552
  REMARK    GeneRIF: These findings suggest that Spatial may play a role in
            neuronal morphogenesis and synaptic plasticity through its
            interaction with the kinesin motor KIF17 in dendrites.
REFERENCE   5  (bases 1 to 999)
  AUTHORS   Saade,M., Irla,M., Govin,J., Victorero,G., Samson,M. and Nguyen,C.
  TITLE     Dynamic distribution of Spatial during mouse spermatogenesis and
            its interaction with the kinesin KIF17b
  JOURNAL   Exp Cell Res 313 (3), 614-626 (2007)
   PUBMED   17196196
  REMARK    GeneRIF: Together, these findings imply a function of Spatial in
            spermatid differentiation as a new cargo of kinesin KIF17b, in a
            microtubule-dependent mechanism specific to the manchette and the
            principal piece of the sperm tail.
REFERENCE   6  (bases 1 to 999)
  AUTHORS   Li,Q., Ishikawa,T.O., Miyoshi,H., Oshima,M. and Taketo,M.M.
  TITLE     A targeted mutation of Nkd1 impairs mouse spermatogenesis
  JOURNAL   J Biol Chem 280 (4), 2831-2839 (2005)
   PUBMED   15546883
REFERENCE   7  (bases 1 to 999)
  AUTHORS   Irla,M., Puthier,D., Granjeaud,S., Saade,M., Victorero,G.,
            Mattei,M.G. and Nguyen,C.
  TITLE     Genomic organization and the tissue distribution of alternatively
            spliced isoforms of the mouse Spatial gene
  JOURNAL   BMC Genomics 5 (1), 41 (2004)
   PUBMED   15236666
  REMARK    GeneRIF: A new short thymus isoform, Spatial-beta, differs from
            other isoforms by an additional alternative exon of 69 bases. This
            new exon encodes an interesting proline-rich signature that could
            confer to the 34 kDa Spatial-beta protein a particular function.
            Publication Status: Online-Only
REFERENCE   8  (bases 1 to 999)
  AUTHORS   Irla,M., Puthier,D., Le Goffic,R., Victorero,G., Freeman,T.,
            Naquet,P., Samson,M. and Nguyen,C.
  TITLE     Spatial, a new nuclear factor tightly regulated during mouse
            spermatogenesis
  JOURNAL   Gene Expr Patterns 3 (2), 135-138 (2003)
   PUBMED   12711538
  REMARK    Erratum:[Gene Expr Patterns. 2003 Aug;3(4):539]
REFERENCE   9  (bases 1 to 999)
  AUTHORS   Flomerfelt,F.A., Kim,M.G. and Schwartz,R.H.
  TITLE     Spatial, a gene expressed in thymic stromal cells, depends on
            three-dimensional thymus organization for its expression
  JOURNAL   Genes Immun 1 (6), 391-401 (2000)
   PUBMED   11196687
  REMARK    GeneRIF: provides evidence for non-AUG translation initiation site
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AY243457.1, AJ249392.1 and
            AY243459.1.
            
            Summary: This gene encodes a putative transcription factor that is
            highly expressed in thymic cortical stromal cells, and may be
            involved in T-cell development. Its expression is developmentally
            regulated in the testis, where it is restricted to the haploid
            round spermatids during spermatogenesis, and thus this gene may
            also have a role in the control of male germ cell development.
            Alternative splicing of this gene results in two sets of transcript
            variants: the variants containing 5 additional exons at the 3' end
            encode long isoforms that are highly expressed in the testis, while
            the variants lacking the 3' end exons encode short isoforms that
            are highly expressed in the thymus. Most of the transcripts
            encoding the short isoforms have been shown to initiate translation
            from non-AUG (CUG) start sites. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (6) uses an alternate acceptor
            splice site in one of the coding exons and in the last exon,
            compared to transcript variant 3. The encoded isoform (6, also
            known as Spatial-beta) is missing an internal segment and has a
            different C-terminus compared to short isoform 3. This variant
            initiates translation from a non-AUG (CUG) start site and is highly
            expressed in the thymus.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AY243457.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849375, SAMN00849383
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            non-AUG initiation codon :: PMID: 11196687
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-549               AY243457.1         1-549
            550-615             AJ249392.1         522-587
            616-999             AY243459.1         587-970
FEATURES             Location/Qualifiers
     source          1..999
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="10"
                     /map="10 32.16 cM"
     gene            1..999
                     /gene="Tbata"
                     /gene_synonym="1700021K02Rik; Spatial; Titest"
                     /note="thymus, brain and testes associated"
                     /db_xref="GeneID:65971"
                     /db_xref="MGI:MGI:1923820"
     exon            1..142
                     /gene="Tbata"
                     /gene_synonym="1700021K02Rik; Spatial; Titest"
                     /inference="alignment:Splign:2.1.0"
     CDS             84..671
                     /gene="Tbata"
                     /gene_synonym="1700021K02Rik; Spatial; Titest"
                     /note="isoform 6 is encoded by transcript variant 6;
                     non-AUG (CUG) translation initiation codon; stromal
                     protein associated with thymii and lymph nodes; protein
                     SPATIAL; thymus and testis specific nuclear protein;
                     thymus, brain and testes-associated protein; protein
                     TBATA"
                     /codon_start=1
                     /product="protein TBATA isoform 6"
                     /protein_id="NP_001017409.1"
                     /db_xref="GeneID:65971"
                     /db_xref="MGI:MGI:1923820"
                     /translation="MFLGNVYKGSLAPRRDEVTSPKAEPQPETKPENLPRSHGDVGLQ
                     KETVVPGIVDFELIHEELKTTKPQTSQPTPSAYRFGRLSHHSFFSRHHPQPQRVTHIQ
                     DIAGKPVCVVRDEFSLSALTQPTFLSRCLMGMPTISVPIGDPQSNRNPQLSTSVLKTQ
                     GGQTTPTAPHPHLSCPLRHLEEETEGPGFPSDCLH"
     exon            143..390
                     /gene="Tbata"
                     /gene_synonym="1700021K02Rik; Spatial; Titest"
                     /inference="alignment:Splign:2.1.0"
     exon            391..549
                     /gene="Tbata"
                     /gene_synonym="1700021K02Rik; Spatial; Titest"
                     /inference="alignment:Splign:2.1.0"
     exon            550..982
                     /gene="Tbata"
                     /gene_synonym="1700021K02Rik; Spatial; Titest"
                     /inference="alignment:Splign:2.1.0"
     regulatory      956..961
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tbata"
                     /gene_synonym="1700021K02Rik; Spatial; Titest"
                     /note="hexamer: AATAAA"
     polyA_site      982
                     /gene="Tbata"
                     /gene_synonym="1700021K02Rik; Spatial; Titest"
                     /note="major polyA site"
ORIGIN      
        1 tcttgaggtt gccaattttt tttttttttt tttttttttt tttttttttt ggtttgggga
       61 gaaacttgtg ttggaaccag cccctgtttc tggggaatgt atataagggg agtttagcac
      121 ctcgtaggga tgaggtgact agtccaaagg cagagcccca gccagagacg aagccggaga
      181 accttccaag gagccacggg gatgttgggc tccagaaaga gactgtggtc ccaggcattg
      241 tggatttcga gctgatccat gaggagctga agaccacaaa gccccaaaca tcacaaccaa
      301 cacccagtgc ctaccgcttt ggacgcctaa gccaccattc cttcttctcg aggcaccacc
      361 cccaaccaca gcgagtgact catatccaag atatcgctgg gaagcctgtc tgcgtggtca
      421 gggacgagtt ctctctgtcg gccttgactc agcccacatt cttatcccgc tgtctgatgg
      481 ggatgcccac catctctgtc cccattgggg atccacagtc caatcggaac ccccagcttt
      541 ctacttctgt cctgaagaca cagggaggac aaacaacacc taccgccccc cacccccatc
      601 tttcctgtcc tctcagacac ctggaggaag aaactgaagg acctggcttc ccgagtgact
      661 gtcttcacta aggaaatcca gccaaagccc gatgaggttg gtgttgcaca aagaatggag
      721 cctagaaaaa aaaggccttc ttaagtctcc ccaatgctca gctgctggca cgggagggga
      781 aggaccctca taacctcgaa ggtgacagcg aaaatcaaag aaacacaaaa tcacacctag
      841 cagagaaatc caagaagggt tcccagaaac accctctaaa gcaactgttc ccaacctgtc
      901 taatgccttg acccttgaat acagtttctc acactgcagt aacccctgcc cccgaaataa
      961 aattattttc attactactt caaaaaaaaa aaaaaaaaa
//
