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Tbata thymus, brain and testes associated [ Mus musculus (house mouse) ]

Gene ID: 65971, updated on 2-Nov-2024

Summary

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Official Symbol
Tbataprovided by MGI
Official Full Name
thymus, brain and testes associatedprovided by MGI
Primary source
MGI:MGI:1923820
See related
Ensembl:ENSMUSG00000020096 AllianceGenome:MGI:1923820
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Titest; Spatial; 1700021K02Rik
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]
Expression
Biased expression in testis adult (RPKM 135.3) and thymus adult (RPKM 109.1) See more
Orthologs
human all
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Genomic context

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See Tbata in Genome Data Viewer
Location:
10 B4; 10 32.16 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (61007743..61024620)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (61171964..61188841)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene pterin 4 alpha carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 1 Neighboring gene sphingosine phosphate lyase 1 Neighboring gene STARR-positive B cell enhancer ABC_E8337 Neighboring gene STARR-positive B cell enhancer mm9_chr10:60610293-60610594 Neighboring gene STARR-seq mESC enhancer starr_26826 Neighboring gene STARR-positive B cell enhancer mm9_chr10:60662268-60662569 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 14 Neighboring gene predicted gene, 29861 Neighboring gene CapStarr-seq enhancer MGSCv37_chr10:60697146-60697393 Neighboring gene perforin 1 (pore forming protein)

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Spatial gene's (Tbata) implication in neurite outgrowth and dendrite patterning in hippocampal neurons. Yammine M, et al. Mol Cell Neurosci, 2014 Mar. PMID 24361585
  2. Genomic organization and the tissue distribution of alternatively spliced isoforms of the mouse Spatial gene. Irla M, et al. BMC Genomics, 2004 Jul 5. PMID 15236666, Free PMC Article
  3. Spatial, a new nuclear factor tightly regulated during mouse spermatogenesis. Irla M, et al. Gene Expr Patterns, 2003 May. PMID 12711538
  4. Identification of differentially expressed genes by restriction endonuclease-based gene expression fingerprinting. Ivanova NB, et al. Nucleic Acids Res, 1995 Aug 11. PMID 7659517, Free PMC Article
  5. Dynamic distribution of Spatial during mouse spermatogenesis and its interaction with the kinesin KIF17b. Saade M, et al. Exp Cell Res, 2007 Feb 1. PMID 17196196

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Spatial, through its transport by Kif17, is crucial for neuronal polarization.
    Title: Spatial gene's (Tbata) implication in neurite outgrowth and dendrite patterning in hippocampal neurons.
  2. Tbata modulates thymus function by regulating stromal cell proliferation via the Nedd8 pathway.
    Title: Tbata modulates thymic stromal cell proliferation and thymus function.
  3. Data show that Spatial expression is independent of thymocyte-derived signals during thymus organogenesis.
    Title: Spatial (Tbata) expression in mature medullary thymic epithelial cells.
  4. 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.
    Title: Neuronal distribution of spatial in the developing cerebellum and hippocampus and its somatodendritic association with the kinesin motor KIF17.
  5. 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.
    Title: Genomic organization and the tissue distribution of alternatively spliced isoforms of the mouse Spatial gene.
  6. 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.
    Title: Dynamic distribution of Spatial during mouse spermatogenesis and its interaction with the kinesin KIF17b.
  7. provides evidence for non-AUG translation initiation site
    Title: Spatial, a gene expressed in thymic stromal cells, depends on three-dimensional thymus organization for its expression.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 
  • Targeted (1)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in spermatid differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein TBATA
Names
protein SPATIAL
stromal protein associated with thymii and lymph node
stromal protein associated with thymii and lymph nodes
thymus and testis specific nuclear protein
thymus, brain and testes-associated protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001017407.1 → NP_001017407.1  protein TBATA isoform 5

    See identical proteins and their annotated locations for NP_001017407.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate, in-frame acceptor splice site in one of the coding exons compared to transcript variant 3, resulting in an isoform (5, also known as Spatial-gamma) that is missing an internal segment compared to short isoform 3. This variant initiates translation from a non-AUG (CUG) start site and is highly expressed in the thymus.
    Source sequence(s)
    AF257503, AJ249392
    UniProtKB/Swiss-Prot
    Q7TSD4
    UniProtKB/TrEMBL
    Q91YF1
    Conserved Domains (1) summary
    pfam15256
    Location:87 → 196
    SPATIAL; SPATIAL

  2. NM_001017409.1 → NP_001017409.1  protein TBATA isoform 6

    Status: REVIEWED

    Description
    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.
    Source sequence(s)
    AJ249392, AY243457, AY243459
    UniProtKB/TrEMBL
    Q91YF1
    Conserved Domains (1) summary
    pfam15256
    Location:87 → 155
    SPATIAL; SPATIAL

  3. NM_001017419.2 → NP_001017419.1  protein TBATA isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate, in-frame acceptor splice site in one of the coding exons compared to transcript variant 1, resulting in an isoform (2, also known as Spatial-delta) that is missing an internal segment compared to long isoform 1, and like the latter, it is highly expressed in the testis.
    Source sequence(s)
    AF521591, AK132793, AW490515
    Consensus CDS
    CCDS48572.1
    UniProtKB/Swiss-Prot
    Q7TSD4
    Related
    ENSMUSP00000113902.2, ENSMUST00000122261.8
    Conserved Domains (1) summary
    pfam15256
    Location:82 → 281
    SPATIAL; SPATIAL

  4. NM_001017433.2 → NP_001017433.1  protein TBATA isoform 1

    See identical proteins and their annotated locations for NP_001017433.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1, also known as Spatial-epsilon) that is highly expressed in the testis.
    Source sequence(s)
    AF521592, AK132793, AW490515
    Consensus CDS
    CCDS23873.1
    UniProtKB/Swiss-Prot
    B2ZA64, Q6XBG6, Q6XBG7, Q6XBG8, Q7TSD4, Q7TSD5, Q8BYU0, Q9EQE4, Q9EQE5
    Related
    ENSMUSP00000036422.6, ENSMUST00000035894.12
    Conserved Domains (1) summary
    pfam15256
    Location:82 → 315
    SPATIAL; SPATIAL

  5. NM_001017441.2 → NP_001017441.2  protein TBATA isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, 5' coding region and mid-coding region, compared to variant 3. The encoded isoform (4) is shorter and has a different N-terminus, compared to short isoform 3.
    Source sequence(s)
    AJ249392, AK132793
    Consensus CDS
    CCDS23874.2
    UniProtKB/TrEMBL
    Q91YF1
    Related
    ENSMUSP00000113253.2, ENSMUST00000121297.8
    Conserved Domains (1) summary
    pfam15256
    Location:82 → 191
    SPATIAL; SPATIAL

  6. NM_023064.3 → NP_075551.3  protein TBATA isoform 3

    See identical proteins and their annotated locations for NP_075551.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes the longest of the short isoforms (3, also known as Spatial-alpha). It initiates translation from a non-AUG (CUG) start site and is highly expressed in the thymus.
    Source sequence(s)
    AF257502, AJ249392
    Consensus CDS
    CCDS48573.1
    UniProtKB/Swiss-Prot
    Q7TSD4
    UniProtKB/TrEMBL
    G5E8I6, Q91YF1
    Conserved Domains (1) summary
    pfam15256
    Location:87 → 230
    SPATIAL; SPATIAL

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    61007743..61024620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7TSD4.2 GenPept UniProtKB/Swiss-Prot:Q7TSD4

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