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

Summary

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

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_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Tbata modulates thymus function by regulating stromal cell proliferation via the Nedd8 pathway.
Title: Tbata modulates thymic stromal cell proliferation and thymus function.
Data show that Spatial expression is independent of thymocyte-derived signals during thymus organogenesis.
Title: Spatial (Tbata) expression in mature medullary thymic epithelial cells.
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.
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.
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.
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)

Targeted (1) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:489237

AI428928 (e-PCR)
- UniSTS:165690

1700021K02Rik (e-PCR), detects polymorphism
- UniSTS:471171

D10Mit258 (e-PCR), detects polymorphism
- UniSTS:126163

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in spermatid differentiation	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed

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)

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
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
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
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
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
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