This gene encodes a protein that regulates thymic epithelial cell proliferation and thymus size. It has been identified as a ligand for the class I human leukocyte antigen (HLA-I) in thymus. Studies of the orthologous mouse protein suggest that it may also play a role in spermatid differentiation, as well as in neuronal morphogenesis and synaptic plasticity. Polymorphisms in th... See more...

Aliases for TBATA Gene

Aliases for TBATA Gene

  • Thymus, Brain And Testes Associated 2 3 5
  • Stromal Protein Associated With Thymii And Lymph Node Homolog 3 4
  • Thymus, Brain And Testes-Associated Protein 3 4
  • Protein TBATA 3 4
  • C10orf27 3 4
  • SPATIAL 3 4
  • Chromosome 10 Open Reading Frame 27 2
  • Protein SPATIAL 4
  • FLJ32820 2
  • Spatial 2
  • TBATA 5

External Ids for TBATA Gene

Previous HGNC Symbols for TBATA Gene

  • C10orf27

Previous GeneCards Identifiers for TBATA Gene

  • GC10M072531

Summaries for TBATA Gene

Entrez Gene Summary for TBATA Gene

  • This gene encodes a protein that regulates thymic epithelial cell proliferation and thymus size. It has been identified as a ligand for the class I human leukocyte antigen (HLA-I) in thymus. Studies of the orthologous mouse protein suggest that it may also play a role in spermatid differentiation, as well as in neuronal morphogenesis and synaptic plasticity. Polymorphisms in this gene are associated with susceptibility for multiple sclerosis (MS). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

GeneCards Summary for TBATA Gene

TBATA (Thymus, Brain And Testes Associated) is a Protein Coding gene. Diseases associated with TBATA include Hirschsprung Disease 1 and Janus Kinase-3 Deficiency.

UniProtKB/Swiss-Prot Summary for TBATA Gene

  • May play a role in spermatid differentiation. Modulates thymic stromal cell proliferation and thymus function.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TBATA Gene

Genomics for TBATA Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TBATA Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J070779 Promoter/Enhancer 1.4 EPDnew FANTOM5 Ensembl ENCODE 255.5 +3.0 3000 8 REST BHLHE40 ARNT PRDM10 SPI1 RAD51 NRF1 HDAC8 RFX1 L3MBTL2 TBATA SAR1A ADAMTS14 SGPL1 HSALNG0078670
GH10J070786 Enhancer 0.3 Ensembl ENCODE 250.7 -1.6 -1599 0.8 TBATA SGPL1 lnc-TBATA-1
GH10J070759 Enhancer 1 Ensembl ENCODE 12.5 +25.8 25828 1.4 MYC ZNF654 IKZF1 ZIC2 REST CEBPB TRIM22 CTCF SIN3A ARNT TBATA PCBD1 TYSND1 ADAMTS14 lnc-PCBD1-5 piR-52438-011
GH10J070760 Enhancer 0.7 Ensembl ENCODE 17.8 +23.2 23203 3.2 CTCF RXRA RAD21 HNF4A CEBPB POLR2A SP1 TBATA ADAMTS14 lnc-PCBD1-5 piR-52438-011
GH10J070756 Enhancer 0.8 Ensembl ENCODE dbSUPER 12 +28.5 28475 0.9 FOSL2 ATF4 CEBPB ATF3 NR2F1 CEBPG ADAMTS14 TBATA PCBD1 lnc-PCBD1-5 piR-52438-011
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TBATA on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TBATA

Genomic Locations for TBATA Gene

Latest Assembly
chr10:70,771,237-70,785,401
(GRCh38/hg38)
Size:
14,165 bases
Orientation:
Minus strand

Previous Assembly
chr10:72,530,994-72,545,133
(GRCh37/hg19 by Entrez Gene)
Size:
14,140 bases
Orientation:
Minus strand

chr10:72,530,995-72,545,157
(GRCh37/hg19 by Ensembl)
Size:
14,163 bases
Orientation:
Minus strand

Genomic View for TBATA Gene

Genes around TBATA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBATA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBATA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBATA Gene

Proteins for TBATA Gene

  • Protein details for TBATA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96M53-TBATA_HUMAN
    Recommended name:
    Protein TBATA
    Protein Accession:
    Q96M53
    Secondary Accessions:
    • A4QPA8
    • B2RPQ2
    • Q5T4G2

    Protein attributes for TBATA Gene

    Size:
    351 amino acids
    Molecular mass:
    39460 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for TBATA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBATA Gene

Post-translational modifications for TBATA Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TBATA Gene

Domains & Families for TBATA Gene

Gene Families for TBATA Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for TBATA Gene

InterPro:

Suggested Antigen Peptide Sequences for TBATA Gene

GenScript: Design optimal peptide antigens:
  • C10orf27 protein (B7ZMN4_HUMAN)
  • C10orf27 protein (B7ZMN5_HUMAN)
  • Chromosome 10 open reading frame 27 (Q5T4G3_HUMAN)
  • Stromal protein associated with thymii and lymph node homolog (SPATL_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96M53

UniProtKB/Swiss-Prot:

TBATA_HUMAN :
  • Belongs to the TBATA family.
Family:
  • Belongs to the TBATA family.
genes like me logo Genes that share domains with TBATA: view

Function for TBATA Gene

Molecular function for TBATA Gene

UniProtKB/Swiss-Prot Function:
May play a role in spermatid differentiation. Modulates thymic stromal cell proliferation and thymus function.

Phenotypes From GWAS Catalog for TBATA Gene

Gene Ontology (GO) - Molecular Function for TBATA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with TBATA: view
genes like me logo Genes that share phenotypes with TBATA: view

Animal Models for TBATA Gene

MGI Knock Outs for TBATA:

miRNA for TBATA Gene

miRTarBase miRNAs that target TBATA

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBATA

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TBATA Gene

Localization for TBATA Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBATA Gene

Cytoplasm, cytosol.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TBATA gene
Compartment Confidence
cytoskeleton 4
cytosol 4
nucleus 2
plasma membrane 1
extracellular 1
mitochondrion 0

Gene Ontology (GO) - Cellular Components for TBATA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol ISS --
GO:0036064 ciliary basal body IDA 29257953
genes like me logo Genes that share ontologies with TBATA: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TBATA Gene

Pathways & Interactions for TBATA Gene

PathCards logo

SuperPathways for TBATA Gene

No Data Available

Interacting Proteins for TBATA Gene

STRING Interaction Network Preview (showing top 1 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: Q96M53-TBATA_HUMAN ENSP00000299290 for TBATA Gene via UniProtKB STRING IID

Gene Ontology (GO) - Biological Process for TBATA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007283 spermatogenesis IEA --
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with TBATA: view

No data available for Pathways by source and SIGNOR curated interactions for TBATA Gene

Drugs & Compounds for TBATA Gene

No Compound Related Data Available

Transcripts for TBATA Gene

mRNA/cDNA for TBATA Gene

4 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBATA

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for TBATA Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d · 8e ^ 9a · 9b · 9c ^ 10a · 10b · 10c · 10d · 10e ^
SP1: - - - - - -
SP2: - - - -
SP3:
SP4: - - - - - - - -
SP5: - - - - - - - -
SP6: - -
SP7: - -
SP8: - - -
SP9: - - - -
SP10: - -
SP11: - - - - - - - - - -
SP12:
SP13: - - -
SP14: - - -

ExUns: 11 ^ 12a · 12b
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for TBATA Gene

GeneLoc Exon Structure for
TBATA

Expression for TBATA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TBATA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TBATA Gene

This gene is overexpressed in Testis (x47.1).

Protein differential expression in normal tissues from HIPED for TBATA Gene

This gene is overexpressed in Cerebrospinal fluid (67.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TBATA Gene



Protein tissue co-expression partners for TBATA Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TBATA

SOURCE GeneReport for Unigene cluster for TBATA Gene:

Hs.386698
genes like me logo Genes that share expression patterns with TBATA: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for TBATA Gene

Orthologs for TBATA Gene

This gene was present in the common ancestor of chordates.

Orthologs for TBATA Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TBATA 29 30
  • 98.67 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TBATA 29 30
  • 81.91 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TBATA 29 30
  • 81.32 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Tbata 29 16 30
  • 74.22 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tbata 29
  • 72.53 (n)
Oppossum
(Monodelphis domestica)
Mammalia TBATA 30
  • 42 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TBATA 30
  • 41 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TBATA 30
  • 37 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC101731705 29
  • 54.6 (n)
Str.15612 29
Zebrafish
(Danio rerio)
Actinopterygii tbata 29 30
  • 48.71 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.7069 30
  • 23 (a)
OneToOne
Species where no ortholog for TBATA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for TBATA Gene

ENSEMBL:
Gene Tree for TBATA (if available)
TreeFam:
Gene Tree for TBATA (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TBATA: view image
Alliance of Genome Resources:
Additional Orthologs for TBATA

Paralogs for TBATA Gene

(1) SIMAP similar genes for TBATA Gene using alignment to 3 proteins:

  • TBATA_HUMAN
  • F5H4G4_HUMAN
  • Q5T4G3_HUMAN
genes like me logo Genes that share paralogs with TBATA: view

No data available for Paralogs for TBATA Gene

Variants for TBATA Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TBATA Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs2254433 Uncertain Significance: Hirschsprung disease 70,777,180(-) A/G
NM_001318241.1(TBATA):c.666T>C (p.Ala222=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs759944122 Likely Pathogenic: Hirschsprung disease 1 70,781,921(-) G/A
NM_152710.4(TBATA):c.157C>T (p.Arg53Cys)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs2254174 -- p.Arg237Gln

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TBATA Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TBATA Gene

Variant ID Type Subtype PubMed ID
esv32737 CNV gain+loss 17666407
esv3302857 CNV tandem duplication 20981092
esv3891856 CNV gain 25118596
nsv1043245 CNV loss 25217958
nsv524058 CNV loss 19592680
nsv831909 CNV loss 17160897

Variation tolerance for TBATA Gene

Residual Variation Intolerance Score: 89.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.88; 35.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBATA Gene

Human Gene Mutation Database (HGMD)
TBATA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBATA
Leiden Open Variation Database (LOVD)
TBATA

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBATA Gene

Disorders for TBATA Gene

MalaCards: The human disease database

(4) MalaCards diseases for TBATA Gene - From: CVR, COP, and GCD

Disorder Aliases PubMed IDs
hirschsprung disease 1
  • hirschsprung disease, susceptibility to, 1
janus kinase-3 deficiency
multiple sclerosis
  • multiple sclerosis, susceptibility to
megacystis-microcolon-intestinal hypoperistalsis syndrome
  • mmihs
- elite association - COSMIC cancer census association via MalaCards
Search TBATA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TBATA

genes like me logo Genes that share disorders with TBATA: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TBATA Gene

Publications for TBATA Gene

  1. Tbata modulates thymic stromal cell proliferation and thymus function. (PMID: 20937703) Flomerfelt FA … Gress RE (The Journal of experimental medicine 2010) 2 3
  2. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways. (PMID: 29257953) Sigg MA … Reiter JF (Developmental cell 2017) 3

Products for TBATA Gene

Sources for TBATA Gene