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TUB Gene(Protein Coding)

Tubby Bipartite Transcription Factor

GCID:
GC11P008040
GIFtS:
52
Genes Participants
UDN Logo

Aliases for TUB Gene

Aliases for TUB Gene

  • Tubby Bipartite Transcription Factor 2 3 5
  • Tubby (Mouse) Homolog 2
  • Tubby Homolog (Mouse) 2
  • Tubby Protein Homolog 3
  • Tubby Homologue 3
  • Tubby Homolog 3
  • RDOB 3
  • Rd5 3

External Ids for TUB Gene

Previous GeneCards Identifiers for TUB Gene

  • GC11P008828
  • GC11P008520
  • GC11P007999
  • GC11P008024
  • GC11P008016
  • GC11P007727

Summaries for TUB Gene

Entrez Gene Summary for TUB Gene

  • This gene encodes a member of the Tubby family of bipartite transcription factors. The encoded protein may play a role in obesity and sensorineural degradation. The crystal structure has been determined for a similar protein in mouse, and it functions as a membrane-bound transcription regulator that translocates to the nucleus in response to phosphoinositide hydrolysis. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for TUB Gene

TUB (Tubby Bipartite Transcription Factor) is a Protein Coding gene. Diseases associated with TUB include Retinal Dystrophy And Obesity and Retinitis Pigmentosa. Among its related pathways are Transcription_Transcription factor Tubby signaling pathways and Presynaptic function of Kainate receptors. Gene Ontology (GO) annotations related to this gene include protein complex binding and G-protein coupled photoreceptor activity. An important paralog of this gene is TULP3.

UniProtKB/Swiss-Prot for TUB Gene

  • Functions in signal transduction from heterotrimeric G protein-coupled receptors. Binds to membranes containing phosphatidylinositol 4,5-bisphosphate. Can bind DNA (in vitro). May contribute to the regulation of transcription in the nucleus. Could be involved in the hypothalamic regulation of body weight (By similarity). Contribute to stimulation of phagocytosis of apoptotic retinal pigment epithelium (RPE) cells and macrophages.

Gene Wiki entry for TUB Gene

Additional gene information for TUB Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TUB Gene

Genomics for TUB Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for TUB Gene

Promoters and enhancers for TUB 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
GH11I008080 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 566.7 +62.9 62937 3.5 KLF17 SIN3A ZNF335 ZNF121 GLIS2 ZNF143 RCOR1 EGR2 SP3 ZNF398 TUB CASC23 ENSG00000254921 LOC100506258 TRIM66 RIC3 ENSG00000279391 PIR31183 GC11P008020
GH11I008018 Promoter/Enhancer 1.5 FANTOM5 Ensembl ENCODE 567.1 +0.3 269 1.8 SIN3A BMI1 ZNF335 GLIS2 ZNF366 SCRT2 FOS EGR2 ZNF398 CBX8 TUB GC11P008020 RIC3 OR10A3
GH11I008038 Promoter 0.7 EPDnew 550.4 +19.5 19512 0.1 MXI1 RFX1 BMI1 ENSG00000254921 TUB GC11P008020
GH11I007985 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.3 -32.0 -31991 2.7 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 EIF3F SNORA3B OLFML1 TMEM9B-AS1 ZNF214 RPL27A ST5 CASC23 TUB COX6CP5
GH11I008067 Enhancer 1 Ensembl ENCODE 17.8 +49.8 49797 2.1 PKNOX1 MZF1 FEZF1 RFX5 YY1 RCOR1 FOS RXRA USF2 REST TUB ENSG00000254921 CASC23 TUB-AS1 ENSG00000279391 GC11P008020
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TUB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TUB gene promoter:

Genomic Locations for TUB Gene

Genomic Locations for TUB Gene
chr11:8,019,180-8,106,241
(GRCh38/hg38)
Size:
87,062 bases
Orientation:
Plus strand
chr11:8,040,791-8,127,659
(GRCh37/hg19)

Genomic View for TUB Gene

Genes around TUB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for TUB Gene

Proteins for TUB Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P50607-TUB_HUMAN
    Recommended name:
    Tubby protein homolog
    Protein Accession:
    P50607
    Secondary Accessions:
    • D3DQU4
    • O00293
    • Q6B007

    Protein attributes for TUB Gene

    Size:
    506 amino acids
    Molecular mass:
    55651 Da
    Quaternary structure:
    • Interacts with GNAQ. Interacts with TULP1.

    Three dimensional structures from OCA and Proteopedia for TUB Gene

    Alternative splice isoforms for TUB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TUB Gene

Protein Expression for TUB Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TUB Gene

No Post-translational modifications

Other Protein References for TUB Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TUB Gene

Domains & Families for TUB Gene

Gene Families for TUB Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for TUB Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TUB Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P50607

UniProtKB/Swiss-Prot:

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

Function for TUB Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for TUB Gene

GENATLAS Biochemistry:
tubby gene homolog of mouse (Tub) of mild naturity onset obesity,progressive retinal and cochlear degeneration,expressed in cochlea,retina,brain,testis
UniProtKB/Swiss-Prot Function:
Functions in signal transduction from heterotrimeric G protein-coupled receptors. Binds to membranes containing phosphatidylinositol 4,5-bisphosphate. Can bind DNA (in vitro). May contribute to the regulation of transcription in the nucleus. Could be involved in the hypothalamic regulation of body weight (By similarity). Contribute to stimulation of phagocytosis of apoptotic retinal pigment epithelium (RPE) cells and macrophages.

Phenotypes From GWAS Catalog for TUB Gene

Gene Ontology (GO) - Molecular Function for TUB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032403 protein complex binding IDA 20889716
GO:0035091 phosphatidylinositol binding IBA --
genes like me logo Genes that share ontologies with TUB: view
genes like me logo Genes that share phenotypes with TUB: view

Human Phenotype Ontology for TUB Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TUB Gene

MGI Knock Outs for TUB:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TUB Gene

Localization for TUB Gene

Subcellular locations from UniProtKB/Swiss-Prot for TUB Gene

Cytoplasm. Nucleus. Secreted. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Note=Binds phospholipid and is anchored to the plasma membrane through binding phosphatidylinositol 4,5-bisphosphate. Is released upon activation of phospholipase C. Translocates from the plasma membrane to the nucleus upon activation of guanine nucleotide-binding protein G(q) subunit alpha. Does not have a cleavable signal peptide and is secreted by a non-conventional pathway (By similarity). {ECO:0000250}.

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 TUB gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 4
plasma membrane 3
cytoskeleton 3
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (2)
  • Microtubule organizing center (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TUB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005634 nucleus TAS,IEA --
GO:0005737 cytoplasm TAS 11000483
GO:0005829 cytosol IEA --
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with TUB: view

Pathways & Interactions for TUB Gene

genes like me logo Genes that share pathways with TUB: view

Pathways by source for TUB Gene

1 GeneGo (Thomson Reuters) pathway for TUB Gene
1 Qiagen pathway for TUB Gene

Gene Ontology (GO) - Biological Process for TUB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006909 phagocytosis IEA --
GO:0006910 phagocytosis, recognition IEA --
GO:0007605 sensory perception of sound IEA --
GO:0009725 response to hormone IEA --
GO:0045494 photoreceptor cell maintenance IEA --
genes like me logo Genes that share ontologies with TUB: view

No data available for SIGNOR curated interactions for TUB Gene

Drugs & Compounds for TUB Gene

Products:

  1. Drug

(1) Drugs for TUB Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Alpha-Glycerophospho-D-Myo-Inositol-4,5-Bis-Phosphate Experimental Pharma Target 0
genes like me logo Genes that share compounds with TUB: view

Transcripts for TUB Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TUB Gene

(4) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(72) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TUB Gene

Tubby homolog (mouse):
Representative Sequences:

Clone Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17
SP1: - - - - - -
SP2:
SP3: -
SP4:

Relevant External Links for TUB Gene

GeneLoc Exon Structure for
TUB
ECgene alternative splicing isoforms for
TUB

Expression for TUB Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for TUB Gene
mRNA expression by BioGPS for TUB GenemRNA expression by GTEx for TUB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TUB Gene

This gene is overexpressed in Fetal Brain (31.7) and Retina (31.6).

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



Protein tissue co-expression partners for TUB Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TUB Gene:

TUB

SOURCE GeneReport for Unigene cluster for TUB Gene:

Hs.568986

Evidence on tissue expression from TISSUES for TUB Gene

  • Nervous system(4.7)
  • Skin(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TUB Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
Pelvis:
  • penis
  • testicle
General:
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with TUB: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for TUB Gene

Orthologs for TUB Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TUB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TUB 33 34
  • 99.58 (n)
dog
(Canis familiaris)
 Mammalia TUB 33 34
  • 91.67 (n)
mouse
(Mus musculus)
 Mammalia Tub 33 16 34
  • 90.85 (n)
rat
(Rattus norvegicus)
 Mammalia Tub 33
  • 90.04 (n)
cow
(Bos Taurus)
 Mammalia TUB 33 34
  • 90.02 (n)
oppossum
(Monodelphis domestica)
 Mammalia TUB 34
  • 75 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia TUB 34
  • 66 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves TUB 33 34
  • 71.9 (n)
lizard
(Anolis carolinensis)
 Reptilia TUB 34
  • 75 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia tub 33
  • 74.53 (n)
Str.12141 33
zebrafish
(Danio rerio)
 Actinopterygii TUB 34
  • 75 (a)
 OneToOne
tub 33
  • 73.92 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Tulp 35
  • 63 (a)
king-tubby 34
  • 44 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea tub-1 35 33 34
  • 57.18 (n)
Alicante grape
(Vitis vinifera)
 eudicotyledons Vvi.6835 33
rice
(Oryza sativa)
 Liliopsida Os03g0351400 33
  • 52.01 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 62 (a)
 OneToMany
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.13886 33
Species where no ortholog for TUB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)

Evolution for TUB Gene

ENSEMBL:
Gene Tree for TUB (if available)
TreeFam:
Gene Tree for TUB (if available)

Paralogs for TUB Gene

Paralogs for TUB Gene

(3) SIMAP similar genes for TUB Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with TUB: view

Variants for TUB Gene

Sequence variations from dbSNP and Humsavar for TUB Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs727502810 pathogenic, Retinal dystrophy and obesity 8,100,575(+) GAGAGAG/GAGAG coding_sequence_variant, frameshift
rs1000006631 -- 8,092,818(+) G/A intron_variant
rs1000036415 -- 8,099,076(+) G/A intron_variant
rs1000060116 -- 8,086,407(+) G/A intron_variant
rs1000066580 -- 8,068,617(+) C/T genic_upstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
nsv7215 OTHER inversion 18451855
nsv499766 OTHER inversion 21111241
nsv473005 CNV novel sequence insertion 20440878
nsv428249 CNV loss 18775914
esv3579353 CNV loss 25503493
esv3579352 CNV loss 25503493
esv25122 CNV loss 19812545
esv1001231 CNV insertion 20482838

Variation tolerance for TUB Gene

Residual Variation Intolerance Score: 16.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.06; 50.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TUB Gene

Human Gene Mutation Database (HGMD)
TUB
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TUB

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

Disorders for TUB Gene

MalaCards: The human disease database

(5) MalaCards diseases for TUB Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search TUB in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TUB_HUMAN
  • Retinal dystrophy and obesity (RDOB) [MIM:616188]: A disease characterized by obesity, night blindness, decreased visual acuity, and electrophysiological features of a rod cone dystrophy. {ECO:0000269 PubMed:24375934}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TUB

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TUB: view

No data available for Genatlas for TUB Gene

Publications for TUB Gene

  1. Molecular characterization of TUB, TULP1, and TULP2, members of the novel tubby gene family and their possible relation to ocular diseases. (PMID: 9096357) North MA … Nishina PM (Proceedings of the National Academy of Sciences of the United States of America 1997) 3 4 22 58
  2. Identification and characterization of the mouse obesity gene tubby: a member of a novel gene family. (PMID: 8612280) Kleyn PW … Moore KJ (Cell 1996) 2 3 4 58
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  4. Inherited genetic variant predisposes to aggressive but not indolent prostate cancer. (PMID: 20080650) Xu J … Isaacs WB (Proceedings of the National Academy of Sciences of the United States of America 2010) 3 44 58
  5. Identification of tubby and tubby-like protein 1 as eat-me signals by phage display. (PMID: 19837063) Caberoy NB … Li W (Experimental cell research 2010) 3 4 58

Products for TUB Gene

Sources for TUB Gene

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