This gene encodes a member of the tubby gene family of bipartite transcription factors. Members of this family have been identified in plants, vertebrates, and invertebrates, and they share a conserved N-terminal transcription activation region and a conserved C-terminal DNA and phosphatidylinositol-phosphate binding region. The encoded protein binds to phosphoinositides in the... See more...

Aliases for TULP3 Gene

Aliases for TULP3 Gene

  • TUB Like Protein 3 2 3 5
  • Tubby-Related Protein 3 3 4
  • Tubby Like Protein 3 2 3
  • TUBL3 3 4
  • Tubby-Like Protein 3 4

External Ids for TULP3 Gene

Previous GeneCards Identifiers for TULP3 Gene

  • GC12P002872
  • GC12P003000
  • GC12P002987
  • GC12P002989

Summaries for TULP3 Gene

Entrez Gene Summary for TULP3 Gene

  • This gene encodes a member of the tubby gene family of bipartite transcription factors. Members of this family have been identified in plants, vertebrates, and invertebrates, and they share a conserved N-terminal transcription activation region and a conserved C-terminal DNA and phosphatidylinositol-phosphate binding region. The encoded protein binds to phosphoinositides in the plasma membrane via its C-terminal region and probably functions as a membrane-bound transcription regulator that translocates to the nucleus in response to phosphoinositide hydrolysis, for instance, induced by G-protein-coupled-receptor signaling. It plays an important role in neuronal development and function. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, May 2009]

GeneCards Summary for TULP3 Gene

TULP3 (TUB Like Protein 3) is a Protein Coding gene. Diseases associated with TULP3 include Joubert Syndrome 1 and Ellis-Van Creveld Syndrome. Among its related pathways are Signaling by GPCR and Signaling by Hedgehog. Gene Ontology (GO) annotations related to this gene include enzyme binding and phosphatidylinositol binding. An important paralog of this gene is TUB.

UniProtKB/Swiss-Prot Summary for TULP3 Gene

  • Negative regulator of the Shh signaling transduction pathway: recruited to primary cilia via association with the IFT complex A (IFT-A) and is required for recruitment of G protein-coupled receptor GPR161 to cilia, a promoter of PKA-dependent basal repression machinery in Shh signaling. Binds to phosphorylated inositide (phosphoinositide) lipids. Both IFT-A- and phosphoinositide-binding properties are required to regulate ciliary G protein-coupled receptor trafficking. Not involved in ciliogenesis.

Additional gene information for TULP3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TULP3 Gene

Genomics for TULP3 Gene

GeneHancer (GH) Regulatory Elements for TULP3 Gene

Promoters and enhancers for TULP3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TULP3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TULP3

Top Transcription factor binding sites by QIAGEN in the TULP3 gene promoter:
  • CREB
  • deltaCREB
  • E2F
  • YY1

Genomic Locations for TULP3 Gene

Genomic Locations for TULP3 Gene
chr12:2,877,223-2,941,140
(GRCh38/hg38)
Size:
63,918 bases
Orientation:
Plus strand
chr12:2,986,389-3,050,306
(GRCh37/hg19)
Size:
63,918 bases
Orientation:
Plus strand

Genomic View for TULP3 Gene

Genes around TULP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TULP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TULP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TULP3 Gene

Proteins for TULP3 Gene

  • Protein details for TULP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75386-TULP3_HUMAN
    Recommended name:
    Tubby-related protein 3
    Protein Accession:
    O75386
    Secondary Accessions:
    • B3KNB7
    • B7Z6A2
    • D3DUQ4
    • F8WBZ9
    • Q8N5B0

    Protein attributes for TULP3 Gene

    Size:
    442 amino acids
    Molecular mass:
    49642 Da
    Quaternary structure:
    • Associates with the IFT complex A (IFT-A).

    Alternative splice isoforms for TULP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TULP3 Gene

Post-translational modifications for TULP3 Gene

  • Ubiquitination at Lys245, Lys277, and Lys316
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TULP3 Gene

Domains & Families for TULP3 Gene

Gene Families for TULP3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for TULP3 Gene

Blocks:
  • Tubby
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TULP3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ54520, highly similar to Homo sapiens tubby like protein 3 (TULP3), mRNA (B7Z1E7_HUMAN)
  • cDNA FLJ60873, highly similar to Tubby-related protein 3 (B7Z6A2_HUMAN)
  • Tubby-like protein 3 (TULP3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75386

UniProtKB/Swiss-Prot:

TULP3_HUMAN :
  • Belongs to the TUB family.
Family:
  • Belongs to the TUB family.
genes like me logo Genes that share domains with TULP3: view

Function for TULP3 Gene

Molecular function for TULP3 Gene

UniProtKB/Swiss-Prot Function:
Negative regulator of the Shh signaling transduction pathway: recruited to primary cilia via association with the IFT complex A (IFT-A) and is required for recruitment of G protein-coupled receptor GPR161 to cilia, a promoter of PKA-dependent basal repression machinery in Shh signaling. Binds to phosphorylated inositide (phosphoinositide) lipids. Both IFT-A- and phosphoinositide-binding properties are required to regulate ciliary G protein-coupled receptor trafficking. Not involved in ciliogenesis.
GENATLAS Biochemistry:
tubby-like protein 3,expressed in testis,ovary,thyroid,spinal cord,brain,and in retina,at a moderate level,only in the inner nuclear and ganglion cell layers

Phenotypes From GWAS Catalog for TULP3 Gene

Gene Ontology (GO) - Molecular Function for TULP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001664 G protein-coupled receptor binding IDA 28154160
GO:0005515 protein binding IPI 22190034
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding NAS 11375483
GO:0019899 enzyme binding IPI 23382074
GO:0035091 phosphatidylinositol binding IDA 20889716
genes like me logo Genes that share ontologies with TULP3: view
genes like me logo Genes that share phenotypes with TULP3: view

Animal Models for TULP3 Gene

MGI Knock Outs for TULP3:
  • Tulp3 Tulp3<tm1Jng>
  • Tulp3 Tulp3<tm1b(EUCOMM)Hmgu>

Animal Model Products

  • Taconic Biosciences Mouse Models for TULP3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TULP3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TULP3 Gene

Localization for TULP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TULP3 Gene

Nucleus. Cell membrane. Cell projection, cilium. Cytoplasm. Secreted. Note=Does not have a cleavable signal peptide and is secreted by a non-conventional pathway (By similarity). Translocates from the plasma membrane to the nucleus upon activation of guanine nucleotide-binding protein G(q) subunit alpha. {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 TULP3 gene
Compartment Confidence
plasma membrane 5
nucleus 5
extracellular 3
cytoskeleton 3
cytosol 2
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TULP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005634 nucleus NAS 11375483
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with TULP3: view

Pathways & Interactions for TULP3 Gene

PathCards logo

SuperPathways for TULP3 Gene

genes like me logo Genes that share pathways with TULP3: view

Pathways by source for TULP3 Gene

SIGNOR curated interactions for TULP3 Gene

Activates:

Gene Ontology (GO) - Biological Process for TULP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001841 neural tube formation IEA --
GO:0001843 neural tube closure IEA --
GO:0006355 regulation of transcription, DNA-templated NAS 11375483
GO:0007186 G protein-coupled receptor signaling pathway NAS 11375483
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with TULP3: view

Drugs & Compounds for TULP3 Gene

No Compound Related Data Available

Transcripts for TULP3 Gene

mRNA/cDNA for TULP3 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TULP3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TULP3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13
SP1: -
SP2: - -
SP3: - - - - - - - -
SP4:
SP5: -

Relevant External Links for TULP3 Gene

GeneLoc Exon Structure for
TULP3

Expression for TULP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TULP3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TULP3 Gene

This gene is overexpressed in Ovary (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TULP3 Gene



Protein tissue co-expression partners for TULP3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TULP3

SOURCE GeneReport for Unigene cluster for TULP3 Gene:

Hs.655333

mRNA Expression by UniProt/SwissProt for TULP3 Gene:

O75386-TULP3_HUMAN
Tissue specificity: Expressed at high levels in testis, ovaries, thyroid, and spinal chord.

Evidence on tissue expression from TISSUES for TULP3 Gene

  • Eye(4.3)
genes like me logo Genes that share expression patterns with TULP3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TULP3 Gene

Orthologs for TULP3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TULP3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TULP3 31
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TULP3 31 30
  • 80.76 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TULP3 31 30
  • 75.13 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Tulp3 17 31 30
  • 74.17 (n)
rat
(Rattus norvegicus)
Mammalia Tulp3 30
  • 71.74 (n)
oppossum
(Monodelphis domestica)
Mammalia TULP3 31
  • 63 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TULP3 31
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves TULP3 31 30
  • 69.09 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TULP3 31
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tulp3 30
  • 63.79 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC566221 30
  • 62.77 (n)
TULP3 31
  • 49 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011959 30
  • 58.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta king-tubby 31 30
  • 53.61 (n)
OneToMany
Tulp 32
  • 50 (a)
worm
(Caenorhabditis elegans)
Secernentea tub-1 31 32
  • 40 (a)
OneToMany
corn
(Zea mays)
Liliopsida Zm.3378 30
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 56 (a)
OneToMany
Species where no ortholog for TULP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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 (Oryza sativa)
  • 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 TULP3 Gene

ENSEMBL:
Gene Tree for TULP3 (if available)
TreeFam:
Gene Tree for TULP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TULP3: view image

Paralogs for TULP3 Gene

Paralogs for TULP3 Gene

(3) SIMAP similar genes for TULP3 Gene using alignment to 7 proteins:

  • TULP3_HUMAN
  • B7Z6A2_HUMAN
  • F5GWL5_HUMAN
  • F5H7B9_HUMAN
  • F8WBZ9_HUMAN
  • H0YFU8_HUMAN
  • H0YG12_HUMAN

Pseudogenes.org Pseudogenes for TULP3 Gene

genes like me logo Genes that share paralogs with TULP3: view

Variants for TULP3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TULP3 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
768504 Benign: not provided 2,938,229(+) G/A MISSENSE_VARIANT
784226 Benign: not provided 2,934,524(+) C/A MISSENSE_VARIANT
784227 Benign: not provided 2,940,631(+) G/T NONSENSE,THREE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for TULP3 Gene

Structural Variations from Database of Genomic Variants (DGV) for TULP3 Gene

Variant ID Type Subtype PubMed ID
dgv19n68 CNV loss 17160897
esv2648236 CNV deletion 19546169
esv3628321 CNV gain 21293372
esv3628326 CNV gain 21293372
esv3628327 CNV loss 21293372
esv3628328 CNV loss 21293372
nsv1122687 CNV deletion 24896259
nsv1125182 CNV insertion 24896259
nsv470261 CNV loss 18288195
nsv579 CNV insertion 18451855
nsv832311 CNV loss 17160897

Variation tolerance for TULP3 Gene

Residual Variation Intolerance Score: 78.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.31; 70.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TULP3 Gene

Human Gene Mutation Database (HGMD)
TULP3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TULP3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TULP3 Gene

Disorders for TULP3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for TULP3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
joubert syndrome 1
  • jbts1
ellis-van creveld syndrome
  • evc
neural tube defects
  • neural tube defects, susceptibility to
meckel syndrome, type 1
  • mks1
bardet-biedl syndrome
  • biedl-bardet syndrome
- elite association - COSMIC cancer census association via MalaCards
Search TULP3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TULP3

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 TULP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TULP3 Gene

Publications for TULP3 Gene

  1. Molecular characterization of a novel tubby gene family member, TULP3, in mouse and humans. (PMID: 9828123) Nishina PM … Naggert JK (Genomics 1998) 2 3 4 23 54
  2. Intraflagellar transport-A complex mediates ciliary entry and retrograde trafficking of ciliary G protein-coupled receptors. (PMID: 27932497) Hirano T … Nakayama K (Molecular biology of the cell 2017) 3 4 54
  3. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 41 54
  4. TULP3 bridges the IFT-A complex and membrane phosphoinositides to promote trafficking of G protein-coupled receptors into primary cilia. (PMID: 20889716) Mukhopadhyay S … Jackson PK (Genes & development 2010) 3 4 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54

Products for TULP3 Gene

Sources for TULP3 Gene