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Aliases for TULP3 Gene

Aliases for TULP3 Gene

  • TUB Like Protein 3 2 3
  • Tubby Like Protein 3 2 3 5
  • Tubby-Related Protein 3 3 4
  • 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. Among its related pathways are Signaling by Hedgehog and Signaling by GPCR. 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 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 , fRNAdb sequence ontologies and piRNA Summary for TULP3 Gene

Genomics for TULP3 Gene

GeneHancer (GH) Regulatory Elements for TULP3 Gene

Promoters and enhancers for TULP3 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
GH12J002889 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 639 +14.4 14443 4.2 ZNF652 SP1 ZKSCAN8 MNT NKRF POLR2A ZNF121 CSDE1 ZNF687 ZSCAN21 TULP3 RHNO1 NRIP2 ITFG2 DCP1B PIR60635 GC12M002940
GH12J002876 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 641.8 -0.3 -257 4.7 ZFX CBFA2T2 NKRF ZNF121 CEBPG ZNF384 ZNF687 ZSCAN21 AHR TFE3 TULP3 RHNO1 FOXM1 ITFG2 DCP1B CBX3P4 NRIP2 ENSG00000227081 FKBP4 GC12M002869
GH12J002256 Enhancer 1.3 Ensembl ENCODE dbSUPER 136.6 -620.5 -620525 1.6 ZNF473 ZNF121 IKZF1 ZNF680 ZNF704 ZNF547 ZNF488 ZNF544 ZNF300 ZNF776 ITFG2 TULP3 DCP1B CBX3P4 IQSEC3P1 ENSG00000227081 CACNA1C-AS4 NRIP2 LINC00942 CACNA1C-IT3
GH12J001924 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 97.5 -952.4 -952413 0.8 ZNF121 ZNF687 ZSCAN21 ZBTB7A YY1 SP7 ZNF548 MZF1 ZNF680 IKZF1 ITFG2 TULP3 RAD52 DCP1B LRTM2 ERC1 CBX3P4 CACNA2D4 GC12M001928
GH12J002811 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 24.7 -64.1 -64116 3 ZNF652 SP1 ZFX CTCF ELF3 MNT NKRF POLR2A MLLT1 ZNF121 ITFG2 ITFG2-AS1 DCP1B TULP3 NRIP2
- 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

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 isoforms=2245, posLast=316316, and isoforms=2277
  • 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

Protein Domains for TULP3 Gene

Blocks:
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 IBA,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

  • Applied Biological Materials (abm): Clones for TULP3 - Now 50% OFF >
  • * TULP3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * TULP3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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
nucleus 5
plasma membrane 4
extracellular 3
cytoskeleton 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (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:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane NAS 11375483
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

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

No data available for SIGNOR curated interactions for TULP3 Gene

Drugs & Compounds for TULP3 Gene

No Compound Related Data Available

Transcripts for TULP3 Gene

mRNA/cDNA for TULP3 Gene

Unigene Clusters for TULP3 Gene

Tubby like protein 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

  • Applied Biological Materials (abm): Clones for TULP3 - Now 50% OFF >
  • * TULP3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * TULP3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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
ECgene alternative splicing isoforms for
TULP3

Expression for TULP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of TULP3 Gene:

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 35
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TULP3 35 34
  • 80.76 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TULP3 35 34
  • 75.13 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Tulp3 17 35 34
  • 74.17 (n)
rat
(Rattus norvegicus)
Mammalia Tulp3 34
  • 71.74 (n)
oppossum
(Monodelphis domestica)
Mammalia TULP3 35
  • 63 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TULP3 35
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves TULP3 35 34
  • 69.09 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TULP3 35
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tulp3 34
  • 63.79 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC566221 34
  • 62.77 (n)
TULP3 35
  • 49 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011959 34
  • 58.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta king-tubby 35 34
  • 53.61 (n)
OneToMany
Tulp 36
  • 50 (a)
worm
(Caenorhabditis elegans)
Secernentea tub-1 35 36
  • 40 (a)
OneToMany
corn
(Zea mays)
Liliopsida Zm.3378 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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 from dbSNP and Humsavar for TULP3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000054094 -- 2,925,477(+) G/T intron_variant
rs1000090821 -- 2,932,115(+) C/T intron_variant
rs1000100380 -- 2,894,682(+) T/A intron_variant
rs1000261461 -- 2,894,362(+) C/T intron_variant
rs1000298001 -- 2,937,096(+) CTCT/CT intron_variant

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

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

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

Disorder Aliases PubMed IDs
joubert syndrome 1
  • jbts1
- 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 58
  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 58
  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 45 58
  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 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for TULP3 Gene

Sources for TULP3 Gene

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