TULP3 TUB like protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TULP3provided by HGNC
Official Full Name: TUB like protein 3provided by HGNC
Primary source: HGNC:HGNC:12425
See related: Ensembl:ENSG00000078246 MIM:604730; AllianceGenome:HGNC:12425
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HRCDF; TUBL3
Summary: 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]
Expression: Ubiquitous expression in ovary (RPKM 20.1), endometrium (RPKM 13.4) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.33

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (2890891..2941138)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (2896833..2947229)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (3000057..3050304)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TULP3 silencing suppresses cell proliferation, migration and invasion in gastric cancer via the PTEN/Akt/Snail pathway.
Title: TULP3 silencing suppresses cell proliferation, migration and invasion in gastric cancer via the PTEN/Akt/Snail pathway.
Progressive liver, kidney, and heart degeneration in children and adults affected by TULP3 mutations.
Title: Progressive liver, kidney, and heart degeneration in children and adults affected by TULP3 mutations.
MicroRNA-506 has a suppressive effect on the tumorigenesis of nonsmall-cell lung cancer by regulating tubby-like protein 3.
Title: MicroRNA-506 has a suppressive effect on the tumorigenesis of nonsmall-cell lung cancer by regulating tubby-like protein 3.
TULP3 expression levels were increased in colorectal cancer when compared to the adjacent non-tumoral tissue. In addition, higher TULP3 gene expression was associated to lymphatic and vascular invasion in colon adenocarcinoma and rectum adenocarcinoma, respectively.
Title: TULP3: A potential biomarker in colorectal cancer?
Formation of primary cilia is downregulated in TULP3-knockout (KO) RPE1 cells. ARL13B and INPP5E fail to localize to primary cilia in TULP3-KO cells.
Title: TULP3 is required for localization of membrane-associated proteins ARL13B and INPP5E to primary cilia.
Data demonstrated that pancreatic cancer patients exhibiting high transcriptional levels of TULP3 showed a poor overall survival rate.
Title: Computational analyses reveal a prognostic impact of TULP3 as a transcriptional master regulator in pancreatic ductal adenocarcinoma.
Observational study of gene-disease association. (HuGE Navigator)
Title: Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hepatorenocardiac degenerative fibrosis MedGen: C5676996 OMIM: 619902 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	HIV-1 Vpr is identified to have a physical interaction with tubby like protein 3 (TULP3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G17615 (e-PCR)
- UniSTS:73748

RH44963 (e-PCR)
- UniSTS:2874

STS-N62451 (e-PCR)
- UniSTS:74684

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables G protein-coupled receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables intraciliary transport particle A binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-4,5-bisphosphate binding	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
involved_in bone development	IEA Inferred from Electronic Annotation more info
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in bronchus morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in central nervous system neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in embryonic camera-type eye development	IEA Inferred from Electronic Annotation more info
involved_in embryonic digit morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic neurocranium morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in ganglion development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of smoothened signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in neural tube closure	IEA Inferred from Electronic Annotation more info
involved_in protein localization to cilium	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein localization to cilium	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein localization to cilium	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within protein localization to cilium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within regulation of G protein-coupled receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of G protein-coupled receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of G protein-coupled receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in smoothened signaling pathway involved in dorsal/ventral neural tube patterning	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in 9+0 non-motile cilium	IDA Inferred from Direct Assay more info	PubMed
located_in axoneme	IEA Inferred from Electronic Annotation more info
located_in ciliary base	IDA Inferred from Direct Assay more info	PubMed
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	TAS Traceable Author Statement more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: tubby-related protein 3

Names: tubby like protein 3

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_001160408.2 → NP_001153880.1 tubby-related protein 3 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a longer and distinct C-terminus compared to isoform 1.

Source sequence(s)

AC005911, AK024246, BP392987

Consensus CDS

CCDS53737.1

UniProtKB/Swiss-Prot

O75386

Related

ENSP00000380321.2, ENST00000397132.6

Conserved Domains (2) summary

pfam01167
Location:195 → 435

Tub; Tub family

pfam16322
Location:31 → 169

Tub_N; Tubby N-terminal
NM_003324.5 → NP_003315.2 tubby-related protein 3 isoform 1

See identical proteins and their annotated locations for NP_003315.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript but encodes the shorter isoform (1).

Source sequence(s)

AK024246, AK293285, BC032587

Consensus CDS

CCDS8519.1

UniProtKB/Swiss-Prot

B3KNB7, B7Z6A2, D3DUQ4, F8WBZ9, O75386, Q8N5B0

Related

ENSP00000410051.2, ENST00000448120.7

Conserved Domains (2) summary

pfam01167
Location:195 → 435

Tub; Tub family

pfam16322
Location:31 → 169

Tub_N; Tubby N-terminal