TUB TUB bipartite transcription factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: TUBprovided by HGNC
Official Full Name: TUB bipartite transcription factorprovided by HGNC
Primary source: HGNC:HGNC:12406
See related: Ensembl:ENSG00000166402 MIM:601197; AllianceGenome:HGNC:12406
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: rd5; RDOB
Summary: 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]
Expression: Broad expression in brain (RPKM 18.8), endometrium (RPKM 10.0) and 21 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 11p15.4

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (8019059..8106243)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (8098231..8185410)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (8060180..8127790)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Common genetic variants associated with obesity in an African-American and Hispanic/Latino population.
Title: Common genetic variants associated with obesity in an African-American and Hispanic/Latino population.
Biallelic Inactivating TUB Variants Cause Retinal Ciliopathy Impairing Biogenesis and the Structure of the Primary Cilium.
Title: Biallelic Inactivating TUB Variants Cause Retinal Ciliopathy Impairing Biogenesis and the Structure of the Primary Cilium.
A novel homozygous TUB mutation associated with autosomal recessive retinitis pigmentosa in a consanguineous Chinese family.
Title: A novel homozygous TUB mutation associated with autosomal recessive retinitis pigmentosa in a consanguineous Chinese family.
Lnc-OIP5-AS1 exacerbates aorta wall injury during the development of aortic dissection through upregulating TUB via sponging miR-143-3p.
Title: Lnc-OIP5-AS1 exacerbates aorta wall injury during the development of aortic dissection through upregulating TUB via sponging miR-143-3p.
Candidate variants in TUB are associated with familial tremor.
Title: Candidate variants in TUB are associated with familial tremor.
Studied the expression and distribution patterns of tubby bipartite transcription factor (TUB) in the hypothalamus and in adipose tissue in obese and healthy controls.
Title: TUB gene expression in hypothalamus and adipose tissue and its association with obesity in humans.
Tubby and Tulp1 mediated phagocytosis through MerTK-dependent signaling with non-muscle myosin II redistribution leading to colocalization of phagocytosed vesicles with rearranged NMMIIA.
Title: Synergistic interaction of tubby and tubby-like protein 1 (Tulp1).
Tubby and Tulp1 are bridging molecules with their N-terminal region as MERTK-binding domain and C-terminal region as phagocytosis prey-binding domain.
Title: Tubby and tubby-like protein 1 are new MerTK ligands for phagocytosis.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Tubby and Tulp1 function as phagocytosis sigmals (eat-me) for retinal pigment epithelium cells and other phagocytes.
Title: Identification of tubby and tubby-like protein 1 as eat-me signals by phage display.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Phenotypes

Go to the top of the page Help

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
Retinal dystrophy and obesity MedGen: C4015424 OMIM: 616188 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Both HIV-1 Tat 47-59 and FITC-labeled Tat 47-59 peptides downregulate gene expression of tubby homolog, mouse (TUB) in U-937 macrophages	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

PMC310777P16 (e-PCR)
- UniSTS:272683

PMC20333P1 (e-PCR)
- UniSTS:271931

PMC20333P2 (e-PCR)
- UniSTS:271932

RH36564 (e-PCR)
- UniSTS:55145

G02283 (e-PCR)
- UniSTS:14444

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables G protein-coupled receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables intraciliary transport particle A binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within intraciliary transport	IDA Inferred from Direct Assay more info	PubMed
involved_in phagocytosis, recognition	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of phagocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to cilium	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein localization to photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
involved_in receptor localization to non-motile cilium	IEA Inferred from Electronic Annotation more info
involved_in regulation of G protein-coupled receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in retina development in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
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 cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: tubby protein homolog

Names: tubby bipartite transcription factor; tubby homolog; tubby homologue

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

Genomic

NG_029912.2 RefSeqGene

Range

67154..92186

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_003320.5 → NP_003311.2 tubby protein homolog isoform a

See identical proteins and their annotated locations for NP_003311.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript, and encodes the longer isoform (a).

Source sequence(s)

AC116456, BC075032, BM992151, U82467

Consensus CDS

CCDS7786.1

UniProtKB/TrEMBL

E9PQR4

Related

ENSP00000305426.4, ENST00000305253.8

Conserved Domains (2) summary

pfam01167
Location:313 → 554

Tub; Tub family

pfam16322
Location:84 → 292

Tub_N; Tubby N-terminal
NM_177972.3 → NP_813977.1 tubby protein homolog isoform b

See identical proteins and their annotated locations for NP_813977.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. This results in a shorter isoform (b) with a distinct N-terminus, compared to isoform a.

Source sequence(s)

AC116456, BM679358, BM992151, U54644

Consensus CDS

CCDS7787.1

UniProtKB/Swiss-Prot

D3DQU4, O00293, P50607, Q6B007

UniProtKB/TrEMBL

E9PQR4

Related

ENSP00000299506.3, ENST00000299506.3

Conserved Domains (2) summary

pfam01167
Location:258 → 499

Tub; Tub family

pfam16322
Location:29 → 237

Tub_N; Tubby N-terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

8019059..8106243

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005253109.4 → XP_005253166.1 tubby protein homolog isoform X1

UniProtKB/TrEMBL

E9PQR4

Related

ENSP00000434400.1, ENST00000534099.5

Conserved Domains (2) summary

pfam01167
Location:300 → 541

Tub; Tub family

pfam16322
Location:71 → 279

Tub_N; Tubby N-terminal
XM_047427512.1 → XP_047283468.1 tubby protein homolog isoform X3

UniProtKB/TrEMBL

E9PQR4
XM_047427513.1 → XP_047283469.1 tubby protein homolog isoform X4

UniProtKB/TrEMBL

E9PQR4
XM_047427515.1 → XP_047283471.1 tubby protein homolog isoform X6
XM_047427517.1 → XP_047283473.1 tubby protein homolog isoform X8

UniProtKB/TrEMBL

Q9H4D2
XM_047427514.1 → XP_047283470.1 tubby protein homolog isoform X5

UniProtKB/TrEMBL

E9PQR4
XM_047427516.1 → XP_047283472.1 tubby protein homolog isoform X7
XM_011520344.3 → XP_011518646.1 tubby protein homolog isoform X2

See identical proteins and their annotated locations for XP_011518646.1

UniProtKB/TrEMBL

E9PQR4

Conserved Domains (2) summary

pfam01167
Location:270 → 511

Tub; Tub family

pfam16322
Location:41 → 249

Tub_N; Tubby N-terminal

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

8098231..8185410

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054369807.1 → XP_054225782.1 tubby protein homolog isoform X1

UniProtKB/TrEMBL

E9PQR4
XM_054369809.1 → XP_054225784.1 tubby protein homolog isoform X3

UniProtKB/TrEMBL

E9PQR4
XM_054369810.1 → XP_054225785.1 tubby protein homolog isoform X4

UniProtKB/TrEMBL

E9PQR4
XM_054369812.1 → XP_054225787.1 tubby protein homolog isoform X6
XM_054369814.1 → XP_054225789.1 tubby protein homolog isoform X8

UniProtKB/TrEMBL

Q9H4D2
XM_054369811.1 → XP_054225786.1 tubby protein homolog isoform X5

UniProtKB/TrEMBL

E9PQR4
XM_054369813.1 → XP_054225788.1 tubby protein homolog isoform X7
XM_054369808.1 → XP_054225783.1 tubby protein homolog isoform X2

UniProtKB/TrEMBL

E9PQR4