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

Gene ID: 7275, updated on 1-Mar-2024

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
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Genomic context

See TUB in Genome Data Viewer
Location:
11p15.4
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (8019059..8106243)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (8098231..8185410)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (8060180..8127790)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:8008582-8009121 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:8009122-8009660 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:8016231-8017430 Neighboring gene eukaryotic translation initiation factor 3 subunit F Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3112 Neighboring gene cancer susceptibility 23 Neighboring gene uncharacterized LOC124902627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8057222-8057786 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:8093711-8094487 Neighboring gene TUB antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8104709-8105272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8111641-8112141 Neighboring gene RIC3 acetylcholine receptor chaperone Neighboring gene RIC3 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 8819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8214713-8215283 Neighboring gene VISTA enhancer hs1859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8244025-8244526 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8248695-8249355 Neighboring gene uncharacterized LOC105376536 Neighboring gene LIM domain only 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

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 response to stimulus 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

Preferred Names
tubby protein homolog
Names
tubby bipartite transcription factor
tubby homolog
tubby homologue

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.

Genomic

  1. NG_029912.2 RefSeqGene

    Range
    67154..92186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_003320.5NP_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
    B4DE99
    Related
    ENSP00000305426.4, ENST00000305253.8
    Conserved Domains (2) summary
    pfam01167
    Location:313554
    Tub; Tub family
    pfam16322
    Location:84292
    Tub_N; Tubby N-terminal
  2. NM_177972.3NP_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
    B4DE99
    Related
    ENSP00000299506.3, ENST00000299506.3
    Conserved Domains (2) summary
    pfam01167
    Location:258499
    Tub; Tub family
    pfam16322
    Location:29237
    Tub_N; Tubby N-terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    8019059..8106243
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    B4DE99
    Related
    ENSP00000434400.1, ENST00000534099.5
    Conserved Domains (2) summary
    pfam01167
    Location:300541
    Tub; Tub family
    pfam16322
    Location:71279
    Tub_N; Tubby N-terminal
  2. XM_047427512.1XP_047283468.1  tubby protein homolog isoform X3

    UniProtKB/TrEMBL
    B4DE99
  3. XM_047427513.1XP_047283469.1  tubby protein homolog isoform X4

  4. XM_047427515.1XP_047283471.1  tubby protein homolog isoform X6

  5. XM_047427517.1XP_047283473.1  tubby protein homolog isoform X8

    UniProtKB/TrEMBL
    Q9H4D2
  6. XM_047427514.1XP_047283470.1  tubby protein homolog isoform X5

    UniProtKB/TrEMBL
    B4DE99
  7. XM_047427516.1XP_047283472.1  tubby protein homolog isoform X7

  8. XM_011520344.3XP_011518646.1  tubby protein homolog isoform X2

    See identical proteins and their annotated locations for XP_011518646.1

    UniProtKB/TrEMBL
    B4DE99
    Conserved Domains (2) summary
    pfam01167
    Location:270511
    Tub; Tub family
    pfam16322
    Location:41249
    Tub_N; Tubby N-terminal

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    8098231..8185410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    B4DE99
  2. XM_054369809.1XP_054225784.1  tubby protein homolog isoform X3

    UniProtKB/TrEMBL
    B4DE99
  3. XM_054369810.1XP_054225785.1  tubby protein homolog isoform X4

  4. XM_054369812.1XP_054225787.1  tubby protein homolog isoform X6

  5. XM_054369814.1XP_054225789.1  tubby protein homolog isoform X8

    UniProtKB/TrEMBL
    Q9H4D2
  6. XM_054369811.1XP_054225786.1  tubby protein homolog isoform X5

    UniProtKB/TrEMBL
    B4DE99
  7. XM_054369813.1XP_054225788.1  tubby protein homolog isoform X7

  8. XM_054369808.1XP_054225783.1  tubby protein homolog isoform X2

    UniProtKB/TrEMBL
    B4DE99