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TUBB6 tubulin beta 6 class V [ Homo sapiens (human) ]

Gene ID: 84617, updated on 7-Apr-2024

Summary

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Official Symbol
TUBB6provided by HGNC
Official Full Name
tubulin beta 6 class Vprovided by HGNC
Primary source
HGNC:HGNC:20776
See related
Ensembl:ENSG00000176014 MIM:615103; AllianceGenome:HGNC:20776
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FPVEPD; TUBB-5; HsT1601
Summary
Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Located in microtubule. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 41.4), esophagus (RPKM 38.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
18p11.21
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (12307669..12329826)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (12470687..12492842)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (12307668..12329825)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12258258-12258758 Neighboring gene cell death inducing DFFA like effector a Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9307 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12276271-12276894 Neighboring gene VISTA enhancer hs1751 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12287027-12288022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12288023-12289016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12289267-12290030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9309 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9310 Neighboring gene RNA, U6 small nuclear 170, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12318543-12319043 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12327565-12328414 Neighboring gene uncharacterized LOC107985154 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12334195-12335050 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12335909-12336764 Neighboring gene AFG3 like matrix AAA peptidase subunit 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:12377463-12377994 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:12377995-12378524 Neighboring gene RNA, U7 small nuclear 129 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Quantitative proteomics identifies TUBB6 as a biomarker of muscle-invasion and poor prognosis in bladder cancer. Kim B, et al. Int J Cancer, 2023 Jan 15. PMID 36054443
  2. Discovery and Validation of Methylation Biomarkers for Ulcerative Colitis Associated Neoplasia. Beggs AD, et al. Inflamm Bowel Dis, 2018 Jun 8. PMID 29762666, Free PMC Article
  3. A cellular genome-wide association study reveals human variation in microtubule stability and a role in inflammatory cell death. Salinas RE, et al. Mol Biol Cell, 2014 Jan. PMID 24173717, Free PMC Article
  4. Characterization of a human βV-tubulin antibody and expression of this isotype in normal and malignant human tissue. Chao SK, et al. Cytoskeleton (Hoboken), 2012 Aug. PMID 22903939, Free PMC Article
  5. Detection of human betaV-tubulin expression in epithelial cancer cell lines by tubulin proteomics. Verdier-Pinard P, et al. Biochemistry, 2005 Dec 6. PMID 16313188

See all (171) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Quantitative proteomics identifies TUBB6 as a biomarker of muscle-invasion and poor prognosis in bladder cancer.
    Title: Quantitative proteomics identifies TUBB6 as a biomarker of muscle-invasion and poor prognosis in bladder cancer.
  2. Primary myeloid cell proteomics and transcriptomics: importance of beta-tubulin isotypes for osteoclast function.
    Title: Primary myeloid cell proteomics and transcriptomics: importance of β-tubulin isotypes for osteoclast function.
  3. Methylation in the beta-tubulin TUBB6 correlated with the presence of dysplasia and accurately discriminated between dysplasia and nondysplastic tissue, even in the apparently normal field mucosa downstream from dysplastic lesions. Methylation in TUBB6 is a potential biomarker for Ulcerative colitis (UC) - associated dysplasia.
    Title: Discovery and Validation of Methylation Biomarkers for Ulcerative Colitis Associated Neoplasia.
  4. Findings enlarge the spectrum of tubulinopathies and emphasize that mutations of TUBB6 should be considered in patients with congenital non-progressive facial palsy.
    Title: A TUBB6 mutation is associated with autosomal dominant non-progressive congenital facial palsy, bilateral ptosis and velopharyngeal dysfunction.
  5. TUBB6 is an inhibitor of pyroptosis.
    Title: A cellular genome-wide association study reveals human variation in microtubule stability and a role in inflammatory cell death.
  6. Data indicate that leucine-rich repeat kinase 2 (LRRK2) selectively interacts with three beta-tubulin isoforms: TUBB, TUBB4, and TUBB6.
    Title: A direct interaction between leucine-rich repeat kinase 2 and specific β-tubulin isoforms regulates tubulin acetylation.
  7. betaV-tubulin expression is a potentially promising prognostic marker of malignancy.
    Title: Characterization of a human βV-tubulin antibody and expression of this isotype in normal and malignant human tissue.
  8. in colorectal cancer patients, there was a link between poor survival, the expression of TUBB3/TUBB6, and androgen receptor only in females
    Title: Gender influences the class III and V β-tubulin ability to predict poor outcome in colorectal cancer.
  9. The TUBB6 expression was largely decreased in most tumors.
    Title: Tumoral and tissue-specific expression of the major human beta-tubulin isotypes.
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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
Facial palsy, congenital, with ptosis and velopharyngeal dysfunction
MedGen: C4540277 OMIM: 617732 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev Rev acts to depolymerize microtubules that are formed by tubulin, an effect that is observed during HIV-1 infection PubMed
Tat tat HIV-1 Tat K29A, K50R, and K51R lysine mutations downregulate the proportion of soluble tubulin in cells, while the majority of other lysine mutations upregulate the percentage of soluble tubulin compared with the wild-type PubMed
tat In Jurkat cells expressing HIV-1 Tat, decreased expression levels are found for basic cytoskeletal proteins such as actin, beta-tubulin, annexin, cofilin, gelsolin, and Rac/Rho-GDI complex PubMed
tat HIV-1 Tat (amino acids 36-39) binds tubulin alpha/beta dimers and polymerized microtubules leading to the alteration of microtubule dynamics and activation of a mitochondria-dependent apoptotic pathway that is facilitated by the Bcl-2 relative Bim PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC4083, MGC132410

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables structural constituent of cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in microtubule cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular exosome HDA PubMed 
located_in intercellular bridge IDA
Inferred from Direct Assay
more info
  
is_active_in microtubule IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in microtubule IDA
Inferred from Direct Assay
more info
 PubMed 
located_in microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
  
located_in mitotic spindle IDA
Inferred from Direct Assay
more info
  
located_in nucleus HDA PubMed 

General protein information

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Preferred Names
tubulin beta-6 chain
Names
class V beta-tubulin
tubulin beta MGC4083
tubulin beta class V
tubulin, beta 6

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)

  1. NM_001303524.1 → NP_001290453.1  tubulin beta-6 chain isoform 1

    See identical proteins and their annotated locations for NP_001290453.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AK001295, CD364877, DB271698
    Consensus CDS
    CCDS11858.1
    UniProtKB/Swiss-Prot
    B3KM76, Q9BUF5, Q9HA42
    UniProtKB/TrEMBL
    B4DP54
    Conserved Domains (1) summary
    PLN00220
    Location:1 → 432
    PLN00220; tubulin beta chain; Provisional

  2. NM_001303525.2 → NP_001290454.1  tubulin beta-6 chain isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 5'-terminal exon compared to variant 1. This results in a novel 3' coding region and 3' UTR. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK001295, BC039717, CX866060
    Consensus CDS
    CCDS77153.1
    UniProtKB/TrEMBL
    K7EJ64, K7ESQ3
    Related
    ENSP00000465040.1, ENST00000591909.5
    Conserved Domains (1) summary
    PTZ00010
    Location:1 → 93
    PTZ00010; tubulin beta chain; Provisional

  3. NM_001303526.2 → NP_001290455.1  tubulin beta-6 chain isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter compared to isoform 1.
    Source sequence(s)
    AK001295, BP268791, CD364877, CX866060
    UniProtKB/TrEMBL
    B4DP54
    Related
    ENSP00000468777.1, ENST00000590103.5
    Conserved Domains (2) summary
    PLN00220
    Location:1 → 395
    PLN00220; tubulin beta chain; Provisional
    cd02187
    Location:2 → 389
    beta_tubulin; The beta-tubulin family

  4. NM_001303527.2 → NP_001290456.1  tubulin beta-6 chain isoform 4

    See identical proteins and their annotated locations for NP_001290456.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon in its 5' UTR and uses a downstream start codon compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AK001295, CD364877, CN367565, CX866060
    UniProtKB/TrEMBL
    B3KS31, B4DQN9, B7ZAK1
    Conserved Domains (1) summary
    PLN00220
    Location:1 → 360
    PLN00220; tubulin beta chain; Provisional

  5. NM_001303528.2 → NP_001290457.1  tubulin beta-6 chain isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains an alternate internal exon, which results in a distinct 5' UTR and the use of an alternate start codon, compared to variant 1. The encoded isoform (5) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AK001295, AP005264, CD364877, DA693982
    UniProtKB/TrEMBL
    Q9BUU9
    Conserved Domains (1) summary
    PLN00220
    Location:28 → 367
    PLN00220; tubulin beta chain; Provisional

  6. NM_001303529.3 → NP_001290458.1  tubulin beta-6 chain isoform 6

    See identical proteins and their annotated locations for NP_001290458.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate splice site in the 3'-terminal exon compared to variant 1. This results in a distinct 5' UTR and the use of a downstream in-frame start codon. The encoded isoform (6) has a shorter N-terminus compared to isoform 1. Both variants 7 and 8 encode the same isoform.
    Source sequence(s)
    AK001295, AK311364, CD364877, CX866060, DA765796
    UniProtKB/TrEMBL
    B4E386, Q9UGA2
    Conserved Domains (1) summary
    PLN00220
    Location:1 → 286
    PLN00220; tubulin beta chain; Provisional

  7. NM_001303530.3 → NP_001290459.1  tubulin beta-6 chain isoform 6

    See identical proteins and their annotated locations for NP_001290459.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) contains an alternate exon in its 5' UTR and uses an alternate splice site in the 3'-terminal exon, compared to variant 1. This results in a distinct 5' UTR and the use of a downstream in-frame start codon. The encoded isoform (6) has a shorter N-terminus compared to isoform 1. Both variants 7 and 8 encode the same isoform.
    Source sequence(s)
    AK001295, AK311364, AP005264, CD364877
    UniProtKB/TrEMBL
    B4E386, Q9UGA2
    Conserved Domains (1) summary
    PLN00220
    Location:1 → 286
    PLN00220; tubulin beta chain; Provisional

  8. NM_032525.3 → NP_115914.1  tubulin beta-6 chain isoform 1

    See identical proteins and their annotated locations for NP_115914.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Both variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AK001295, CD364877
    Consensus CDS
    CCDS11858.1
    UniProtKB/Swiss-Prot
    B3KM76, Q9BUF5, Q9HA42
    UniProtKB/TrEMBL
    B4DP54
    Related
    ENSP00000318697.4, ENST00000317702.10
    Conserved Domains (1) summary
    PLN00220
    Location:1 → 432
    PLN00220; tubulin beta chain; Provisional

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    12307669..12329826
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    12470687..12492842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BUF5.1 GenPept UniProtKB/Swiss-Prot:Q9BUF5

Gene LinkOut

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