TUBD1 tubulin delta 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TUBD1provided by HGNC
Official Full Name: tubulin delta 1provided by HGNC
Primary source: HGNC:HGNC:16811
See related: Ensembl:ENSG00000108423 MIM:607344; AllianceGenome:HGNC:16811
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: TUBD
Summary: Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization; mitotic cell cycle; and positive regulation of smoothened signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in esophagus (RPKM 3.8), thyroid (RPKM 3.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q23.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (59859479..59892943, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (60728231..60761691, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (57936840..57970304, complement)

Chromosome 17 - NC_000017.11 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?

Here, the authors report that centrioles in delta-tubulin and epsilon-tubulin null mutant human cells lack triplet microtubules and fail to undergo centriole maturation.
Title: Centriole triplet microtubules are required for stable centriole formation and inheritance in human cells.
our data suggest that TUBD1 mRNA isoform expression profile in peripheral blood could be an accessible biomarker for predicting the risk for diabetic retinopathy development.
Title: Genome-wide mRNA analysis reveals a TUBD1 isoform profile as a potential biomarker for diabetic retinopathy development.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Centrosome-related genes, genetic variation, and risk of breast cancer.

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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
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	HIV-1 Tat (specifically, amino acids 38-72), enhances tubulin polymerization and triggers the mitochondrial pathway to induce T cell apoptosis as shown in vitro by the release of cytochrome c from isolated mitochondria	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

D11S2921 (e-PCR)
- UniSTS:152074

PMC156606P1 (e-PCR)
- UniSTS:271408

L18426 (e-PCR)
- UniSTS:34648

G42217 (e-PCR)
- UniSTS:93320

SHGC-30060 (e-PCR)
- UniSTS:25047

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTP binding	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cell projection organization	IEA Inferred from Electronic Annotation more info
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
involved_in positive regulation of smoothened signaling pathway	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in centriole	IEA Inferred from Electronic Annotation more info
located_in cilium	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
is_active_in microtubule	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: tubulin delta chain

Names: delta-tubulin

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_001193609.2 → NP_001180538.1 tubulin delta chain isoform 2

See identical proteins and their annotated locations for NP_001180538.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate, in-frame, segment, compared to variant 1. The resulting protein (isoform 2) is shorter when it is compared to isoform 1.

Source sequence(s)

AK024741, BC000258, BG682935, BX119803

Consensus CDS

CCDS54153.1

UniProtKB/TrEMBL

Q5KU37

Related

ENSP00000342399.5, ENST00000340993.10

Conserved Domains (1) summary

cd02189
Location:2 → 397

delta_zeta_tubulin-like; The delta- and zeta-tubulin families
NM_001193610.2 → NP_001180539.1 tubulin delta chain isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate, in-frame, segment and uses a different splice site in the 3' coding region, compared to variant 1. The resulting protein (isoform 3) is shorter when it is compared to isoform 1.

Source sequence(s)

AB030837, AK024741, AK298492, BG682935, BX119803

Consensus CDS

CCDS54154.1

UniProtKB/TrEMBL

B3KMV1

Related

ENSP00000377785.3, ENST00000394239.7

Conserved Domains (2) summary

cd02189
Location:2 → 395

delta_zeta_tubulin-like; The delta- and zeta-tubulin families

pfam00091
Location:2 → 213

Tubulin; Tubulin/FtsZ family, GTPase domain
NM_001193611.2 → NP_001180540.1 tubulin delta chain isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks two alternate, in-frame, segments in the 3' coding region, compared to variant 1. The resulting protein (isoform 4) is shorter when it is compared to isoform 1.

Source sequence(s)

AB030837, AB031045, AK024741, BG682935, BX119803, DA607129

Consensus CDS

CCDS54152.1

UniProtKB/TrEMBL

Q5KU37

Related

ENSP00000480387.1, ENST00000613721.4

Conserved Domains (2) summary

cd02189
Location:2 → 350

delta_zeta_tubulin-like; The delta- and zeta-tubulin families

pfam00091
Location:2 → 213

Tubulin; Tubulin/FtsZ family, GTPase domain
NM_001193612.2 → NP_001180541.1 tubulin delta chain isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (5) contains an alternate exon in the 5' end, which results in the use of a downstream start codon, and lacks an alternate, in-frame segment in the 3' coding region, compared to variant 1. The resulting protein (isoform 5) has a shorter N-terminus when it is compared to isoform 1.

Source sequence(s)

AB030837, AK024741, AK315172, BG682935, BX119803, DA607129

UniProtKB/Swiss-Prot

Q9UJT1

Conserved Domains (2) summary

cd02189
Location:1 → 278

delta_zeta_tubulin-like; The delta- and zeta-tubulin families

pfam00091
Location:1 → 94

Tubulin; Tubulin/FtsZ family, GTPase domain
NM_001193613.2 → NP_001180542.1 tubulin delta chain isoform 6

See identical proteins and their annotated locations for NP_001180542.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) lacks three alternate exons in the 5' coding region, which results in the use of a downstream start codon, compared to variant 1. The resulting protein (isoform 6) has a shorter N-terminus when it is compared to isoform 1.

Source sequence(s)

AB030837, AK024741, AK301312, BG682935, BX119803

Consensus CDS

CCDS54151.1

UniProtKB/Swiss-Prot

Q9UJT1

Related

ENSP00000441757.1, ENST00000539018.5

Conserved Domains (1) summary

cd02189
Location:1 → 236

delta_zeta_tubulin-like; The delta- and zeta-tubulin families
NM_016261.4 → NP_057345.2 tubulin delta chain isoform 1

See identical proteins and their annotated locations for NP_057345.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and it encodes the longest protein (isoform 1).

Source sequence(s)

AB030837, AK024741, BG682935, BX119803, DA607129

Consensus CDS

CCDS11620.1

UniProtKB/Swiss-Prot

B4DPT8, B4DW01, D3DU02, E9PCA7, E9PCQ8, Q5KU36, Q9BWG9, Q9H7Z8, Q9UJT1

UniProtKB/TrEMBL

B3KMV1

Related

ENSP00000320797.3, ENST00000325752.8

Conserved Domains (2) summary

cd02189
Location:2 → 452

delta_zeta_tubulin-like; The delta- and zeta-tubulin families

pfam00091
Location:2 → 213

Tubulin; Tubulin/FtsZ family, GTPase domain

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

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

59859479..59892943 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047436202.1 → XP_047292158.1 tubulin delta chain isoform X5
XM_047436200.1 → XP_047292156.1 tubulin delta chain isoform X3
XM_011524871.4 → XP_011523173.1 tubulin delta chain isoform X1

UniProtKB/TrEMBL

B3KMV1

Conserved Domains (2) summary

cd02189
Location:2 → 405

delta_zeta_tubulin-like; The delta- and zeta-tubulin families

pfam00091
Location:2 → 213

Tubulin; Tubulin/FtsZ family, GTPase domain
XM_017024716.3 → XP_016880205.1 tubulin delta chain isoform X2
XM_047436201.1 → XP_047292157.1 tubulin delta chain isoform X4