Human Gene TUBD1 (uc002ixw.2)
  Description: Homo sapiens tubulin, delta 1 (TUBD1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr17:57,936,841-57,970,306 Size: 33,466 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr17:57,937,683-57,968,363 Size: 30,681 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:57,936,841-57,970,306)mRNA (may differ from genome)Protein (453 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TBD_HUMAN
DESCRIPTION: RecName: Full=Tubulin delta chain; AltName: Full=Delta-tubulin;
FUNCTION: In the elongating spermatid it is associated with the manchette, a specialized microtubule system present during reshaping of the sperm head (By similarity).
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, centrosome, centriole. Cytoplasm. Nucleus. Note=Associated with centrioles. Both cytoplasmic and nuclear.
SIMILARITY: Belongs to the tubulin family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TUBD1
CDC HuGE Published Literature: TUBD1

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.67 RPKM in Ovary
Total median expression: 137.27 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -77.14288-0.268 Picture PostScript Text
3' UTR -223.66842-0.266 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002967 - Delta_tubulin
IPR008280 - Tub_FtsZ_C
IPR000217 - Tubulin
IPR023123 - Tubulin_C
IPR017975 - Tubulin_CS
IPR003008 - Tubulin_FtsZ_GTPase

Pfam Domains:
PF00091 - Tubulin/FtsZ family, GTPase domain

SCOP Domains:
52490 - Tubulin nucleotide-binding domain-like
55307 - Tubulin C-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q9UJT1
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005200 structural constituent of cytoskeleton
GO:0005525 GTP binding

Biological Process:
GO:0007010 cytoskeleton organization
GO:0007017 microtubule-based process
GO:0007275 multicellular organism development
GO:0030030 cell projection organization
GO:0045880 positive regulation of smoothened signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005814 centriole
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005929 cilium
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AK024741 - Homo sapiens cDNA: FLJ21088 fis, clone CAS03335, highly similar to AF201333 Homo sapiens delta-tubulin mRNA.
AK024096 - Homo sapiens cDNA FLJ14034 fis, clone HEMBA1004499, weakly similar to Homo sapiens delta-tubulin mRNA.
BC000258 - Homo sapiens tubulin, delta 1, mRNA (cDNA clone MGC:2619 IMAGE:3358263), complete cds.
AK298492 - Homo sapiens cDNA FLJ60775 complete cds, highly similar to Tubulin delta chain.
AK022771 - Homo sapiens cDNA FLJ12709 fis, clone NT2RP1001033, highly similar to Tubulin delta chain.
AB030837 - Homo sapiens mRNA for delta tubulin, complete cds.
AB031044 - Homo sapiens mRNA for delta-tubulin isoform, complete cds.
AB031045 - Homo sapiens mRNA for delta-tubulin isoform, complete cds.
AK301312 - Homo sapiens cDNA FLJ57211 complete cds, highly similar to Tubulin delta chain.
AF201333 - Homo sapiens delta-tubulin mRNA, complete cds.
AK315172 - Homo sapiens cDNA, FLJ96147.
KJ893841 - Synthetic construct Homo sapiens clone ccsbBroadEn_03235 TUBD1 gene, encodes complete protein.
CU674110 - Synthetic construct Homo sapiens gateway clone IMAGE:100018216 5' read TUBD1 mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DU02, NM_016261, NP_001180542, Q9BWG9, Q9H7Z8, Q9UJT1, TBD_HUMAN, TUBD
UCSC ID: uc002ixw.2
RefSeq Accession: NM_016261
Protein: Q9UJT1 (aka TBD_HUMAN)
CCDS: CCDS11620.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016261.3
exon count: 9CDS single in 3' UTR: no RNA size: 2505
ORF size: 1362CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2543.00frame shift in genome: no % Coverage: 99.48
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.