Human Gene TPGS1 (uc002lou.3)
  Description: Homo sapiens tubulin polyglutamylase complex subunit 1 (TPGS1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:507,497-519,654 Size: 12,158 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr19:507,507-519,423 Size: 11,917 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:507,497-519,654)mRNA (may differ from genome)Protein (290 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TPGS1_HUMAN
DESCRIPTION: RecName: Full=Tubulin polyglutamylase complex subunit 1; Short=PGs1;
FUNCTION: May act in the targeting of the tubulin polyglutamylase complex. Required for the development of the spermatid flagellum (By similarity).
SUBUNIT: Part of the neuronal tubulin polyglutamylase complex which contains TPGS1, TPGS2, TTLL1, LRRC49 and NICN1 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, cilium axoneme. Cytoplasm, cytoskeleton, flagellum axoneme. Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, flagellum basal body. Cell projection, axon. Cell projection, dendrite. Cytoplasm, cytoskeleton, centrosome. Note=Associated with microtubules from neurites, centrosomes, basal bodies and axonemes (By similarity).

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 11.46 RPKM in Cervix - Endocervix
Total median expression: 384.45 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
3' UTR -122.80231-0.532 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
  ModBase Predicted Comparative 3D Structure on Q6ZTW0
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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:0008017 microtubule binding
GO:0015631 tubulin binding
GO:0070740 tubulin-glutamic acid ligase activity

Biological Process:
GO:0007268 chemical synaptic transmission
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0007288 sperm axoneme assembly
GO:0018095 protein polyglutamylation
GO:0030154 cell differentiation
GO:0030534 adult behavior
GO:0051648 vesicle localization

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005929 cilium
GO:0030424 axon
GO:0030425 dendrite
GO:0031514 motile cilium
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AK126170 - Homo sapiens cDNA FLJ44182 fis, clone THYMU2038369, highly similar to Mus musculus GTRGEO22 (Gtrgeo22) mRNA.
AK125401 - Homo sapiens cDNA FLJ43412 fis, clone OCBBF2021323.
AB463513 - Synthetic construct DNA, clone: pF1KB7452, Homo sapiens C19orf20 gene for chromosome 19 open reading frame 20, without stop codon, in Flexi system.
BC148687 - Synthetic construct Homo sapiens clone IMAGE:100015733, MGC:183160 chromosome 19 open reading frame 20 (C19orf20) mRNA, encodes complete protein.
BC152801 - Synthetic construct Homo sapiens clone IMAGE:100016032, MGC:184102 chromosome 19 open reading frame 20 (C19orf20) mRNA, encodes complete protein.
JD485621 - Sequence 466645 from Patent EP1572962.
BC009520 - Homo sapiens chromosome 19 open reading frame 20, mRNA (cDNA clone IMAGE:3637796), partial cds.
JD486921 - Sequence 467945 from Patent EP1572962.
JD119020 - Sequence 100044 from Patent EP1572962.
JD472020 - Sequence 453044 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6ZTW0 (Reactome details) participates in the following event(s):

R-HSA-8955869 Polyglutamylase complex (TTLL1) polyglutamylates alpha subunits of tubulin
R-HSA-8955332 Carboxyterminal post-translational modifications of tubulin
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: C19orf20, NM_033513, NP_277048, Q6ZTW0, Q96GE2, TPGS1_HUMAN
UCSC ID: uc002lou.3
RefSeq Accession: NM_033513
Protein: Q6ZTW0 (aka TPGS1_HUMAN)
CCDS: CCDS42454.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_033513.2
exon count: 2CDS single in 3' UTR: no RNA size: 1134
ORF size: 873CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1411.00frame shift in genome: no % Coverage: 98.24
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # 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.