Human Gene TBL3 (uc002cnu.1)
  Description: Homo sapiens transducin (beta)-like 3 (TBL3), mRNA.
RefSeq Summary (NM_006453): The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This gene has multiple polyadenylation sites. It might have multiple alternatively spliced transcript variants but the variants have not been fully described yet. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr16:2,022,064-2,028,751 Size: 6,688 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr16:2,022,166-2,028,686 Size: 6,521 Coding Exon Count: 22 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:2,022,064-2,028,751)mRNA (may differ from genome)Protein (808 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TBL3_HUMAN
DESCRIPTION: RecName: Full=Transducin beta-like protein 3; AltName: Full=WD repeat-containing protein SAZD;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Contains 13 WD repeats.
SEQUENCE CAUTION: Sequence=AAA18945.1; Type=Frameshift; Positions=Several; Sequence=BAD92410.1; Type=Erroneous initiation;

-  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): TBL3
CDC HuGE Published Literature: TBL3

-  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: 48.83 RPKM in Testis
Total median expression: 763.48 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 -42.40102-0.416 Picture PostScript Text
3' UTR -16.0065-0.246 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
IPR020472 - G-protein_beta_WD-40_rep
IPR013934 - SSU_processome_Utp13
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF08625 - Utp13 specific WD40 associated domain

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q12788
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0030515 snoRNA binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0032040 small-subunit processome
GO:0034388 Pwp2p-containing subcomplex of 90S preribosome


-  Descriptions from all associated GenBank mRNAs
  KJ898252 - Synthetic construct Homo sapiens clone ccsbBroadEn_07646 TBL3 gene, encodes complete protein.
AK095076 - Homo sapiens cDNA FLJ37757 fis, clone BRHIP2023860, highly similar to WD-REPEAT PROTEIN SAZD.
BC010231 - Homo sapiens transducin (beta)-like 3, mRNA (cDNA clone MGC:17508 IMAGE:3455740), complete cds.
BC021563 - Homo sapiens transducin (beta)-like 3, mRNA (cDNA clone IMAGE:4811252), with apparent retained intron.
BC014007 - Homo sapiens transducin (beta)-like 3, mRNA (cDNA clone MGC:20031 IMAGE:4040312), complete cds.
AB209173 - Homo sapiens mRNA for transducin beta-like 3 variant protein.
BC035409 - Homo sapiens transducin (beta)-like 3, mRNA (cDNA clone MGC:35053 IMAGE:5165833), complete cds.
U02609 - Human transducin-like protein mRNA, complete cds.
JD443995 - Sequence 425019 from Patent EP1572962.
JD407326 - Sequence 388350 from Patent EP1572962.
CU679657 - Synthetic construct Homo sapiens gateway clone IMAGE:100020455 5' read TBL3 mRNA.
CU680738 - Synthetic construct Homo sapiens gateway clone IMAGE:100023488 5' read TBL3 mRNA.
CU690084 - Synthetic construct Homo sapiens gateway clone IMAGE:100023264 5' read TBL3 mRNA.
AB384871 - Synthetic construct DNA, clone: pF1KB3889, Homo sapiens TBL3 gene for WD repeat protein SAZD, complete cds, without stop codon, in Flexi system.
BC002361 - Homo sapiens cDNA clone IMAGE:2961321, containing frame-shift errors.
BC007620 - Homo sapiens transducin (beta)-like 3, mRNA (cDNA clone IMAGE:3355545), partial cds.
JD157435 - Sequence 138459 from Patent EP1572962.
JD126406 - Sequence 107430 from Patent EP1572962.
JD251472 - Sequence 232496 from Patent EP1572962.

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

Protein Q12788 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006453, NP_006444, Q12788, Q59GD6, Q8IVB7, Q96A78, SAZD, TBL3_HUMAN
UCSC ID: uc002cnu.1
RefSeq Accession: NM_006453
Protein: Q12788 (aka TBL3_HUMAN)
CCDS: CCDS10453.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006453.2
exon count: 22CDS single in 3' UTR: no RNA size: 2618
ORF size: 2427CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5047.00frame shift in genome: no % Coverage: 99.08
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.