Human Gene TBC1D2B (uc002bda.3)
  Description: Homo sapiens TBC1 domain family, member 2B (TBC1D2B), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr15:78,294,840-78,309,628 Size: 14,789 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr15:78,295,638-78,309,018 Size: 13,381 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:78,294,840-78,309,628)mRNA (may differ from genome)Protein (312 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedUniProtKB
BioGrid CRISPR DB

-  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): TBC1D2B
CDC HuGE Published Literature: TBC1D2B

-  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: 36.06 RPKM in Ovary
Total median expression: 681.89 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 -181.71610-0.298 Picture PostScript Text
3' UTR -265.04798-0.332 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
  Pfam Domains:
PF00566 - Rab-GTPase-TBC domain

SCOP Domains:
47923 - Ypt/Rab-GAP domain of gyp1p

ModBase Predicted Comparative 3D Structure on Q9UPU7-3
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC033712 - Homo sapiens TBC1 domain family, member 2B, mRNA (cDNA clone IMAGE:4400762), complete cds.
BC152465 - Homo sapiens TBC1 domain family, member 2B, mRNA (cDNA clone MGC:176722 IMAGE:8862601), complete cds.
AB028978 - Homo sapiens mRNA for KIAA1055 protein, partial cds.
BC140766 - Homo sapiens TBC1 domain family, member 2B, mRNA (cDNA clone MGC:176443 IMAGE:9021634), complete cds.
BC144482 - Homo sapiens TBC1 domain family, member 2B, mRNA (cDNA clone MGC:178026 IMAGE:9053009), complete cds.
KJ902282 - Synthetic construct Homo sapiens clone ccsbBroadEn_11676 TBC1D2B gene, encodes complete protein.
AB463304 - Synthetic construct DNA, clone: pF1KB9777, Homo sapiens TBC1D2B gene for TBC1 domain family, member 2B, without stop codon, in Flexi system.
LF208576 - JP 2014500723-A/16079: Polycomb-Associated Non-Coding RNAs.
AK000173 - Homo sapiens cDNA FLJ20166 fis, clone COL09511.
JD425287 - Sequence 406311 from Patent EP1572962.
JD425286 - Sequence 406310 from Patent EP1572962.
JD425289 - Sequence 406313 from Patent EP1572962.
LF378054 - JP 2014500723-A/185557: Polycomb-Associated Non-Coding RNAs.
LF378056 - JP 2014500723-A/185559: Polycomb-Associated Non-Coding RNAs.
DQ574184 - Homo sapiens piRNA piR-42296, complete sequence.
JD206975 - Sequence 187999 from Patent EP1572962.
MA444153 - JP 2018138019-A/16079: Polycomb-Associated Non-Coding RNAs.
MA613631 - JP 2018138019-A/185557: Polycomb-Associated Non-Coding RNAs.
MA613633 - JP 2018138019-A/185559: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK000173, KIAA1055, NM_015079, NP_055894, Q9UPU7-3
UCSC ID: uc002bda.3
RefSeq Accession: NM_015079
Protein: Q9UPU7-3, splice isoform of Q9UPU7

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK000173.1
exon count: 4CDS single in 3' UTR: no RNA size: 2364
ORF size: 939CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 1642.00frame shift in genome: no % Coverage: 99.28
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: 1354# 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.