Human Gene TBC1D5 (uc003cbe.3)
  Description: Homo sapiens TBC1 domain family, member 5 (TBC1D5), transcript variant 3, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:17,198,654-17,784,240 Size: 585,587 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg19 chr3:17,202,455-17,550,062 Size: 347,608 Coding Exon Count: 20 

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 (chr3:17,198,654-17,784,240)mRNA (may differ from genome)Protein (795 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIneXtProtPubMedTreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: TBCD5_HUMAN
DESCRIPTION: RecName: Full=TBC1 domain family member 5;
FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).
INTERACTION: P54253:ATXN1; NbExp=2; IntAct=EBI-742381, EBI-930964;
SIMILARITY: Contains 1 Rab-GAP TBC domain.
SEQUENCE CAUTION: Sequence=BAA13201.2; 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): TBC1D5
CDC HuGE Published Literature: TBC1D5
Positive Disease Associations: Heart Failure , Walking
Related Studies:
  1. Heart Failure
    , , . [PubMed 0]
  2. Walking
    Kathryn L Lunetta et al. BMC medical genetics 2007, Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study., BMC medical genetics. [PubMed 17903295]
    Longevity and aging traits are associated with SNPs on the Affymetrix 100K GeneChip. None of the associations achieved genome-wide significance. These data generate hypotheses and serve as a resource for replication as more genes and biologic pathways are proposed as contributing to longevity and healthy aging.
  3. Walking
    Kathryn L Lunetta et al. BMC medical genetics 2007, Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study., BMC medical genetics. [PubMed 17903295]
    Longevity and aging traits are associated with SNPs on the Affymetrix 100K GeneChip. None of the associations achieved genome-wide significance. These data generate hypotheses and serve as a resource for replication as more genes and biologic pathways are proposed as contributing to longevity and healthy aging.
           more ... click here to view the complete list

-  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: 10.97 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 299.61 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 -200.32427-0.469 Picture PostScript Text
3' UTR -1200.393801-0.316 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
IPR000195 - Rab-GTPase-TBC_dom

Pfam Domains:
PF00566 - Rab-GTPase-TBC domain

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

ModBase Predicted Comparative 3D Structure on Q92609
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 orthologGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
 Gene Details Gene DetailsGene Details 
 Gene Sorter Gene SorterGene Sorter 
 RGD FlyBaseWormBase 
 Protein Sequence Protein SequenceProtein Sequence 
 Alignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0017137 Rab GTPase binding
GO:0035612 AP-2 adaptor complex binding
GO:1905394 retromer complex binding

Biological Process:
GO:0002092 positive regulation of receptor internalization
GO:0006886 intracellular protein transport
GO:0006914 autophagy
GO:0015031 protein transport
GO:0016236 macroautophagy
GO:0031338 regulation of vesicle fusion
GO:0042147 retrograde transport, endosome to Golgi
GO:0042594 response to starvation
GO:0090630 activation of GTPase activity
GO:1902017 regulation of cilium assembly

Cellular Component:
GO:0005768 endosome
GO:0005776 autophagosome
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030904 retromer complex
GO:0031410 cytoplasmic vesicle
GO:0043231 intracellular membrane-bounded organelle
GO:0030122 AP-2 adaptor complex
GO:1990316 ATG1/ULK1 kinase complex


-  Descriptions from all associated GenBank mRNAs
  D86965 - Homo sapiens mRNA for KIAA0210 gene.
BC013145 - Homo sapiens TBC1 domain family, member 5, mRNA (cDNA clone MGC:21104 IMAGE:4510019), complete cds.
AK097990 - Homo sapiens cDNA FLJ40671 fis, clone THYMU2021361.
AK310539 - Homo sapiens cDNA, FLJ17581.
KJ892847 - Synthetic construct Homo sapiens clone ccsbBroadEn_02241 TBC1D5 gene, encodes complete protein.
JF432743 - Synthetic construct Homo sapiens clone IMAGE:100073987 TBC1 domain family, member 5 (TBC1D5) gene, encodes complete protein.
AB449886 - Homo sapiens TBC1D5 mRNA for TBC1 domain family, member 5, complete cds.
AB383800 - Synthetic construct DNA, clone: pF1KSDA0210, Homo sapiens TBC1D5 gene for TBC1 domain family member 5, complete cds, without stop codon, in Flexi system.
AK309374 - Homo sapiens cDNA, FLJ99415.
JD239553 - Sequence 220577 from Patent EP1572962.
JD376200 - Sequence 357224 from Patent EP1572962.
JD051807 - Sequence 32831 from Patent EP1572962.
JD403229 - Sequence 384253 from Patent EP1572962.
JD387166 - Sequence 368190 from Patent EP1572962.
JD386083 - Sequence 367107 from Patent EP1572962.
JD231417 - Sequence 212441 from Patent EP1572962.
JD487715 - Sequence 468739 from Patent EP1572962.
JD403977 - Sequence 385001 from Patent EP1572962.
JD243044 - Sequence 224068 from Patent EP1572962.
JD474607 - Sequence 455631 from Patent EP1572962.
DQ599921 - Homo sapiens piRNA piR-37987, complete sequence.
JD419174 - Sequence 400198 from Patent EP1572962.
JD290970 - Sequence 271994 from Patent EP1572962.
JD377790 - Sequence 358814 from Patent EP1572962.
JD235274 - Sequence 216298 from Patent EP1572962.
JD226993 - Sequence 208017 from Patent EP1572962.
JD532505 - Sequence 513529 from Patent EP1572962.
JD087963 - Sequence 68987 from Patent EP1572962.
JD051740 - Sequence 32764 from Patent EP1572962.
JD373395 - Sequence 354419 from Patent EP1572962.
JD317976 - Sequence 299000 from Patent EP1572962.
JD418636 - Sequence 399660 from Patent EP1572962.
JD088758 - Sequence 69782 from Patent EP1572962.
JD253369 - Sequence 234393 from Patent EP1572962.
JD098149 - Sequence 79173 from Patent EP1572962.
JD135035 - Sequence 116059 from Patent EP1572962.
JD516299 - Sequence 497323 from Patent EP1572962.
JD060900 - Sequence 41924 from Patent EP1572962.
JD200952 - Sequence 181976 from Patent EP1572962.
JD083646 - Sequence 64670 from Patent EP1572962.
JD328872 - Sequence 309896 from Patent EP1572962.
JD314428 - Sequence 295452 from Patent EP1572962.
JD181327 - Sequence 162351 from Patent EP1572962.
JD127654 - Sequence 108678 from Patent EP1572962.
JD216790 - Sequence 197814 from Patent EP1572962.
JD436753 - Sequence 417777 from Patent EP1572962.
JD051726 - Sequence 32750 from Patent EP1572962.
DQ570045 - Homo sapiens piRNA piR-30157, complete sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NP25, KIAA0210, NM_001134380, NP_055559, Q92609, TBCD5_HUMAN
UCSC ID: uc003cbe.3
RefSeq Accession: NM_001134380
Protein: Q92609 (aka TBCD5_HUMAN or TBC5_HUMAN)
CCDS: CCDS33714.1, CCDS46770.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001134380.1
exon count: 22CDS single in 3' UTR: no RNA size: 6631
ORF size: 2388CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4940.00frame shift in genome: no % Coverage: 99.77
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.