Human Gene TBC1D20 (uc002wds.3) Description and Page Index
  Description: Homo sapiens TBC1 domain family, member 20 (TBC1D20), mRNA.
RefSeq Summary (NM_144628): This gene encodes a protein that belongs to a family of GTPase activator proteins of Rab-like small GTPases. The encoded protein and its cognate GTPase, Rab1, bind the nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) to mediate viral replication. Depletion of this protein inhibits replication of the virus and HCV infection. Mutations in this gene are associated with Warburg micro syndrome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014].
Transcript (Including UTRs)
   Position: hg19 chr20:416,124-443,187 Size: 27,064 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr20:419,230-443,049 Size: 23,820 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:416,124-443,187)mRNA (may differ from genome)Protein (403 aa)
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UniProtKB

-  Comments and Description Text from UniProtKB
  ID: TBC20_HUMAN
DESCRIPTION: RecName: Full=TBC1 domain family member 20;
FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).
SUBUNIT: Directly interacts with the N-terminal amphipathic helix of hepatitis C virus (HCV) NS5A.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
SIMILARITY: Contains 1 Rab-GAP TBC domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TBC1D20
CDC HuGE Published Literature: TBC1D20
Positive Disease Associations: Stroke
Related Studies:
  1. Stroke
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: TBC1D20
Diseases sorted by gene-association score: warburg micro syndrome 4* (1038), warburg micro syndrome (28), warburg micro syndrome 1 (13), hepatitis c virus (13), spastic diplegia (8)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.64 RPKM in Brain - Cerebellum
Total median expression: 700.97 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -77.60138-0.562 Picture PostScript Text
3' UTR -1060.903106-0.342 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 Q96BZ9
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 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:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0017137 Rab GTPase binding

Biological Process:
GO:0001675 acrosome assembly
GO:0002088 lens development in camera-type eye
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0007030 Golgi organization
GO:0007283 spermatogenesis
GO:0008584 male gonad development
GO:0016032 viral process
GO:0019068 virion assembly
GO:0034389 lipid particle organization
GO:0043010 camera-type eye development
GO:0043547 positive regulation of GTPase activity
GO:0044829 positive regulation by host of viral genome replication
GO:0046726 positive regulation by virus of viral protein levels in host cell
GO:0048208 COPII vesicle coating
GO:0070309 lens fiber cell morphogenesis
GO:0072520 seminiferous tubule development
GO:0090110 cargo loading into COPII-coated vesicle
GO:1902953 positive regulation of ER to Golgi vesicle-mediated transport
GO:1902017 regulation of cilium assembly

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030173 integral component of Golgi membrane
GO:0031965 nuclear membrane
GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane


-  Descriptions from all associated GenBank mRNAs
  BC014648 - Homo sapiens TBC1 domain family, member 20, mRNA (cDNA clone IMAGE:4561546), with apparent retained intron.
BX647370 - Homo sapiens mRNA; cDNA DKFZp686B10111 (from clone DKFZp686B10111).
BC014983 - Homo sapiens TBC1 domain family, member 20, mRNA (cDNA clone MGC:23197 IMAGE:4861869), complete cds.
AF116909 - Homo sapiens clone HH419 unknown mRNA.
AK092063 - Homo sapiens cDNA FLJ34744 fis, clone MESAN2009081.
JD232271 - Sequence 213295 from Patent EP1572962.
JD055911 - Sequence 36935 from Patent EP1572962.
JD102703 - Sequence 83727 from Patent EP1572962.
JD251647 - Sequence 232671 from Patent EP1572962.
JD444751 - Sequence 425775 from Patent EP1572962.
JD372430 - Sequence 353454 from Patent EP1572962.
JD200187 - Sequence 181211 from Patent EP1572962.
JD439790 - Sequence 420814 from Patent EP1572962.
JD265450 - Sequence 246474 from Patent EP1572962.
JD264865 - Sequence 245889 from Patent EP1572962.
BC047616 - Homo sapiens TBC1 domain family, member 20, mRNA (cDNA clone IMAGE:4939252), with apparent retained intron.
AK055488 - Homo sapiens cDNA FLJ30926 fis, clone FEBRA2006667.
AK095110 - Homo sapiens cDNA FLJ37791 fis, clone BRHIP3000131.
AK127062 - Homo sapiens cDNA FLJ45119 fis, clone BRAWH3035914.
DQ600872 - Homo sapiens piRNA piR-38938, complete sequence.
DQ588114 - Homo sapiens piRNA piR-55226, complete sequence.
JD364381 - Sequence 345405 from Patent EP1572962.
JD115477 - Sequence 96501 from Patent EP1572962.
JD364382 - Sequence 345406 from Patent EP1572962.
JD213033 - Sequence 194057 from Patent EP1572962.
JD533829 - Sequence 514853 from Patent EP1572962.
JD213032 - Sequence 194056 from Patent EP1572962.
JD407554 - Sequence 388578 from Patent EP1572962.
JD337570 - Sequence 318594 from Patent EP1572962.
JD371271 - Sequence 352295 from Patent EP1572962.
JD427100 - Sequence 408124 from Patent EP1572962.
JD142991 - Sequence 124015 from Patent EP1572962.
DQ586516 - Homo sapiens piRNA piR-53628, complete sequence.
AK055573 - Homo sapiens cDNA FLJ31011 fis, clone HLUNG2000176.
AK291648 - Homo sapiens cDNA FLJ77323 complete cds, highly similar to Homo sapiens TBC1 domain family, member 20 (TBC1D20), mRNA.
AB449906 - Homo sapiens TBC1D20 mRNA for TBC1 domain family, member 20, complete cds.
KJ895451 - Synthetic construct Homo sapiens clone ccsbBroadEn_04845 TBC1D20 gene, encodes complete protein.
JD443492 - Sequence 424516 from Patent EP1572962.

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

Protein Q96BZ9 (Reactome details) participates in the following event(s):

R-HSA-6814831 TBC1D20 binds RAB1:GTP
R-HSA-8854290 TBC1D20 binds NS5A
R-HSA-6814833 TBC1D20 stimulates GTPase activity of RAB1, resulting in hydrolysis of GTP
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-8854214 TBC/RABGAPs
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-9007101 Rab regulation of trafficking
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6I3, C20orf140, NM_144628, NP_653229, Q5JWQ7, Q6ZSY8, Q96BZ9, Q96NE1, Q9BYM7, Q9H140, TBC20_HUMAN
UCSC ID: uc002wds.3
RefSeq Accession: NM_144628
Protein: Q96BZ9 (aka TBC20_HUMAN or CTE0_HUMAN)
CCDS: CCDS13002.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TBC1D20:
rab18-def (RAB18 Deficiency)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_144628.2
exon count: 8CDS single in 3' UTR: no RNA size: 4456
ORF size: 1212CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2506.50frame shift in genome: no % Coverage: 100.00
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: 3070# 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.