Human Gene RAB6D (uc002tsr.3)
  Description: Homo sapiens RAB6C-like (RAB6D), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:132,118,065-132,121,731 Size: 3,667 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr2:132,120,529-132,121,293 Size: 765 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:132,118,065-132,121,731)mRNA (may differ from genome)Protein (254 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsHPRDLynx
MGIPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q53S08_HUMAN
DESCRIPTION: SubName: Full=Putative uncharacterized protein RAB6C; SubName: Full=Rab6C; SubName: Full=WTH3DI;
SIMILARITY: Belongs to the small GTPase superfamily. Rab family.

-  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


+  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: 0.80 RPKM in Testis
Total median expression: 6.72 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 -220.40438-0.503 Picture PostScript Text
3' UTR -546.442464-0.222 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
IPR005225 - Small_GTP-bd_dom
IPR001806 - Small_GTPase
IPR003579 - Small_GTPase_Rab_type

Pfam Domains:
PF00025 - ADP-ribosylation factor family
PF00071 - Ras family
PF08477 - Ras of Complex, Roc, domain of DAPkinase

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q53S08
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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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005525 GTP binding

Cellular Component:
GO:0005794 Golgi apparatus


-  Descriptions from all associated GenBank mRNAs
  AB232598 - Homo sapiens Rab6C mRNA for Rab6C, complete cds.
BC148667 - Synthetic construct Homo sapiens clone IMAGE:100015622, MGC:183133 RAB6C-like (LOC150786) mRNA, encodes complete protein.
BC153205 - Synthetic construct Homo sapiens clone IMAGE:100016523, MGC:184337 RAB6C-like (LOC150786) mRNA, encodes complete protein.
JD331496 - Sequence 312520 from Patent EP1572962.
JD259950 - Sequence 240974 from Patent EP1572962.
JD345981 - Sequence 327005 from Patent EP1572962.
JD046875 - Sequence 27899 from Patent EP1572962.
JD042212 - Sequence 23236 from Patent EP1572962.
JD309441 - Sequence 290465 from Patent EP1572962.
JD083997 - Sequence 65021 from Patent EP1572962.
JD088047 - Sequence 69071 from Patent EP1572962.
JD084244 - Sequence 65268 from Patent EP1572962.
JD539766 - Sequence 520790 from Patent EP1572962.
JD181946 - Sequence 162970 from Patent EP1572962.
JD316041 - Sequence 297065 from Patent EP1572962.
JD272194 - Sequence 253218 from Patent EP1572962.
JD403165 - Sequence 384189 from Patent EP1572962.
JD424560 - Sequence 405584 from Patent EP1572962.
JD346028 - Sequence 327052 from Patent EP1572962.
JD035875 - Sequence 16899 from Patent EP1572962.
JD477871 - Sequence 458895 from Patent EP1572962.
JD488241 - Sequence 469265 from Patent EP1572962.
JD543784 - Sequence 524808 from Patent EP1572962.
JD132187 - Sequence 113211 from Patent EP1572962.
JD175394 - Sequence 156418 from Patent EP1572962.
JD205166 - Sequence 186190 from Patent EP1572962.
JD200169 - Sequence 181193 from Patent EP1572962.
JD462667 - Sequence 443691 from Patent EP1572962.
JD214406 - Sequence 195430 from Patent EP1572962.
JD489538 - Sequence 470562 from Patent EP1572962.
JD457939 - Sequence 438963 from Patent EP1572962.
JD218297 - Sequence 199321 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001077637, NP_001071105, Q53S08, Q53S08_HUMAN, RAB6C, Rab6C, WTH3DI
UCSC ID: uc002tsr.3
RefSeq Accession: NM_001077637
Protein: Q53S08

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001077637.1
exon count: 1CDS single in 3' UTR: no RNA size: 3672
ORF size: 765CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 965.00frame shift in genome: no % Coverage: 99.86
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.