Human Gene RAB5C (ENST00000346213.9_7) from GENCODE V47lift37
  Description: RAB5C, member RAS oncogene family, transcript variant 1 (from RefSeq NM_201434.3)
Gencode Transcript: ENST00000346213.9_7
Gencode Gene: ENSG00000108774.15_12
Transcript (Including UTRs)
   Position: hg19 chr17:40,276,997-40,307,007 Size: 30,011 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr17:40,277,801-40,282,520 Size: 4,720 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:40,276,997-40,307,007)mRNA (may differ from genome)Protein (216 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RAB5C_HUMAN
DESCRIPTION: RecName: Full=Ras-related protein Rab-5C; AltName: Full=L1880; AltName: Full=RAB5L;
FUNCTION: Protein transport. Probably involved in vesicular traffic (By similarity).
SUBUNIT: Binds EEA1.
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor; Cytoplasmic side (By similarity). Early endosome membrane; Lipid-anchor (By similarity). Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
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


-  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: 13.50 RPKM in Spleen
Total median expression: 461.26 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 -61.60185-0.333 Picture PostScript Text
3' UTR -274.70804-0.342 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
IPR005225 - Small_GTP-bd_dom
IPR001806 - Small_GTPase
IPR003579 - Small_GTPase_Rab_type

Pfam Domains:
PF00025 - ADP-ribosylation factor family
PF00071 - Ras family
PF01926 - 50S ribosome-binding GTPase
PF04670 - Gtr1/RagA G protein conserved region
PF08477 - Ras of Complex, Roc, domain of DAPkinase

SCOP Domains:
51735 - NAD(P)-binding Rossmann-fold domains
52540 - P-loop containing nucleoside triphosphate hydrolases
56300 - Metallo-dependent phosphatases

ModBase Predicted Comparative 3D Structure on P51148
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0019003 GDP binding

Biological Process:
GO:0015031 protein transport
GO:0030100 regulation of endocytosis
GO:0043312 neutrophil degranulation
GO:0048227 plasma membrane to endosome transport

Cellular Component:
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005769 early endosome
GO:0005811 lipid particle
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030139 endocytic vesicle
GO:0031901 early endosome membrane
GO:0035577 azurophil granule membrane
GO:0042470 melanosome
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  U11293 - Human Rab5c-like protein mRNA, complete cds.
AK025474 - Homo sapiens cDNA: FLJ21821 fis, clone HEP01311, highly similar to HSU18420 Human ras-related small GTP binding protein Rab5 (rab5) mRNA.
U18420 - Human ras-related small GTP binding protein Rab5 (rab5) mRNA, complete cds.
BC106039 - Homo sapiens RAB5C, member RAS oncogene family, mRNA (cDNA clone MGC:117217 IMAGE:4938169), complete cds.
JD300405 - Sequence 281429 from Patent EP1572962.
JD055610 - Sequence 36634 from Patent EP1572962.
JD095138 - Sequence 76162 from Patent EP1572962.
JD041499 - Sequence 22523 from Patent EP1572962.
BC114439 - Homo sapiens RAB5C, member RAS oncogene family, mRNA (cDNA clone MGC:138857 IMAGE:40083572), complete cds.
JD514620 - Sequence 495644 from Patent EP1572962.
JD073918 - Sequence 54942 from Patent EP1572962.
JD220867 - Sequence 201891 from Patent EP1572962.
JD219033 - Sequence 200057 from Patent EP1572962.
JD329621 - Sequence 310645 from Patent EP1572962.
JD177295 - Sequence 158319 from Patent EP1572962.
JD252870 - Sequence 233894 from Patent EP1572962.
JD555519 - Sequence 536543 from Patent EP1572962.
JD381820 - Sequence 362844 from Patent EP1572962.
JD164934 - Sequence 145958 from Patent EP1572962.
JD237559 - Sequence 218583 from Patent EP1572962.
AK310234 - Homo sapiens cDNA, FLJ17276.
JD174603 - Sequence 155627 from Patent EP1572962.
JD293836 - Sequence 274860 from Patent EP1572962.
AF141304 - Homo sapiens small GTPase (RAB5C) mRNA, complete cds.
AF498938 - Homo sapiens small GTP binding protein RAB5C (RAB5C) mRNA, complete cds.
CR541901 - Homo sapiens full open reading frame cDNA clone RZPDo834B1233D for gene RAB5C, RAB5C, member RAS oncogene family; complete cds, incl. stopcodon.
EU832102 - Synthetic construct Homo sapiens clone HAIB:100067131; DKFZo008B0425 RAB5C, member RAS oncogene family protein (RAB5C) gene, encodes complete protein.
EU832196 - Synthetic construct Homo sapiens clone HAIB:100067225; DKFZo004B0426 RAB5C, member RAS oncogene family protein (RAB5C) gene, encodes complete protein.
BT019484 - Homo sapiens RAB5C, member RAS oncogene family mRNA, complete cds.
KJ891972 - Synthetic construct Homo sapiens clone ccsbBroadEn_01366 RAB5C gene, encodes complete protein.
AB528716 - Synthetic construct DNA, clone: pF1KB6969, Homo sapiens RAB5C gene for RAB5C, member RAS oncogene family, without stop codon, in Flexi system.
JD439053 - Sequence 420077 from Patent EP1572962.
JD493761 - Sequence 474785 from Patent EP1572962.
JD116731 - Sequence 97755 from Patent EP1572962.
JD487557 - Sequence 468581 from Patent EP1572962.

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

Protein P51148 (Reactome details) participates in the following event(s):

R-HSA-421836 trans-Golgi Network Derived Vesicle Uncoating
R-HSA-421833 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture
R-HSA-6798739 Exocytosis of azurophil granule membrane proteins
R-HSA-421835 trans-Golgi Network Vesicle Scission
R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-8870466 RGGT:CHM binds RABs
R-HSA-8875320 RAB5 GEFs exchange GTP for GDP on RAB5
R-HSA-8854222 TBC1D3 associates with RAB5
R-HSA-8870469 RGGT geranylgeranylates RAB proteins
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-6798695 Neutrophil degranulation
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-168249 Innate Immune System
R-HSA-8873719 RAB geranylgeranylation
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-168256 Immune System
R-HSA-8854214 TBC/RABGAPs
R-HSA-597592 Post-translational protein modification
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-9007101 Rab regulation of trafficking
R-HSA-199991 Membrane Trafficking
R-HSA-392499 Metabolism of proteins
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000346213.1, ENST00000346213.2, ENST00000346213.3, ENST00000346213.4, ENST00000346213.5, ENST00000346213.6, ENST00000346213.7, ENST00000346213.8, F8W1H5, NM_201434, P51148, Q6FH55, Q9P0Y5, RAB5C_HUMAN, RABL, uc317xii.1, uc317xii.2
UCSC ID: ENST00000346213.9_7
RefSeq Accession: NM_004583.4
Protein: P51148 (aka RAB5C_HUMAN or RB5C_HUMAN)

-  Gene Model Information
  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.