Human Gene RABGAP1 (ENST00000373647.9) from GENCODE V44
  Description: Homo sapiens RAB GTPase activating protein 1 (RABGAP1), mRNA. (from RefSeq NM_012197)
Gencode Transcript: ENST00000373647.9
Gencode Gene: ENSG00000011454.18
Transcript (Including UTRs)
   Position: hg38 chr9:122,941,020-123,104,866 Size: 163,847 Total Exon Count: 26 Strand: +
Coding Region
   Position: hg38 chr9:122,957,060-123,103,213 Size: 146,154 Coding Exon Count: 25 

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RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:122,941,020-123,104,866)mRNA (may differ from genome)Protein (1069 aa)
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-  Comments and Description Text from UniProtKB
  ID: RBGP1_HUMAN
DESCRIPTION: RecName: Full=Rab GTPase-activating protein 1; AltName: Full=GAP and centrosome-associated protein; AltName: Full=Rab6 GTPase-activating protein GAPCenA;
FUNCTION: May act as a GTPase-activating protein of RAB6A. May play a role in microtubule nucleation by centrosome. May participate in a RAB6A-mediated pathway involved in the metaphase- anaphase transition.
SUBUNIT: Interacts with RAB6A and tubulin gamma.
INTERACTION: Q9H0R8:GABARAPL1; NbExp=2; IntAct=EBI-1057545, EBI-746969;
SUBCELLULAR LOCATION: Cytoplasm, cytosol. Cytoplasm, cytoskeleton, centrosome. Note=Predominantly cytosolic but also associated with the centrosome.
SIMILARITY: Contains 1 PID domain.
SIMILARITY: Contains 1 Rab-GAP TBC domain.
SEQUENCE CAUTION: Sequence=AAF28917.1; Type=Frameshift; Positions=Several; Sequence=AAH20609.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH54492.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AK022408; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=CAB40267.2; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: RABGAP1
Diseases sorted by gene-association score: warburg micro syndrome 1 (3)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.91 RPKM in Artery - Tibial
Total median expression: 790.53 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 -36.20123-0.294 Picture PostScript Text
3' UTR -485.101653-0.293 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
IPR022164 - Kinesin-like
IPR011993 - PH_like_dom
IPR006020 - PTyr_interaction_dom
IPR000195 - Rab-GTPase-TBC_dom

Pfam Domains:
PF12473 - Kinesin protein
PF00640 - Phosphotyrosine interaction domain (PTB/PID)
PF00566 - Rab-GTPase-TBC domain

ModBase Predicted Comparative 3D Structure on Q9Y3P9
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-  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
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Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
AlignmentAlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0015631 tubulin binding
GO:0017137 Rab GTPase binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0007049 cell cycle
GO:0031338 regulation of vesicle fusion
GO:0043087 regulation of GTPase activity
GO:0043547 positive regulation of GTPase activity
GO:0090630 activation of GTPase activity
GO:1902017 regulation of cilium assembly

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005875 microtubule associated complex
GO:0012505 endomembrane system


-  Descriptions from all associated GenBank mRNAs
  AK131449 - Homo sapiens cDNA FLJ16595 fis, clone TESTI4005317, highly similar to Homo sapiens rab6 GTPase activating protein (GAP and centrosome-associated) (GAPCENA).
BC020609 - Homo sapiens RAB GTPase activating protein 1, mRNA (cDNA clone IMAGE:4768130), partial cds.
LP895616 - Sequence 480 from Patent EP3253886.
AK022408 - Homo sapiens cDNA FLJ12346 fis, clone MAMMA1002297.
BC054492 - Homo sapiens RAB GTPase activating protein 1, mRNA (cDNA clone MGC:54135 IMAGE:5785896), complete cds.
AF161357 - Homo sapiens HSPC094 mRNA, partial cds.
AJ011679 - Homo sapiens mRNA for Rab6 GTPase activating protein.
AB449897 - Homo sapiens TBC1D11 mRNA for TBC1 domain family, member 11, complete cds.
AK294531 - Homo sapiens cDNA FLJ53389 complete cds, highly similar to Homo sapiens RAB GTPase activating protein 1 (RABGAP1), mRNA.
JD083006 - Sequence 64030 from Patent EP1572962.
JD301667 - Sequence 282691 from Patent EP1572962.
AL050195 - Homo sapiens mRNA; cDNA DKFZp586D2123 (from clone DKFZp586D2123); partial cds.
JD362119 - Sequence 343143 from Patent EP1572962.
JD205521 - Sequence 186545 from Patent EP1572962.
JD137615 - Sequence 118639 from Patent EP1572962.
JD548972 - Sequence 529996 from Patent EP1572962.
JD507200 - Sequence 488224 from Patent EP1572962.
JD084270 - Sequence 65294 from Patent EP1572962.
JD269813 - Sequence 250837 from Patent EP1572962.
JD349557 - Sequence 330581 from Patent EP1572962.
JD433503 - Sequence 414527 from Patent EP1572962.
JD060457 - Sequence 41481 from Patent EP1572962.
JD429082 - Sequence 410106 from Patent EP1572962.
JD324146 - Sequence 305170 from Patent EP1572962.
JD057815 - Sequence 38839 from Patent EP1572962.
JD469996 - Sequence 451020 from Patent EP1572962.
JD546928 - Sequence 527952 from Patent EP1572962.
JD059447 - Sequence 40471 from Patent EP1572962.
AF088073 - Homo sapiens full length insert cDNA clone ZD96A04.
JD373759 - Sequence 354783 from Patent EP1572962.
JD519387 - Sequence 500411 from Patent EP1572962.
JD382831 - Sequence 363855 from Patent EP1572962.
JD491131 - Sequence 472155 from Patent EP1572962.

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

Protein Q9Y3P9 (Reactome details) participates in the following event(s):

R-HSA-8854303 TBC1D11 binds RAB6
R-HSA-8854214 TBC/RABGAPs
R-HSA-9007101 Rab regulation of trafficking
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: B9A6L2, ENST00000373647.1, ENST00000373647.2, ENST00000373647.3, ENST00000373647.4, ENST00000373647.5, ENST00000373647.6, ENST00000373647.7, ENST00000373647.8, HSPC094, NM_012197, Q05CW2, Q6ZMY1, Q9HA28, Q9P0E2, Q9UG67, Q9Y3P9, RBGP1_HUMAN, uc011lzh.1, uc011lzh.2, uc011lzh.3, uc011lzh.4
UCSC ID: ENST00000373647.9
RefSeq Accession: NM_012197
Protein: Q9Y3P9 (aka RBGP1_HUMAN)
CCDS: CCDS6848.2

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.