Human Gene RGP1 (ENST00000378078.5_4) from GENCODE V47lift37
  Description: RGP1 homolog, RAB6A GEF complex partner 1 (from RefSeq NM_001080496.3)
Gencode Transcript: ENST00000378078.5_4
Gencode Gene: ENSG00000107185.10_7
Transcript (Including UTRs)
   Position: hg19 chr9:35,749,284-35,758,582 Size: 9,299 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr9:35,749,753-35,752,871 Size: 3,119 Coding Exon Count: 8 

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 (chr9:35,749,284-35,758,582)mRNA (may differ from genome)Protein (391 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RGP1_HUMAN
DESCRIPTION: RecName: Full=Retrograde Golgi transport protein RGP1 homolog;
SIMILARITY: Belongs to the RGP1 family.
SEQUENCE CAUTION: Sequence=BAA13388.2; 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


-  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: 7.92 RPKM in Cells - Cultured fibroblasts
Total median expression: 236.29 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 -55.50141-0.394 Picture PostScript Text
3' UTR -2171.705711-0.380 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
IPR014848 - Rgp1

Pfam Domains:
PF08737 - Rgp1

SCOP Domains:
81296 - E set domains
55112 - Formylmethanofuran:tetrahydromethanopterin formyltransferase

ModBase Predicted Comparative 3D Structure on Q92546
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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 orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0005515 protein binding
GO:0017112 Rab guanyl-nucleotide exchange factor activity
GO:0017137 Rab GTPase binding

Biological Process:
GO:0042147 retrograde transport, endosome to Golgi
GO:0043547 positive regulation of GTPase activity
GO:1903363 negative regulation of cellular protein catabolic process

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0032588 trans-Golgi network membrane
GO:0032991 macromolecular complex
GO:0034066 RIC1-RGP1 guanyl-nucleotide exchange factor complex


-  Descriptions from all associated GenBank mRNAs
  LF206435 - JP 2014500723-A/13938: Polycomb-Associated Non-Coding RNAs.
AK289566 - Homo sapiens cDNA FLJ76996 complete cds.
D87447 - Homo sapiens mRNA for KIAA0258 gene.
BC001725 - Homo sapiens RGP1 retrograde golgi transport homolog (S. cerevisiae), mRNA (cDNA clone MGC:755 IMAGE:3533857), complete cds.
AB383823 - Synthetic construct DNA, clone: pF1KSDA0258, Homo sapiens KIAA0258 gene for KIAA0258 protein, complete cds, without stop codon, in Flexi system.
CU674846 - Synthetic construct Homo sapiens gateway clone IMAGE:100017163 5' read KIAA0258 mRNA.
HQ447683 - Synthetic construct Homo sapiens clone IMAGE:100071702; CCSB003651_01 KIAA0258 (RGP1) gene, encodes complete protein.
KJ892860 - Synthetic construct Homo sapiens clone ccsbBroadEn_02254 RGP1 gene, encodes complete protein.
DQ600531 - Homo sapiens piRNA piR-38597, complete sequence.
LF354365 - JP 2014500723-A/161868: Polycomb-Associated Non-Coding RNAs.
LF354366 - JP 2014500723-A/161869: Polycomb-Associated Non-Coding RNAs.
JD381922 - Sequence 362946 from Patent EP1572962.
LF206437 - JP 2014500723-A/13940: Polycomb-Associated Non-Coding RNAs.
JD243716 - Sequence 224740 from Patent EP1572962.
JD347359 - Sequence 328383 from Patent EP1572962.
JD279776 - Sequence 260800 from Patent EP1572962.
JD555092 - Sequence 536116 from Patent EP1572962.
JD519743 - Sequence 500767 from Patent EP1572962.
JD393035 - Sequence 374059 from Patent EP1572962.
JD483992 - Sequence 465016 from Patent EP1572962.
JD561060 - Sequence 542084 from Patent EP1572962.
JD120085 - Sequence 101109 from Patent EP1572962.
JD062056 - Sequence 43080 from Patent EP1572962.
JD466295 - Sequence 447319 from Patent EP1572962.
JD278628 - Sequence 259652 from Patent EP1572962.
JD392723 - Sequence 373747 from Patent EP1572962.
JD317217 - Sequence 298241 from Patent EP1572962.
JD135416 - Sequence 116440 from Patent EP1572962.
JD358397 - Sequence 339421 from Patent EP1572962.
JD110539 - Sequence 91563 from Patent EP1572962.
JD223475 - Sequence 204499 from Patent EP1572962.
JD340576 - Sequence 321600 from Patent EP1572962.
JD206292 - Sequence 187316 from Patent EP1572962.
JD256269 - Sequence 237293 from Patent EP1572962.
JD075679 - Sequence 56703 from Patent EP1572962.
LF354368 - JP 2014500723-A/161871: Polycomb-Associated Non-Coding RNAs.
JD271724 - Sequence 252748 from Patent EP1572962.
JD431165 - Sequence 412189 from Patent EP1572962.
JD101604 - Sequence 82628 from Patent EP1572962.
JD280556 - Sequence 261580 from Patent EP1572962.
DQ589555 - Homo sapiens piRNA piR-56667, complete sequence.
JD253757 - Sequence 234781 from Patent EP1572962.
JD272430 - Sequence 253454 from Patent EP1572962.
JD055989 - Sequence 37013 from Patent EP1572962.
JD556803 - Sequence 537827 from Patent EP1572962.
JD235761 - Sequence 216785 from Patent EP1572962.
JD298679 - Sequence 279703 from Patent EP1572962.
JD494687 - Sequence 475711 from Patent EP1572962.
JD218090 - Sequence 199114 from Patent EP1572962.
JD510532 - Sequence 491556 from Patent EP1572962.
JD519689 - Sequence 500713 from Patent EP1572962.
JD465163 - Sequence 446187 from Patent EP1572962.
JD490915 - Sequence 471939 from Patent EP1572962.
JD483539 - Sequence 464563 from Patent EP1572962.
JD446744 - Sequence 427768 from Patent EP1572962.
JD123590 - Sequence 104614 from Patent EP1572962.
JD259836 - Sequence 240860 from Patent EP1572962.
JD437296 - Sequence 418320 from Patent EP1572962.
JD188248 - Sequence 169272 from Patent EP1572962.
JD163636 - Sequence 144660 from Patent EP1572962.
JD298348 - Sequence 279372 from Patent EP1572962.
JD277425 - Sequence 258449 from Patent EP1572962.
JD464134 - Sequence 445158 from Patent EP1572962.
JD218263 - Sequence 199287 from Patent EP1572962.
JD488255 - Sequence 469279 from Patent EP1572962.
JD515103 - Sequence 496127 from Patent EP1572962.
JD262725 - Sequence 243749 from Patent EP1572962.
JD554523 - Sequence 535547 from Patent EP1572962.
JD091818 - Sequence 72842 from Patent EP1572962.
JD089749 - Sequence 70773 from Patent EP1572962.
JD286287 - Sequence 267311 from Patent EP1572962.
JD354494 - Sequence 335518 from Patent EP1572962.
JD310603 - Sequence 291627 from Patent EP1572962.
JD348884 - Sequence 329908 from Patent EP1572962.
JD101504 - Sequence 82528 from Patent EP1572962.
JD538936 - Sequence 519960 from Patent EP1572962.
JD359590 - Sequence 340614 from Patent EP1572962.
JD106994 - Sequence 88018 from Patent EP1572962.
JC506794 - Sequence 162 from Patent EP2733220.
JC737906 - Sequence 162 from Patent WO2014075939.
JD075241 - Sequence 56265 from Patent EP1572962.
JD551756 - Sequence 532780 from Patent EP1572962.
JD333678 - Sequence 314702 from Patent EP1572962.
JD221208 - Sequence 202232 from Patent EP1572962.
JD564909 - Sequence 545933 from Patent EP1572962.
JD048049 - Sequence 29073 from Patent EP1572962.
JD352184 - Sequence 333208 from Patent EP1572962.
JD448737 - Sequence 429761 from Patent EP1572962.
JD566273 - Sequence 547297 from Patent EP1572962.
JD251665 - Sequence 232689 from Patent EP1572962.
JD373876 - Sequence 354900 from Patent EP1572962.
JD175035 - Sequence 156059 from Patent EP1572962.
JD348348 - Sequence 329372 from Patent EP1572962.
JD418594 - Sequence 399618 from Patent EP1572962.
JD439978 - Sequence 421002 from Patent EP1572962.
JD559529 - Sequence 540553 from Patent EP1572962.
JD233217 - Sequence 214241 from Patent EP1572962.
JD498307 - Sequence 479331 from Patent EP1572962.
JD194039 - Sequence 175063 from Patent EP1572962.
JD452226 - Sequence 433250 from Patent EP1572962.
JD485778 - Sequence 466802 from Patent EP1572962.
JD426243 - Sequence 407267 from Patent EP1572962.
JD323779 - Sequence 304803 from Patent EP1572962.
LF354370 - JP 2014500723-A/161873: Polycomb-Associated Non-Coding RNAs.
JD218664 - Sequence 199688 from Patent EP1572962.
JD038633 - Sequence 19657 from Patent EP1572962.
JD199300 - Sequence 180324 from Patent EP1572962.
JD354495 - Sequence 335519 from Patent EP1572962.
JD273022 - Sequence 254046 from Patent EP1572962.
JD484923 - Sequence 465947 from Patent EP1572962.
JD217658 - Sequence 198682 from Patent EP1572962.
JD142403 - Sequence 123427 from Patent EP1572962.
JD476317 - Sequence 457341 from Patent EP1572962.
LF354371 - JP 2014500723-A/161874: Polycomb-Associated Non-Coding RNAs.
JD406063 - Sequence 387087 from Patent EP1572962.
JD066130 - Sequence 47154 from Patent EP1572962.
JD443183 - Sequence 424207 from Patent EP1572962.
LF354372 - JP 2014500723-A/161875: Polycomb-Associated Non-Coding RNAs.
JD265452 - Sequence 246476 from Patent EP1572962.
JD206858 - Sequence 187882 from Patent EP1572962.
JD483428 - Sequence 464452 from Patent EP1572962.
JD381958 - Sequence 362982 from Patent EP1572962.
JD184086 - Sequence 165110 from Patent EP1572962.
JD065465 - Sequence 46489 from Patent EP1572962.
JD499322 - Sequence 480346 from Patent EP1572962.
JD445415 - Sequence 426439 from Patent EP1572962.
JD276823 - Sequence 257847 from Patent EP1572962.
JD494202 - Sequence 475226 from Patent EP1572962.
JD547001 - Sequence 528025 from Patent EP1572962.
LF354374 - JP 2014500723-A/161877: Polycomb-Associated Non-Coding RNAs.
JD188487 - Sequence 169511 from Patent EP1572962.
JD025563 - Sequence 6587 from Patent EP1572962.
JD032651 - Sequence 13675 from Patent EP1572962.
JD034999 - Sequence 16023 from Patent EP1572962.
MA442012 - JP 2018138019-A/13938: Polycomb-Associated Non-Coding RNAs.
MA589942 - JP 2018138019-A/161868: Polycomb-Associated Non-Coding RNAs.
MA589943 - JP 2018138019-A/161869: Polycomb-Associated Non-Coding RNAs.
MA442014 - JP 2018138019-A/13940: Polycomb-Associated Non-Coding RNAs.
MA589945 - JP 2018138019-A/161871: Polycomb-Associated Non-Coding RNAs.
MA589947 - JP 2018138019-A/161873: Polycomb-Associated Non-Coding RNAs.
MA589948 - JP 2018138019-A/161874: Polycomb-Associated Non-Coding RNAs.
MA589949 - JP 2018138019-A/161875: Polycomb-Associated Non-Coding RNAs.
MA589951 - JP 2018138019-A/161877: Polycomb-Associated Non-Coding RNAs.

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

Protein Q92546 (Reactome details) participates in the following event(s):

R-HSA-6811428 RIC1:RGP1 recruits RAB6:GDP to the TGN
R-HSA-8847887 RAB33B:GTP binds RIC1:RGP1
R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
R-HSA-6811429 RIC1:RGP1 stimulates nucleotide RAB6 nucleotide exchange
R-HSA-8876193 RIC1-RGP1 exchanges GTP for GDP on RAB6
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811438 Intra-Golgi traffic
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-199991 Membrane Trafficking
R-HSA-9007101 Rab regulation of trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000378078.1, ENST00000378078.2, ENST00000378078.3, ENST00000378078.4, KIAA0258, NM_001080496, Q5TCV5, Q92546, RGP1 , RGP1_HUMAN, uc318oay.1, uc318oay.2
UCSC ID: ENST00000378078.5_4
RefSeq Accession: NM_001080496.3
Protein: Q92546 (aka RGP1_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.