U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Rabgef1 RAB guanine nucleotide exchange factor 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 360797, updated on 28-Oct-2024

Summary

Official Symbol
Rabgef1provided by RGD
Official Full Name
RAB guanine nucleotide exchange factor 1provided by RGD
Primary source
RGD:1307295
See related
EnsemblRapid:ENSRNOG00000000895 AllianceGenome:RGD:1307295
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable guanyl-nucleotide exchange factor activity; small GTPase binding activity; and ubiquitin protein ligase activity. Predicted to be involved in dendritic transport and protein targeting to membrane. Predicted to act upstream of or within several processes, including negative regulation of macromolecule metabolic process; regulation of signal transduction; and regulation of vesicle-mediated transport. Is active in presynaptic endosome. Orthologous to human RABGEF1 (RAB guanine nucleotide exchange factor 1). [provided by Alliance of Genome Resources, Oct 2024]
Expression
Biased expression in Muscle (RPKM 165.5), Spleen (RPKM 77.1) and 9 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Rabgef1 in Genome Data Viewer
Location:
12q12
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (32096338..32139949, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (26459190..26503790, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (29960132..30004727, complement)

Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene transmembrane protein 248 Neighboring gene transfer RNA leucine (anticodon AAG) 19 Neighboring gene potassium channel tetramerization domain containing 7 Neighboring gene tyrosylprotein sulfotransferase 1

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

General gene information

Markers

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables guanyl-nucleotide exchange factor activity ISO
Inferred from Sequence Orthology
more info
 
enables small GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables small GTPase binding ISO
Inferred from Sequence Orthology
more info
 
enables ubiquitin protein ligase activity ISO
Inferred from Sequence Orthology
more info
 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of Kit signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of Ras protein signal transduction ISO
Inferred from Sequence Orthology
more info
 
involved_in dendritic transport ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of establishment of localization in cell ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of mast cell degranulation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of mast cell migration ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of Kit signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of Ras protein signal transduction ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of inflammatory response ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of interleukin-6 production ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of leukocyte migration ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of mast cell activation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of mast cell cytokine production ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of mast cell degranulation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of protein phosphorylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of receptor-mediated endocytosis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of protein phosphorylation ISO
Inferred from Sequence Orthology
more info
 
involved_in protein targeting to membrane ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of receptor-mediated endocytosis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of Fc receptor mediated stimulatory signaling pathway ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in dendrite ISO
Inferred from Sequence Orthology
more info
 
located_in early endosome ISO
Inferred from Sequence Orthology
more info
 
is_active_in endocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
is_active_in presynaptic endosome IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in presynaptic endosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in vesicle ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
rab5 GDP/GTP exchange factor
Names
RAB guanine nucleotide exchange factor (GEF) 1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001108333.1NP_001101803.1  rab5 GDP/GTP exchange factor

    See identical proteins and their annotated locations for NP_001101803.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473973
    UniProtKB/TrEMBL
    A6J0M5, G3V631
    Conserved Domains (2) summary
    pfam01754
    Location:2851
    zf-A20; A20-like zinc finger
    pfam02204
    Location:281381
    VPS9; Vacuolar sorting protein 9 (VPS9) domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086030.1 Reference GRCr8

    Range
    32096338..32139949 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039089588.2XP_038945516.1  rab5 GDP/GTP exchange factor isoform X6

    UniProtKB/TrEMBL
    A0A8I6ABA8, A6J0M6
    Conserved Domains (3) summary
    pfam02204
    Location:270370
    VPS9; Vacuolar sorting protein 9 (VPS9) domain
    pfam01754
    Location:1739
    zf-A20; A20-like zinc finger
    pfam18151
    Location:158220
    DUF5601; Domain of unknown function (DUF5601)
  2. XM_006249239.5XP_006249301.1  rab5 GDP/GTP exchange factor isoform X5

    See identical proteins and their annotated locations for XP_006249301.1

    Conserved Domains (3) summary
    pfam02204
    Location:271371
    VPS9; Vacuolar sorting protein 9 (VPS9) domain
    pfam01754
    Location:1739
    zf-A20; A20-like zinc finger
    pfam18151
    Location:159221
    DUF5601; Domain of unknown function (DUF5601)
  3. XM_063271493.1XP_063127563.1  rab5 GDP/GTP exchange factor isoform X1

  4. XM_063271494.1XP_063127564.1  rab5 GDP/GTP exchange factor isoform X2

  5. XM_063271495.1XP_063127565.1  rab5 GDP/GTP exchange factor isoform X4

    Related
    ENSRNOP00000090633.2, ENSRNOT00000105396.2
  6. XM_006249240.5XP_006249302.1  rab5 GDP/GTP exchange factor isoform X5

    See identical proteins and their annotated locations for XP_006249302.1

    Conserved Domains (3) summary
    pfam02204
    Location:271371
    VPS9; Vacuolar sorting protein 9 (VPS9) domain
    pfam01754
    Location:1739
    zf-A20; A20-like zinc finger
    pfam18151
    Location:159221
    DUF5601; Domain of unknown function (DUF5601)
  7. XM_039089587.2XP_038945515.1  rab5 GDP/GTP exchange factor isoform X3

    Conserved Domains (3) summary
    pfam02204
    Location:295395
    VPS9; Vacuolar sorting protein 9 (VPS9) domain
    pfam01754
    Location:4163
    zf-A20; A20-like zinc finger
    pfam18151
    Location:183245
    DUF5601; Domain of unknown function (DUF5601)