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

Summary

Official Symbol: Rabgef1provided by RGD
Official Full Name: RAB guanine nucleotide exchange factor 1provided by RGD
Primary source: RGD:1307295
See related: Ensembl: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 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. Predicted to be located in cytosol; early endosome; and nucleolus. Orthologous to human RABGEF1 (RAB guanine nucleotide exchange factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 165.5), Spleen (RPKM 77.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

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_086030.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Our data suggest that RabGEF1 is a negative regulator of TrkA-dependent neuronal differentiation and of NMDA receptor-mediated signaling activation in NGF-differentiated PC12 cells.
Title: RabGEF1/Rabex-5 Regulates TrkA-Mediated Neurite Outgrowth and NMDA-Induced Signaling Activation in NGF-Differentiated PC12 Cells.

Submit: New GeneRIF Correction

General gene information

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Markers

RH143734 (e-PCR)
- UniSTS:232980

d12rat75 (e-PCR)
- UniSTS:120856

BI294189 (e-PCR)
- UniSTS:246052

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
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

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Preferred Names: rab5 GDP/GTP exchange factor

Names: RAB guanine nucleotide exchange factor (GEF) 1

NCBI Reference Sequences (RefSeq)

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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)

NM_001108333.1 → NP_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

Related

ENSRNOP00000001196.3, ENSRNOT00000001196.5

Conserved Domains (2) summary

pfam01754
Location:28 → 51

zf-A20; A20-like zinc finger

pfam02204
Location:281 → 381

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

NC_086030.1 Reference GRCr8

Range

32096338..32139949 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8I6ABA8, A6J0M6

Related

ENSRNOP00000090633.1

Conserved Domains (3) summary

pfam02204
Location:270 → 370

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam01754
Location:17 → 39

zf-A20; A20-like zinc finger

pfam18151
Location:158 → 220

DUF5601; Domain of unknown function (DUF5601)
XM_006249239.5 → XP_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:271 → 371

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam01754
Location:17 → 39

zf-A20; A20-like zinc finger

pfam18151
Location:159 → 221

DUF5601; Domain of unknown function (DUF5601)
XM_063271493.1 → XP_063127563.1 rab5 GDP/GTP exchange factor isoform X1
XM_063271494.1 → XP_063127564.1 rab5 GDP/GTP exchange factor isoform X2
XM_063271495.1 → XP_063127565.1 rab5 GDP/GTP exchange factor isoform X4
XM_006249240.5 → XP_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:271 → 371

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam01754
Location:17 → 39

zf-A20; A20-like zinc finger

pfam18151
Location:159 → 221

DUF5601; Domain of unknown function (DUF5601)
XM_039089587.2 → XP_038945515.1 rab5 GDP/GTP exchange factor isoform X3

Conserved Domains (3) summary

pfam02204
Location:295 → 395

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam01754
Location:41 → 63

zf-A20; A20-like zinc finger

pfam18151
Location:183 → 245

DUF5601; Domain of unknown function (DUF5601)