RGD1359108 similar to RIKEN cDNA 3110043O21 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: RGD1359108provided by RGD
Official Full Name: similar to RIKEN cDNA 3110043O21provided by RGD
Primary source: RGD:1359108
See related: Ensembl:ENSRNOG00000009478 AllianceGenome:RGD:1359108
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: C9orf72
Summary: Predicted to enable small GTPase binding activity. Predicted to contribute to guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including negative regulation of GTP binding activity; regulation of organelle organization; and stress granule assembly. Predicted to be located in several cellular components, including Flemming body; axon; and cytoplasmic ribonucleoprotein granule. Predicted to be part of guanyl-nucleotide exchange factor complex. Predicted to be active in autophagosome and endosome. Human ortholog(s) of this gene implicated in frontotemporal dementia and/or amyotrophic lateral sclerosis-1. Orthologous to human C9orf72 (C9orf72-SMCR8 complex subunit). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 119.7), Brain (RPKM 94.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q21

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (54562570..54587649, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (49766340..49791434, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (50666444..50691523, complement)

Chromosome 5 - NC_086023.1 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?

C9orf72 regulates the unfolded protein response and stress granule formation by interacting with eIF2alpha.
Title: C9orf72 regulates the unfolded protein response and stress granule formation by interacting with eIF2α.
Overexpression of C9orf72 exacerbates Abeta2535induced oxidative stress and apoptosis in PC12 cells.
Title: Overexpression of C9orf72 exacerbates Aβ25‑35‑induced oxidative stress and apoptosis in PC12 cells.
Ablation of C9orf72 together with excitotoxicity induces ALS in rats.
Title: Ablation of C9orf72 together with excitotoxicity induces ALS in rats.
In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.
Title: In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	IEA Inferred from Electronic Annotation more info
contributes_to guanyl-nucleotide exchange factor activity	ISO Inferred from Sequence Orthology more info
enables small GTPase binding	IEA Inferred from Electronic Annotation more info
enables small GTPase binding	ISO Inferred from Sequence Orthology more info
enables small GTPase binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in autophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in autophagy	ISO Inferred from Sequence Orthology more info
involved_in autophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in axon extension	IEA Inferred from Electronic Annotation more info
involved_in axon extension	ISO Inferred from Sequence Orthology more info
involved_in axon extension	ISS Inferred from Sequence or Structural Similarity more info
involved_in endocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in endocytosis	ISO Inferred from Sequence Orthology more info
involved_in endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in late endosome to lysosome transport	IEA Inferred from Electronic Annotation more info
involved_in late endosome to lysosome transport	ISO Inferred from Sequence Orthology more info
involved_in late endosome to lysosome transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein phosphorylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of macroautophagy	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of macroautophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of TORC1 signaling	IEA Inferred from Electronic Annotation more info
involved_in regulation of TORC1 signaling	ISO Inferred from Sequence Orthology more info
involved_in regulation of TORC1 signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of actin filament organization	IEA Inferred from Electronic Annotation more info
involved_in regulation of actin filament organization	ISO Inferred from Sequence Orthology more info
involved_in regulation of actin filament organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of autophagosome assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of autophagosome assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in regulation of autophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of protein localization	IEA Inferred from Electronic Annotation more info
involved_in regulation of protein localization	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic vesicle cycle	ISO Inferred from Sequence Orthology more info
involved_in stress granule assembly	IEA Inferred from Electronic Annotation more info
involved_in stress granule assembly	ISO Inferred from Sequence Orthology more info
involved_in stress granule assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of Atg1/ULK1 kinase complex	IEA Inferred from Electronic Annotation more info
part_of Atg1/ULK1 kinase complex	ISO Inferred from Sequence Orthology more info
part_of Atg1/ULK1 kinase complex	ISS Inferred from Sequence or Structural Similarity more info
located_in Flemming body	IEA Inferred from Electronic Annotation more info
located_in Flemming body	ISO Inferred from Sequence Orthology more info
located_in P-body	IEA Inferred from Electronic Annotation more info
located_in P-body	ISO Inferred from Sequence Orthology more info
located_in P-body	ISS Inferred from Sequence or Structural Similarity more info
is_active_in autophagosome	IBA Inferred from Biological aspect of Ancestor more info
located_in autophagosome	IEA Inferred from Electronic Annotation more info
located_in autophagosome	ISO Inferred from Sequence Orthology more info
located_in autophagosome	ISS Inferred from Sequence or Structural Similarity more info
located_in axonal growth cone	IEA Inferred from Electronic Annotation more info
located_in axonal growth cone	ISO Inferred from Sequence Orthology more info
located_in axonal growth cone	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic stress granule	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic stress granule	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic stress granule	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular space	IEA Inferred from Electronic Annotation more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISS Inferred from Sequence or Structural Similarity more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
part_of guanyl-nucleotide exchange factor complex	IEA Inferred from Electronic Annotation more info
part_of guanyl-nucleotide exchange factor complex	ISO Inferred from Sequence Orthology more info
is_active_in hippocampal mossy fiber to CA3 synapse	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in main axon	IEA Inferred from Electronic Annotation more info
located_in main axon	ISO Inferred from Sequence Orthology more info
located_in main axon	ISS Inferred from Sequence or Structural Similarity more info
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear membrane	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in perikaryon	ISO Inferred from Sequence Orthology more info
located_in perikaryon	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info
is_active_in postsynapse	ISO Inferred from Sequence Orthology more info
located_in postsynapse	ISO Inferred from Sequence Orthology more info
located_in postsynapse	ISS Inferred from Sequence or Structural Similarity more info
located_in presynapse	IEA Inferred from Electronic Annotation more info
located_in presynapse	ISO Inferred from Sequence Orthology more info
located_in presynapse	ISS Inferred from Sequence or Structural Similarity more info
is_active_in presynaptic cytosol	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: guanine nucleotide exchange factor C9orf72 homolog

Names: guanine nucleotide exchange C9orf72 homolog; protein C9orf72 homolog; uncharacterized protein C9orf72 homolog

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_001007702.2 → NP_001007703.1 guanine nucleotide exchange factor C9orf72 homolog

See identical proteins and their annotated locations for NP_001007703.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

Q66HC3

UniProtKB/TrEMBL

A6IIP4, R9PXU1

Related

ENSRNOP00000013181.5, ENSRNOT00000013181.7

Conserved Domains (1) summary

pfam15019
Location:61 → 324

C9orf72-like; C9orf72-like protein family

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_086023.1 Reference GRCr8

Range

54562570..54587649 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109829.2 → XP_038965757.1 guanine nucleotide exchange factor C9orf72 homolog isoform X1

UniProtKB/Swiss-Prot

Q66HC3

UniProtKB/TrEMBL

A6IIP4, R9PXU1

Conserved Domains (1) summary

pfam15019
Location:61 → 324

C9orf72-like; C9orf72-like protein family
XM_039109830.2 → XP_038965758.1 guanine nucleotide exchange factor C9orf72 homolog isoform X2

Conserved Domains (1) summary

pfam15019
Location:61 → 247

C9orf72-like; C9orf72-like protein family