chm CHM Rab escort protein [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: chmprovided by ZNC
Official Full Name: CHM Rab escort proteinprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030318-2
See related: Ensembl:ENSDARG00000003845 AllianceGenome:ZFIN:ZDB-GENE-030318-2
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: eva; REP1; evanescence
Summary: Enables Rab geranylgeranyltransferase activity. Acts upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of sound; iridophore differentiation; and sensory organ development. Predicted to be part of Rab-protein geranylgeranyltransferase complex. Predicted to be active in cytosol and nucleus. Used to study choroideremia. Human ortholog(s) of this gene implicated in choroideremia. Orthologous to human CHM (CHM Rab escort protein). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 21

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	21	NC_007132.7 (34686796..34793908)
105	previous assembly	GRCz10 (GCF_000002035.5)	21	NC_007132.6 (34652306..34759418)

Chromosome 21 - NC_007132.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

REP1 deficiency causes systemic dysfunction of lipid metabolism and oxidative stress in choroideremia.
Title: REP1 deficiency causes systemic dysfunction of lipid metabolism and oxidative stress in choroideremia.
In Choroideremia(Y42X/y) fibroblasts, there was a recovery of prenylation activity following treatment with either PTC124 (42 +/- 5%) or PTC-414 (36 +/- 11%), although an increase in REP1 protein was not detected in these cells, in contrast to the zebrafish model.
Title: Functional rescue of REP1 following treatment with PTC124 and novel derivative PTC-414 in human choroideremia fibroblasts and the nonsense-mediated zebrafish model.
The results of this study propose that in chm(-/-) zebrafish, maternally derived rep allows initial successful development of the embryo, but its gradual loss leads to multisystem disease and invariably to lethality.
Title: Single choroideremia gene in nonmammalian vertebrates explains early embryonic lethality of the zebrafish model of choroideremia.
The degenerative phenotype resulting from a null mutation in the zebrafish gene indicates that hair cells and retinal cells require Rab escort protein 1 for survival.
Title: Mutation of the zebrafish choroideremia gene encoding Rab escort protein 1 devastates hair cells.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables GDP-dissociation inhibitor activity	IEA Inferred from Electronic Annotation more info
enables GTPase activator activity	IEA Inferred from Electronic Annotation more info
enables Rab geranylgeranyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cholesterol metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within compound eye corneal lens development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear auditory receptor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intracellular protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within iridophore differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within maintenance of cell number	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein geranylgeranylation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retina homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina layer formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within small GTPase-mediated signal transduction	IEA Inferred from Electronic Annotation more info
involved_in small GTPase-mediated signal transduction	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within swim bladder inflation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of Rab-protein geranylgeranyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Rab-protein geranylgeranyltransferase complex	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: rab proteins geranylgeranyltransferase component A 1

Names: Rab escort protein 1; choroideremia (Rab escort protein 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_203461.1 → NP_982286.1 rab proteins geranylgeranyltransferase component A 1

See identical proteins and their annotated locations for NP_982286.1

Status: PROVISIONAL

Source sequence(s)

AY500891

UniProtKB/TrEMBL

Q6RFG0

Related

ENSDARP00000019118.8, ENSDART00000005479.9

Conserved Domains (1) summary

cl21454
Location:5 → 513

NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins