depdc5 DEP domain containing 5, GATOR1 subcomplex subunit [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: depdc5provided by ZNC
Official Full Name: DEP domain containing 5, GATOR1 subcomplex subunitprovided by ZNC
Primary source: ZFIN:ZDB-GENE-091204-356
See related: Ensembl:ENSDARG00000078105 AllianceGenome:ZFIN:ZDB-GENE-091204-356
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: si:dkey-106l3.5
Summary: Predicted to contribute to GTPase activator activity. Acts upstream of or within regulation of neuronal action potential and swimming behavior. Predicted to be part of GATOR1 complex. Predicted to be active in lysosomal membrane. Is expressed in central nervous system and notochord. Used to study focal epilepsy. Human ortholog(s) of this gene implicated in focal epilepsy. Orthologous to human DEPDC5 (DEP domain containing 5, GATOR1 subcomplex subunit). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 10

Exon count:: 43

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	10	NC_007121.7 (17171254..17222162, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	10	NC_007121.6 (17213290..17264174, complement)

Chromosome 10 - NC_007121.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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?

Consistently, some defects in depdc5(-/-) could be compensated for by treatment with GABA, corroborating that GABA signaling is indeed involved in DEPDC5 pathogenicity. Further, the mTOR-independent nature of these neurodevelopmental defects was demonstrated by the inability of rapamycin to rescue the GABAergic network defects observed in depdc5(-/-) brains.
Title: Non-canonical mTOR-Independent Role of DEPDC5 in Regulating GABAergic Network Development.

Submit: New GeneRIF Correction

General gene information

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Markers

fc35e01.x1 (e-PCR)
- UniSTS:193631

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables GTPase activator activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to amino acid starvation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intracellular signal transduction	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of TORC1 signaling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuronal action potential propagation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of autophagy	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of neuronal action potential	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within swimming behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within thigmotaxis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of GATOR1 complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: DEP domain-containing protein 5; GATOR1 complex protein DEPDC5

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007121.7 Reference GRCz11 Primary Assembly

Range

17171254..17222162 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_686358.9 → XP_691450.5 GATOR1 complex protein DEPDC5 isoform X3

UniProtKB/TrEMBL

A0A8N7UT47, E7EXM8

Related

ENSDARP00000098526.3, ENSDART00000111088.4

Conserved Domains (2) summary

cd04449
Location:1173 → 1256

DEP_DEPDC5-like; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.

pfam12257
Location:111 → 385

DUF3608; Protein of unknown function (DUF3608)
XM_021479301.2 → XP_021334976.1 GATOR1 complex protein DEPDC5 isoform X2

UniProtKB/TrEMBL

A0A8M9QGW7

Conserved Domains (2) summary

cd04449
Location:1175 → 1258

DEP_DEPDC5-like; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.

pfam12257
Location:111 → 385

IML1; Vacuolar membrane-associated protein Iml1
XM_021479304.2 → XP_021334979.1 GATOR1 complex protein DEPDC5 isoform X5

UniProtKB/TrEMBL

A0A8M9QCD7

Related

ENSDARP00000115238.1, ENSDART00000134059.3

Conserved Domains (2) summary

cd04449
Location:1163 → 1246

DEP_DEPDC5-like; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.

pfam12257
Location:111 → 385

IML1; Vacuolar membrane-associated protein Iml1
XM_021479302.2 → XP_021334977.1 GATOR1 complex protein DEPDC5 isoform X4

UniProtKB/TrEMBL

A0A8M9PTY0

Conserved Domains (2) summary

cd04449
Location:1184 → 1267

DEP_DEPDC5-like; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.

pfam12257
Location:111 → 385

IML1; Vacuolar membrane-associated protein Iml1
XM_021479300.2 → XP_021334975.1 GATOR1 complex protein DEPDC5 isoform X1

UniProtKB/TrEMBL

A0A8M9QKY4

Conserved Domains (2) summary

cd04449
Location:1184 → 1267

DEP_DEPDC5-like; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.

pfam12257
Location:111 → 385

IML1; Vacuolar membrane-associated protein Iml1
XM_068223938.1 → XP_068080039.1 GATOR1 complex protein DEPDC5 isoform X6