Depdc5 DEP domain containing 5, GATOR1 subcomplex subunit [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Depdc5provided by RGD
Official Full Name: DEP domain containing 5, GATOR1 subcomplex subunitprovided by RGD
Primary source: RGD:1311535
See related: EnsemblRapid:ENSRNOG00000018144 AllianceGenome:RGD:1311535
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 small GTPase binding activity. Predicted to be involved in cellular response to amino acid starvation; negative regulation of TORC1 signaling; and positive regulation of autophagy. Predicted to be located in cytosol; lysosome; and perinuclear region of cytoplasm. Predicted to be part of Cul3-RING ubiquitin ligase complex and GATOR1 complex. Predicted to be active in lysosomal membrane. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy and familial focal epilepsy with variable foci 1. Orthologous to human DEPDC5 (DEP domain containing 5, GATOR1 subcomplex subunit). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Adrenal (RPKM 69.8), Spleen (RPKM 46.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14q21

Exon count:: 45

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (81956777..82087392, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (77732297..77862924, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (83089000..83219576, complement)

Chromosome 14 - NC_086032.1 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?

DEP-domain containing 5 knockout rats exhibit multiple features of rodent models of mechanistic target of rapamycin complex 1 (mTOR) mTORopathies, and thus, stand as a relevant model to study their underlying pathogenic mechanisms.
Title: Depdc5 knockout rat: A novel model of mTORopathy.

Submit: New GeneRIF Correction

General gene information

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Markers

RH143825 (e-PCR)
- UniSTS:233071

BI280365 (e-PCR)
- UniSTS:249034

BF413401 (e-PCR)
- UniSTS:248550

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables GTPase activator activity	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables small GTPase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to amino acid starvation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to amino acid starvation	ISO Inferred from Sequence Orthology more info
involved_in 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
involved_in negative regulation of TORC1 signaling	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of autophagy	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of Cul3-RING ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info
part_of GATOR1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of GATOR1 complex	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: GATOR1 complex protein DEPDC5

Names: DEP domain-containing protein 5; GATOR complex protein DEPDC5

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_001107229.1 → NP_001100699.1 GATOR1 complex protein DEPDC5

See identical proteins and their annotated locations for NP_001100699.1

Status: PROVISIONAL

Source sequence(s)

CH473963

UniProtKB/TrEMBL

A0A8I5Y2I2, A6IK73

Conserved Domains (2) summary

cd04449
Location:1032 → 1113

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:1 → 268

DUF3608; Protein of unknown function (DUF3608)

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_086032.1 Reference GRCr8

Range

81956777..82087392 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063273173.1 → XP_063129243.1 GATOR1 complex protein DEPDC5 isoform X7

UniProtKB/TrEMBL

A0A8I6A1L7, D4A362
XM_063273168.1 → XP_063129238.1 GATOR1 complex protein DEPDC5 isoform X2

UniProtKB/TrEMBL

A0A8I5YBC5, A0A8I6A1L7
XM_039091988.2 → XP_038947916.1 GATOR1 complex protein DEPDC5 isoform X1

UniProtKB/TrEMBL

A0A8I6A1L7

Conserved Domains (2) summary

cd04449
Location:1177 → 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:101 → 381

IML1; Vacuolar membrane-associated protein Iml1
XM_063273171.1 → XP_063129241.1 GATOR1 complex protein DEPDC5 isoform X5

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273174.1 → XP_063129244.1 GATOR1 complex protein DEPDC5 isoform X7

UniProtKB/TrEMBL

A0A8I6A1L7, D4A362
XM_063273165.1 → XP_063129235.1 GATOR1 complex protein DEPDC5 isoform X2

UniProtKB/TrEMBL

A0A8I5YBC5, A0A8I6A1L7
XM_039091990.2 → XP_038947918.1 GATOR1 complex protein DEPDC5 isoform X1

UniProtKB/TrEMBL

A0A8I6A1L7

Conserved Domains (2) summary

cd04449
Location:1177 → 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:101 → 381

IML1; Vacuolar membrane-associated protein Iml1
XM_063273182.1 → XP_063129252.1 GATOR1 complex protein DEPDC5 isoform X15

UniProtKB/TrEMBL

A0A8I6A1L7
XM_017599214.3 → XP_017454703.1 GATOR1 complex protein DEPDC5 isoform X13

UniProtKB/TrEMBL

A0A8I6A1L7, A0A8I6A374

Related

ENSRNOP00000086876.1, ENSRNOT00000101652.2

Conserved Domains (2) summary

cd04449
Location:1176 → 1257

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:107 → 381

DUF3608; Protein of unknown function (DUF3608)
XM_039091986.2 → XP_038947914.1 GATOR1 complex protein DEPDC5 isoform X1

UniProtKB/TrEMBL

A0A8I6A1L7

Conserved Domains (2) summary

cd04449
Location:1177 → 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:101 → 381

IML1; Vacuolar membrane-associated protein Iml1
XM_017599213.3 → XP_017454702.1 GATOR1 complex protein DEPDC5 isoform X10

UniProtKB/TrEMBL

A0A8I6A1L7

Conserved Domains (2) summary

cd04449
Location:1145 → 1226

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:107 → 381

DUF3608; Protein of unknown function (DUF3608)
XM_017599211.3 → XP_017454700.1 GATOR1 complex protein DEPDC5 isoform X5

UniProtKB/TrEMBL

A0A8I6A1L7

Conserved Domains (2) summary

cd04449
Location:1167 → 1248

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:107 → 381

DUF3608; Protein of unknown function (DUF3608)
XM_017599212.3 → XP_017454701.1 GATOR1 complex protein DEPDC5 isoform X7

UniProtKB/TrEMBL

A0A8I6A1L7, D4A362

Related

ENSRNOP00000061924.2, ENSRNOT00000067694.4

Conserved Domains (2) summary

cd04449
Location:1154 → 1235

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:107 → 381

DUF3608; Protein of unknown function (DUF3608)
XM_008770289.4 → XP_008768511.1 GATOR1 complex protein DEPDC5 isoform X2

See identical proteins and their annotated locations for XP_008768511.1

UniProtKB/TrEMBL

A0A8I5YBC5, A0A8I6A1L7

Related

ENSRNOP00000076509.1, ENSRNOT00000113787.2

Conserved Domains (2) summary

cd04449
Location:1176 → 1257

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:107 → 381

DUF3608; Protein of unknown function (DUF3608)
XM_063273175.1 → XP_063129245.1 GATOR1 complex protein DEPDC5 isoform X8

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273181.1 → XP_063129251.1 GATOR1 complex protein DEPDC5 isoform X14

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273167.1 → XP_063129237.1 GATOR1 complex protein DEPDC5 isoform X2

UniProtKB/TrEMBL

A0A8I5YBC5, A0A8I6A1L7
XM_063273176.1 → XP_063129246.1 GATOR1 complex protein DEPDC5 isoform X9

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273184.1 → XP_063129254.1 GATOR1 complex protein DEPDC5 isoform X17

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273170.1 → XP_063129240.1 GATOR1 complex protein DEPDC5 isoform X4

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273183.1 → XP_063129253.1 GATOR1 complex protein DEPDC5 isoform X16

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273172.1 → XP_063129242.1 GATOR1 complex protein DEPDC5 isoform X6

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273169.1 → XP_063129239.1 GATOR1 complex protein DEPDC5 isoform X3

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273180.1 → XP_063129250.1 GATOR1 complex protein DEPDC5 isoform X12

UniProtKB/TrEMBL

A0A8I6A1L7
XM_039091987.2 → XP_038947915.1 GATOR1 complex protein DEPDC5 isoform X1

UniProtKB/TrEMBL

A0A8I6A1L7

Conserved Domains (2) summary

cd04449
Location:1177 → 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:101 → 381

IML1; Vacuolar membrane-associated protein Iml1
XM_063273178.1 → XP_063129248.1 GATOR1 complex protein DEPDC5 isoform X11

UniProtKB/TrEMBL

A0A8I6A1L7
XM_063273177.1 → XP_063129247.1 GATOR1 complex protein DEPDC5 isoform X10

UniProtKB/TrEMBL

A0A8I6A1L7
XM_039091991.2 → XP_038947919.1 GATOR1 complex protein DEPDC5 isoform X1

UniProtKB/TrEMBL

A0A8I6A1L7

Conserved Domains (2) summary

cd04449
Location:1177 → 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:101 → 381

IML1; Vacuolar membrane-associated protein Iml1
XM_063273166.1 → XP_063129236.1 GATOR1 complex protein DEPDC5 isoform X2

UniProtKB/TrEMBL

A0A8I5YBC5, A0A8I6A1L7
XM_039091989.2 → XP_038947917.1 GATOR1 complex protein DEPDC5 isoform X1

UniProtKB/TrEMBL

A0A8I6A1L7

Conserved Domains (2) summary

cd04449
Location:1177 → 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:101 → 381

IML1; Vacuolar membrane-associated protein Iml1
XM_039091998.2 → XP_038947926.1 GATOR1 complex protein DEPDC5 isoform X18

UniProtKB/TrEMBL

A0A8I5Y2I2

Conserved Domains (2) summary

cd04449
Location:1008 → 1089

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:1 → 212

IML1; Vacuolar membrane-associated protein Iml1