Pdcd6 programmed cell death 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdcd6provided by RGD
Official Full Name: programmed cell death 6provided by RGD
Primary source: RGD:1311239
See related: Ensembl:ENSRNOG00000014485 AllianceGenome:RGD:1311239
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
Also known as: ALG-2
Summary: Predicted to enable several functions, including metal ion binding activity; protein homodimerization activity; and ubiquitin ligase-substrate adaptor activity. Predicted to be involved in several processes, including mesenchymal cell differentiation; negative regulation of signal transduction; and positive regulation of cellular protein metabolic process. Predicted to act upstream of or within activation of cysteine-type endopeptidase activity involved in apoptotic process and apoptotic process. Predicted to be located in several cellular components, including cytosol; endoplasmic reticulum exit site; and nucleoplasm. Predicted to be part of COPII vesicle coat and Cul3-RING ubiquitin ligase complex. Orthologous to human PDCD6 (programmed cell death 6). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 438.6), Kidney (RPKM 271.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1p11

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (30795105..30810771)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (28966518..28982188)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (31576183..31591852)

Chromosome 1 - NC_086019.1 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?

ALG-2 and peflin regulate COPII targeting and secretion in response to calcium signaling.
Title: ALG-2 and peflin regulate COPII targeting and secretion in response to calcium signaling.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables calcium-dependent protein binding	IEA Inferred from Electronic Annotation more info
enables calcium-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables magnesium ion binding	ISO Inferred from Sequence Orthology more info
enables magnesium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein dimerization activity	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein-macromolecule adaptor activity	ISO Inferred from Sequence Orthology more info
enables protein-membrane adaptor activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-like ligase-substrate adaptor activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-like ligase-substrate adaptor activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in COPII vesicle coating	ISO Inferred from Sequence Orthology more info
involved_in COPII vesicle coating	ISS Inferred from Sequence or Structural Similarity more info
involved_in angiogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in cellular response to heat	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular protein transport	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of TOR signaling	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of vascular endothelial growth factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in neural crest cell development	ISO Inferred from Sequence Orthology more info
involved_in neural crest cell development	ISS Inferred from Sequence or Structural Similarity more info
involved_in neural crest formation	ISO Inferred from Sequence Orthology more info
involved_in neural crest formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein monoubiquitination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein monoubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to calcium ion	ISO Inferred from Sequence Orthology more info
involved_in vascular endothelial growth factor receptor-2 signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of COPII vesicle coat	ISO Inferred from Sequence Orthology more info
part_of COPII vesicle coat	ISS Inferred from Sequence or Structural Similarity more info
part_of Cul3-RING ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info
part_of Cul3-RING ubiquitin ligase complex	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 vesicle	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum exit site	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum exit site	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology 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 perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: programmed cell death protein 6

Names: apoptosis-linked gene 2 protein 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_001107452.1 → NP_001100922.1 programmed cell death protein 6

See identical proteins and their annotated locations for NP_001100922.1

Status: PROVISIONAL

Source sequence(s)

CH474002

UniProtKB/Swiss-Prot

B5DEP1, G3V7W1

UniProtKB/TrEMBL

A0A8I6A7Q9

Related

ENSRNOP00000019735.4, ENSRNOT00000019735.6

Conserved Domains (1) summary

cd16183
Location:27 → 191

EFh_PEF_ALG-2; EF-hand, calcium binding motif, found in apoptosis-linked gene 2 protein (ALG-2) and similar proteins

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_086019.1 Reference GRCr8

Range

30795105..30810771

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006227784.5 → XP_006227846.1 programmed cell death protein 6 isoform X1

See identical proteins and their annotated locations for XP_006227846.1

UniProtKB/TrEMBL

A0A8I6A7Q9

Conserved Domains (3) summary

cd00051
Location:98 → 152

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

pfam13499
Location:96 → 153

EF-hand_7; EF-hand domain pair

cl08302
Location:31 → 120

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...