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PDCD6 programmed cell death 6 [ Homo sapiens (human) ]

Gene ID: 10016, updated on 15-Apr-2019

Summary

Official Symbol
PDCD6provided by HGNC
Official Full Name
programmed cell death 6provided by HGNC
Primary source
HGNC:HGNC:8765
See related
Ensembl:ENSG00000249915 MIM:601057
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ALG2; ALG-2; PEF1B
Summary
This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. Calcium binding is important for homodimerization and for conformational changes required for binding to other protein partners. This gene product participates in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. In mice deficient for this gene product, however, apoptosis was not blocked suggesting this gene product is functionally redundant. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is also located on the short arm of chromosome 5. [provided by RefSeq, May 2012]
Annotation information
Note: ALG2 (Gene ID: 85365) and PDCD6 (Gene ID: 10016) share the ALG2 symbol/alias in common. ALG2 is a widely used alternative name for programmed cell death 6 (PDCD6), whose synonym is apoptosis-linked gene-2. This can be confused with the official symbol for ALG2, alpha-1,3/1,6-mannosyltransferase (ALG2). [31 May 2018]
Expression
Ubiquitous expression in colon (RPKM 23.5), adrenal (RPKM 21.4) and 25 other tissues See more
Orthologs

Genomic context

See PDCD6 in Genome Data Viewer
Location:
5p15.33
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (271621..314974)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (271736..315089)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene succinate dehydrogenase complex flavoprotein subunit A Neighboring gene protein phosphatase 4 regulatory subunit 2 pseudogene Neighboring gene heart tissue-associated transcript 5 Neighboring gene aryl-hydrocarbon receptor repressor Neighboring gene mitochondrial translational initiation factor 3 pseudogene Neighboring gene AHRR intron CAGE-defined high expression enhancer

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC9123, FLJ14113, FLJ42309, FLJ46208, MGC111017, MGC119050

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium-dependent protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
magnesium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
molecular adaptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein dimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein membrane anchor IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
COPII vesicle coating IMP
Inferred from Mutant Phenotype
more info
PubMed 
ER to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
activation of cysteine-type endopeptidase activity involved in apoptotic process IEA
Inferred from Electronic Annotation
more info
 
angiogenesis IEA
Inferred from Electronic Annotation
more info
 
apoptotic signaling pathway TAS
Traceable Author Statement
more info
PubMed 
cellular response to heat IDA
Inferred from Direct Assay
more info
PubMed 
intracellular protein transport IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of TOR signaling IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of protein kinase B signaling IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of vascular endothelial growth factor receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
neural crest cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
neural crest formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of angiogenesis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of endothelial cell migration IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of endothelial cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein monoubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to calcium ion ISS
Inferred from Sequence or Structural Similarity
more info
 
vascular endothelial growth factor receptor-2 signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
COPII vesicle coat IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with Cul3-RING ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum exit site IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum exit site IMP
Inferred from Mutant Phenotype
more info
PubMed 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
endosome IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
programmed cell death protein 6
Names
apoptosis-linked gene 2 protein
apoptosis-linked gene 2 protein homolog
probable calcium-binding protein ALG-2

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001267556.1NP_001254485.1  programmed cell death protein 6 isoform 2

    See identical proteins and their annotated locations for NP_001254485.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK223366, BC012384, BC110291
    Consensus CDS
    CCDS58940.1
    UniProtKB/Swiss-Prot
    O75340
    UniProtKB/TrEMBL
    Q53FC3
    Related
    ENSP00000423815.1, ENST00000507528.5
    Conserved Domains (1) summary
    cd16183
    Location:27189
    EFh_PEF_ALG-2; EF-hand, calcium binding motif, found in apoptosis-linked gene 2 protein (ALG-2) and similar proteins
  2. NM_001267557.1NP_001254486.1  programmed cell death protein 6 isoform 3

    See identical proteins and their annotated locations for NP_001254486.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two consecutive exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AK223366, BC012384, BG390506
    Consensus CDS
    CCDS75222.1
    UniProtKB/Swiss-Prot
    O75340
    UniProtKB/TrEMBL
    A0A087WZ38, Q53FC3
    Related
    ENSP00000482332.1, ENST00000618970.4
    Conserved Domains (2) summary
    cd15897
    Location:2754
    EFh_PEF; EF-hand motif [structural motif]
    cl25352
    Location:27123
    EFh_PEF; The penta-EF hand (PEF) family
  3. NM_001267558.1NP_001254487.1  programmed cell death protein 6 isoform 4

    See identical proteins and their annotated locations for NP_001254487.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK223366, BC012384, DB495449
    Consensus CDS
    CCDS75223.1
    UniProtKB/Swiss-Prot
    O75340
    UniProtKB/TrEMBL
    A0A024QZ42, Q53FC3
    Related
    ENSP00000485024.1, ENST00000614778.4
    Conserved Domains (2) summary
    cd15897
    Location:2453
    EFh_PEF; EF-hand motif [structural motif]
    cl25352
    Location:1121
    EFh_PEF; The penta-EF hand (PEF) family
  4. NM_001267559.1NP_001254488.1  programmed cell death protein 6 isoform 5

    See identical proteins and their annotated locations for NP_001254488.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two consecutive exons in the coding region, which results in a frameshift, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK223366, BC012384, CR983268
    Consensus CDS
    CCDS58941.1
    UniProtKB/Swiss-Prot
    O75340
    UniProtKB/TrEMBL
    Q53FC3
    Related
    ENSP00000422085.1, ENST00000505221.5
    Conserved Domains (2) summary
    cd15897
    Location:2756
    EFh_PEF; EF-hand motif [structural motif]
    cl25352
    Location:2769
    EFh_PEF; The penta-EF hand (PEF) family
  5. NM_013232.4NP_037364.1  programmed cell death protein 6 isoform 1

    See identical proteins and their annotated locations for NP_037364.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK223366, BC012384
    Consensus CDS
    CCDS3854.1
    UniProtKB/Swiss-Prot
    O75340
    UniProtKB/TrEMBL
    Q53FC3
    Related
    ENSP00000264933.4, ENST00000264933.9
    Conserved Domains (1) summary
    cd16183
    Location:27191
    EFh_PEF_ALG-2; EF-hand, calcium binding motif, found in apoptosis-linked gene 2 protein (ALG-2) and similar proteins

RNA

  1. NR_073609.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. This variant (6) is represented as non-coding because the predicted ORF does not meet quality criteria for a protein coding locus with longer protein data.
    Source sequence(s)
    AK223366, AW300963, BC050597
    Related
    ENST00000509581.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    271621..314974
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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