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

    Gene ID: 10016, updated on 9-Dec-2024

    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; AllianceGenome:HGNC:8765
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PDCD6 in Genome Data Viewer
    Location:
    5p15.33
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (271646..314974)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (261673..305205)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (271761..315089)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:218445-219253 Neighboring gene succinate dehydrogenase complex flavoprotein subunit A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:270110-270802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15861 Neighboring gene PDCD6-AHRR readthrough (NMD candidate) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:278988-279488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:279489-279989 Neighboring gene PDCD6 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr5:295122-295292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:296594-297122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:297123-297651 Neighboring gene PPP4R2 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:301361-301866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:301867-302372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:306908-307792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:322065-322632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15867 Neighboring gene aryl hydrocarbon receptor repressor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:372826-373456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22281 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:399561-400760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15871 Neighboring gene mitochondrial translational initiation factor 3 pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85003 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85008 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85009 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85011 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85012 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85017 Neighboring gene AHRR intron CAGE-defined high expression enhancer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_85030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:415251-415804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15872 Neighboring gene EXOC3 antisense RNA 1

    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 Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables calcium-dependent protein binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables calcium-dependent protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables magnesium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein dimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein-macromolecule adaptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables protein-membrane adaptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables ubiquitin-like ligase-substrate adaptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in COPII vesicle coating IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in apoptotic signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cellular response to heat IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of TOR signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of vascular endothelial growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neural crest cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neural crest formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of angiogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cysteine-type endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of endothelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of protein monoubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to calcium ion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to calcium ion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in vascular endothelial growth factor receptor-2 signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of COPII vesicle coat IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of Cul3-RING ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum exit site IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum exit site IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001267556.2NP_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/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_001267557.2NP_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/TrEMBL
      A0A087WZ38
      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_001267558.2NP_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)
      BC012384, DB495449
      Consensus CDS
      CCDS75223.1
      UniProtKB/TrEMBL
      A0A024QZ42
      Related
      ENSP00000485024.1, ENST00000614778.4
      Conserved Domains (2) summary
      cd15897
      Location:2454
      EFh_PEF; EF-hand motif [structural motif]
      cl25352
      Location:1121
      EFh_PEF; The penta-EF hand (PEF) family
    4. NM_001267559.2NP_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/TrEMBL
      A0A6Q8PH81
      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
      B2RD16, E7ESR3, O75340, Q2YDC2, Q5TZS0
      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_073609.2 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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      271646..314974
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      261673..305205
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)