Format

Send to:

Choose Destination

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

Gene ID: 10016, updated on 8-May-2016
Official Symbol
PDCD6provided by HGNC
Official Full Name
programmed cell death 6provided by HGNC
Primary source
HGNC:HGNC:8765
See related
Ensembl:ENSG00000249915 HPRD:03035; MIM:601057; Vega:OTTHUMG00000090283
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]
Orthologs
Location:
5p15.33
Exon count:
7
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 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 uncharacterized LOC105374605 Neighboring gene uncharacterized LOC105374604 Neighboring gene aryl-hydrocarbon receptor repressor Neighboring gene mitochondrial translational initiation factor 3 pseudogene Neighboring gene EXOC3 antisense RNA 1

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
binding, bridging IMP
Inferred from Mutant Phenotype
more info
PubMed 
calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium-dependent cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
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 
protein anchor 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 IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
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 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 IDA
Inferred from Direct Assay
more info
PubMed 
nuclear membrane IEA
Inferred from Electronic Annotation
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
programmed cell death protein 6
Names
apoptosis-linked gene 2 protein
probable calcium-binding protein ALG-2

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, OTTHUMP00000221465, ENST00000507528, OTTHUMT00000367684
    Conserved Domains (3) summary
    cd00051
    Location:98152
    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:100153
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:31120
    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 ...
  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, ENST00000618970
    Conserved Domains (3) summary
    cd00051
    Location:3186
    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:3387
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:68119
    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 ...
  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, ENST00000614778
    Conserved Domains (2) summary
    cd00051
    Location:2884
    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:3085
    EF-hand_7; EF-hand domain pair
  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, OTTHUMP00000221473, ENST00000505221, OTTHUMT00000367694
    Conserved Domains (1) summary
    pfam13405
    Location:2855
    EF-hand_6; EF-hand domain
  5. NM_013232.3NP_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, OTTHUMP00000115318, ENST00000264933, OTTHUMT00000206609
    Conserved Domains (3) summary
    cd00051
    Location:98154
    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:100155
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:31120
    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 ...

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, OTTHUMT00000367646

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p2 Primary Assembly

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

Alternate CHM1_1.1

Genomic

  1. NC_018916.2 Alternate CHM1_1.1

    Range
    267028..314783
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)