Human Gene PDCD6 (ENST00000264933.9_5) from GENCODE V47lift37
  Description: programmed cell death 6, transcript variant 1 (from RefSeq NM_013232.4)
Gencode Transcript: ENST00000264933.9_5
Gencode Gene: ENSG00000249915.9_9
Transcript (Including UTRs)
   Position: hg19 chr5:271,761-315,089 Size: 43,329 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr5:271,836-314,630 Size: 42,795 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:271,761-315,089)mRNA (may differ from genome)Protein (191 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDCD6_HUMAN
DESCRIPTION: RecName: Full=Programmed cell death protein 6; AltName: Full=Apoptosis-linked gene 2 protein; AltName: Full=Probable calcium-binding protein ALG-2;
FUNCTION: Calcium-binding protein required for T-cell receptor-, Fas-, and glucocorticoid-induced cell death. May mediate Ca(2+)- regulated signals along the death pathway (By similarity). Calcium-dependent adapter necessary for the association between PDCD6IP and TSG101. Interaction with DAPK1 can accelerate apoptotic cell death by increasing caspase-3 activity.
SUBUNIT: Self-associates (By similarity). Homodimer. Interacts with PEF1. Interacts with RBM22. Interacts with PLSCR4, ANXA7 and TSG101. Interacts with SEC31A, PDCD6IP, and the N-termini of ANXA11 and PLSCR3 in a calcium-dependent manner. Interacts with DAPK1.
INTERACTION: P53355:DAPK1; NbExp=3; IntAct=EBI-352915, EBI-358616; Q8WUM4:PDCD6IP; NbExp=5; IntAct=EBI-352915, EBI-310624; Q9NRY6:PLSCR3; NbExp=9; IntAct=EBI-352915, EBI-750734; O94979:SEC31A; NbExp=6; IntAct=EBI-352915, EBI-1767898;
SUBCELLULAR LOCATION: Nucleus membrane; Peripheral membrane protein. Endoplasmic reticulum membrane; Peripheral membrane protein. Nucleus. Note=Interaction with RBM22 induces relocalization from the cytoplasm to the nucleus. Translocated from the cytoplasm to the nucleus after heat shock cell treatment. Accumulates in cytoplasmic vesicle-like organelles after heat shock treatment, which may represent stress granules.
SIMILARITY: Contains 5 EF-hand domains.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PDCD6ID43402ch5p15.html";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PDCD6
Diseases sorted by gene-association score: ocular melanoma (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 27.24 RPKM in Adrenal Gland
Total median expression: 963.83 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -29.1075-0.388 Picture PostScript Text
3' UTR -109.90459-0.239 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd

Pfam Domains:
PF00036 - EF hand
PF13202 - EF hand
PF13405 - EF-hand domain
PF13499 - EF-hand domain pair
PF13833 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand
117839 - WWE domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2ZN8 - X-ray MuPIT 2ZN9 - X-ray MuPIT 2ZND - X-ray MuPIT 2ZNE - X-ray MuPIT 2ZRS - X-ray MuPIT 2ZRT - X-ray MuPIT 3AAJ - X-ray MuPIT 3AAK - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O75340
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000287 magnesium ion binding
GO:0004198 calcium-dependent cysteine-type endopeptidase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0043495 protein anchor
GO:0046872 metal ion binding
GO:0046983 protein dimerization activity
GO:0048306 calcium-dependent protein binding
GO:0060090 binding, bridging

Biological Process:
GO:0001525 angiogenesis
GO:0001938 positive regulation of endothelial cell proliferation
GO:0006508 proteolysis
GO:0006886 intracellular protein transport
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0006915 apoptotic process
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0010595 positive regulation of endothelial cell migration
GO:0014029 neural crest formation
GO:0014032 neural crest cell development
GO:0030948 negative regulation of vascular endothelial growth factor receptor signaling pathway
GO:0032007 negative regulation of TOR signaling
GO:0034605 cellular response to heat
GO:0036324 vascular endothelial growth factor receptor-2 signaling pathway
GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0045766 positive regulation of angiogenesis
GO:0048208 COPII vesicle coating
GO:0051592 response to calcium ion
GO:0051898 negative regulation of protein kinase B signaling
GO:0097190 apoptotic signaling pathway
GO:1902527 positive regulation of protein monoubiquitination

Cellular Component:
GO:0000139 Golgi membrane
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0012507 ER to Golgi transport vesicle membrane
GO:0016020 membrane
GO:0030127 COPII vesicle coat
GO:0031410 cytoplasmic vesicle
GO:0070062 extracellular exosome
GO:0070971 endoplasmic reticulum exit site
GO:0031463 Cul3-RING ubiquitin ligase complex


-  Descriptions from all associated GenBank mRNAs
  EU293605 - Homo sapiens aryl hydrocarbon receptor repressor mRNA, complete cds.
AB033060 - Homo sapiens KIAA1234 mRNA for KIAA1234 protein.
BC151852 - Homo sapiens aryl-hydrocarbon receptor repressor, mRNA (cDNA clone MGC:167813 IMAGE:8860492), complete cds.
BC152406 - Homo sapiens aryl-hydrocarbon receptor repressor, mRNA (cDNA clone MGC:176630 IMAGE:8862509), complete cds.
AK315370 - Homo sapiens cDNA, FLJ96416, Homo sapiens programmed cell death 6 (PDCD6), mRNA.
AK223366 - Homo sapiens mRNA for programmed cell death 6 variant, clone: FCC102B09.
AK310347 - Homo sapiens cDNA, FLJ17389.
AK295082 - Homo sapiens cDNA FLJ60532 complete cds, moderately similar to Programmed cell death protein 6.
BC028242 - Homo sapiens programmed cell death 6, mRNA (cDNA clone IMAGE:5243036), with apparent retained intron.
BC012384 - Homo sapiens programmed cell death 6, mRNA (cDNA clone MGC:9123 IMAGE:3859672), complete cds.
BC050597 - Homo sapiens programmed cell death 6, mRNA (cDNA clone IMAGE:6143644), complete cds.
BC110291 - Homo sapiens programmed cell death 6, mRNA (cDNA clone MGC:111017 IMAGE:5187550), complete cds.
AK001917 - Homo sapiens cDNA FLJ11055 fis, clone PLACE1004674, highly similar to PROBABLE CALCIUM-BINDING PROTEIN ALG-2.
AK308872 - Homo sapiens cDNA, FLJ98913.
AF035606 - Homo sapiens calcium binding protein (ALG-2) mRNA, complete cds.
BC106706 - Homo sapiens programmed cell death 6, mRNA (cDNA clone MGC:119050 IMAGE:40003290), complete cds.
U58773 - Human calcium binding protein mRNA, complete cds.
KJ898139 - Synthetic construct Homo sapiens clone ccsbBroadEn_07533 PDCD6 gene, encodes complete protein.
DQ891163 - Synthetic construct clone IMAGE:100003793; FLH170848.01X; RZPDo839C04100D programmed cell death 6 (PDCD6) gene, encodes complete protein.
DQ894344 - Synthetic construct Homo sapiens clone IMAGE:100008804; FLH170844.01L; RZPDo839C0499D programmed cell death 6 (PDCD6) gene, encodes complete protein.
KJ906019 - Synthetic construct Homo sapiens clone ccsbBroadEn_15689 PDCD6 gene, encodes complete protein.
BT020072 - Homo sapiens programmed cell death 6 mRNA, complete cds.
JD056113 - Sequence 37137 from Patent EP1572962.
LP896603 - Sequence 1467 from Patent EP3253886.
AK128087 - Homo sapiens cDNA FLJ46208 fis, clone TESTI4010979.
AK124302 - Homo sapiens cDNA FLJ42309 fis, clone TRACH2006049.
AK124667 - Homo sapiens cDNA FLJ42676 fis, clone BRAMY2033116.
JD049321 - Sequence 30345 from Patent EP1572962.
JD202856 - Sequence 183880 from Patent EP1572962.
JD064944 - Sequence 45968 from Patent EP1572962.
JD229777 - Sequence 210801 from Patent EP1572962.
JD113879 - Sequence 94903 from Patent EP1572962.
JD228332 - Sequence 209356 from Patent EP1572962.
JD250583 - Sequence 231607 from Patent EP1572962.
JD349505 - Sequence 330529 from Patent EP1572962.
JD378493 - Sequence 359517 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ALG2 , B2RD16, E7ESR3, ENST00000264933.1, ENST00000264933.2, ENST00000264933.3, ENST00000264933.4, ENST00000264933.5, ENST00000264933.6, ENST00000264933.7, ENST00000264933.8, NM_013232, O75340, PDCD6_HUMAN, Q2YDC2, Q5TZS0, uc317hwu.1, uc317hwu.2
UCSC ID: ENST00000264933.9_5
RefSeq Accession: NM_013232.4
Protein: O75340 (aka PDCD6_HUMAN or PCD6_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.