Human Gene PDCD7 (ENST00000204549.9_10) from GENCODE V47lift37
  Description: programmed cell death 7 (from RefSeq NM_005707.2)
Gencode Transcript: ENST00000204549.9_10
Gencode Gene: ENSG00000090470.15_12
Transcript (Including UTRs)
   Position: hg19 chr15:65,409,717-65,426,146 Size: 16,430 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr15:65,411,055-65,426,119 Size: 15,065 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:65,409,717-65,426,146)mRNA (may differ from genome)Protein (485 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDCD7_HUMAN
DESCRIPTION: RecName: Full=Programmed cell death protein 7; AltName: Full=ES18; Short=hES18;
FUNCTION: Promotes apoptosis when overexpressed (By similarity).
SUBUNIT: Interacts with RBM40. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome.
SUBCELLULAR LOCATION: Nucleus (Potential).

-  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


-  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: 20.67 RPKM in Testis
Total median expression: 477.19 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -1.4027-0.052 Picture PostScript Text
3' UTR -396.601338-0.296 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
  Pfam Domains:
PF16021 - Programmed cell death protein 7

ModBase Predicted Comparative 3D Structure on Q8N8D1
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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 orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006915 apoptotic process
GO:0008380 RNA splicing
GO:0051384 response to glucocorticoid

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005689 U12-type spliceosomal complex


-  Descriptions from all associated GenBank mRNAs
  BC016992 - Homo sapiens programmed cell death 7, mRNA (cDNA clone IMAGE:4400881), partial cds.
BC092464 - Homo sapiens programmed cell death 7, mRNA (cDNA clone IMAGE:30520477), partial cds.
JD461247 - Sequence 442271 from Patent EP1572962.
JD406665 - Sequence 387689 from Patent EP1572962.
JD523337 - Sequence 504361 from Patent EP1572962.
JD351669 - Sequence 332693 from Patent EP1572962.
JD448267 - Sequence 429291 from Patent EP1572962.
JD332292 - Sequence 313316 from Patent EP1572962.
JD175872 - Sequence 156896 from Patent EP1572962.
JD138277 - Sequence 119301 from Patent EP1572962.
JD063369 - Sequence 44393 from Patent EP1572962.
JD063368 - Sequence 44392 from Patent EP1572962.
JD511938 - Sequence 492962 from Patent EP1572962.
JD076500 - Sequence 57524 from Patent EP1572962.
JD293951 - Sequence 274975 from Patent EP1572962.
AK096970 - Homo sapiens cDNA FLJ39651 fis, clone SMINT2005161, highly similar to Mus musculus ES18 mRNA.
JD466696 - Sequence 447720 from Patent EP1572962.
JD280740 - Sequence 261764 from Patent EP1572962.
BC131704 - Homo sapiens programmed cell death 7, mRNA (cDNA clone IMAGE:40121463), partial cds.
JD130360 - Sequence 111384 from Patent EP1572962.
JD410247 - Sequence 391271 from Patent EP1572962.
JD058557 - Sequence 39581 from Patent EP1572962.
AK225816 - Homo sapiens mRNA for programmed cell death 7 variant, clone: FCC129C02.
AF083930 - Homo sapiens ES18 mRNA, partial cds.
JD283218 - Sequence 264242 from Patent EP1572962.
BT007395 - Homo sapiens programmed cell death 7 mRNA, complete cds.
AK303203 - Homo sapiens cDNA FLJ54213 complete cds, moderately similar to Programmed cell death protein 7.
JD479870 - Sequence 460894 from Patent EP1572962.
JD460828 - Sequence 441852 from Patent EP1572962.
JD336018 - Sequence 317042 from Patent EP1572962.
JD462470 - Sequence 443494 from Patent EP1572962.
JD352793 - Sequence 333817 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8N8D1 (Reactome details) participates in the following event(s):

R-HSA-75080 Formation of AT-AC A complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000204549.1, ENST00000204549.2, ENST00000204549.3, ENST00000204549.4, ENST00000204549.5, ENST00000204549.6, ENST00000204549.7, ENST00000204549.8, NM_005707, PDCD7_HUMAN, Q8N8D1, Q96AK8, Q9Y6D7, uc317cjd.1, uc317cjd.2
UCSC ID: ENST00000204549.9_10
RefSeq Accession: NM_005707.2
Protein: Q8N8D1 (aka PDCD7_HUMAN or PCD7_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.