Human Gene PDCD2L (ENST00000246535.4_5) from GENCODE V47lift37
  Description: programmed cell death 2 like, transcript variant 1 (from RefSeq NM_032346.2)
Gencode Transcript: ENST00000246535.4_5
Gencode Gene: ENSG00000126249.8_9
Transcript (Including UTRs)
   Position: hg19 chr19:34,895,304-34,917,073 Size: 21,770 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr19:34,895,336-34,917,025 Size: 21,690 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:34,895,304-34,917,073)mRNA (may differ from genome)Protein (358 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDD2L_HUMAN
DESCRIPTION: RecName: Full=Programmed cell death protein 2-like;
FUNCTION: Over-expression suppresses AP1, CREB, NFAT, and NF-kB transcriptional activation, and delays cell cycle progression at S phase.
TISSUE SPECIFICITY: Higher expression in lung, colon, mammary gland, cervix, stomach and small intestine.

-  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

+  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: 15.97 RPKM in Testis
Total median expression: 238.86 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 -7.7032-0.241 Picture PostScript Text
3' UTR -2.6048-0.054 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
IPR007320 - PDCD2_C

Pfam Domains:
PF04194 - Programmed cell death protein 2, C-terminal putative domain

ModBase Predicted Comparative 3D Structure on Q9BRP1
FrontTopSide
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 Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007049 cell cycle

Cellular Component:
GO:0005737 cytoplasm
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  BC006146 - Homo sapiens programmed cell death 2-like, mRNA (cDNA clone MGC:13096 IMAGE:3944994), complete cds.
CU675273 - Synthetic construct Homo sapiens gateway clone IMAGE:100023327 5' read PDCD2L mRNA.
HQ448210 - Synthetic construct Homo sapiens clone IMAGE:100071609; CCSB005083_01 programmed cell death 2-like (PDCD2L) gene, encodes complete protein.
KJ894975 - Synthetic construct Homo sapiens clone ccsbBroadEn_04369 PDCD2L gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000246535.1, ENST00000246535.2, ENST00000246535.3, NM_032346, PDD2L_HUMAN, Q9BRP1, uc317etr.1, uc317etr.2
UCSC ID: ENST00000246535.4_5
RefSeq Accession: NM_032346.2
Protein: Q9BRP1 (aka PDD2L_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.