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    PDCD2L programmed cell death 2 like [ Homo sapiens (human) ]

    Gene ID: 84306, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PDCD2Lprovided by HGNC
    Official Full Name
    programmed cell death 2 likeprovided by HGNC
    Primary source
    HGNC:HGNC:28194
    See related
    Ensembl:ENSG00000126249 MIM:615661; AllianceGenome:HGNC:28194
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to be involved in apoptotic process. Located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 7.2), fat (RPKM 2.8) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See PDCD2L in Genome Data Viewer
    Location:
    19q13.11
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (34404399..34426168)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (36948963..36970736)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (34895304..34917073)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene granule associated Rac and RHOG effector 1 Neighboring gene ribosomal protein L29 pseudogene 33 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34801395-34801894 Neighboring gene Sharpr-MPRA regulatory region 14193 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34833051-34833551 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:34850825-34851431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34857175-34857915 Neighboring gene glucose-6-phosphate isomerase Neighboring gene uncharacterized LOC124904695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10502 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10504 Neighboring gene RNA, 7SL, cytoplasmic 154, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr19:34928566-34928723 Neighboring gene MPRA-validated peak3443 silencer Neighboring gene ubiquitin like modifier activating enzyme 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:34971736-34972390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:34972391-34973046 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:34973047-34973701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34988289-34989176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34989177-34990063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34994324-34995145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34996156-34996656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:34996657-34997157 Neighboring gene WT1 interacting protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. The novel MGC13096 protein is correlated with proliferation. Chen Q, et al. Cell Biochem Funct, 2008 Mar-Apr. PMID 17393540
    2. Cloning of cDNAs with PDCD2(C) domain and their expressions during apoptosis of HEK293T cells. Chen Q, et al. Mol Cell Biochem, 2005 Dec. PMID 16311922
    3. Overexpression of the PDCD2-like gene results in inhibited TNF-alpha production in activated Daudi cells. Chen Q, et al. Hum Immunol, 2008 Apr-May. PMID 18486760
    4. USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle. Song N, et al. Mol Carcinog, 2023 Oct. PMID 37314216
    5. Human PDCD2L Is an Export Substrate of CRM1 That Associates with 40S Ribosomal Subunit Precursors. Landry-Voyer AM, et al. Mol Cell Biol, 2016 Dec 15. PMID 27697862, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Findings uncover the existence of an extra-ribosomal complex consisting of PDCD2L, RPS2, and PRMT3 and support a role for PDCD2L in the late maturation of 40S ribosomal subunits.
      Title: Human PDCD2L Is an Export Substrate of CRM1 That Associates with 40S Ribosomal Subunit Precursors.
    2. MGC13096 over-expression restrained proliferation of HEK293T cells. DNA/flow cytometry analysis showed that the over-expression of MGC13096 severely delays cell cycle progression at S phase.
      Title: The novel MGC13096 protein is correlated with proliferation.
    3. Overexpression of PDCD2-like gene attenutates TNF-alpha release in Daudi cells
      Title: Overexpression of the PDCD2-like gene results in inhibited TNF-alpha production in activated Daudi cells.
    4. To study the role of PDCD2_C domain in apoptosis, the cDNAs of two isoforms of PDCD2 and MGC13096 were cloned. PDCD2 (NM_002598) was over expressed when endothelial cells treated with leukotriene D4 or natural killer cells were activated by IL-2.
      Title: Cloning of cDNAs with PDCD2(C) domain and their expressions during apoptosis of HEK293T cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of programmed cell death 2-like (PDCD2L) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC13096

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    programmed cell death protein 2-like

    NCBI Reference Sequences (RefSeq)

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    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_001353433.2 → NP_001340362.1  programmed cell death protein 2-like isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC008747, AC092073
      Conserved Domains (1) summary
      pfam04194
      Location:234 → 348
      PDCD2_C; Programmed cell death protein 2, C-terminal putative domain

    2. NM_032346.2 → NP_115722.1  programmed cell death protein 2-like isoform 1

      See identical proteins and their annotated locations for NP_115722.1

      Status: VALIDATED

      Source sequence(s)
      BC006146
      Consensus CDS
      CCDS12438.1
      UniProtKB/Swiss-Prot
      Q9BRP1
      Related
      ENSP00000246535.1, ENST00000246535.4
      Conserved Domains (1) summary
      pfam04194
      Location:236 → 350
      PDCD2_C; Programmed cell death protein 2, C-terminal putative domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      34404399..34426168
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791809.1 Reference GRCh38.p14 PATCHES

      Range
      69408..91188
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      36948963..36970736
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRP1.1 GenPept UniProtKB/Swiss-Prot:Q9BRP1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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