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PDCD2 programmed cell death 2 [ Homo sapiens (human) ]

Gene ID: 5134, updated on 18-Aug-2020

Summary

Official Symbol
PDCD2provided by HGNC
Official Full Name
programmed cell death 2provided by HGNC
Primary source
HGNC:HGNC:8762
See related
Ensembl:ENSG00000071994 MIM:600866
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
RP8; ZMYND7
Summary
This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]
Expression
Ubiquitous expression in lymph node (RPKM 7.8), thyroid (RPKM 7.5) and 25 other tissues See more
Orthologs

Genomic context

See PDCD2 in Genome Data Viewer
Location:
6q27
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (170575295..170584655, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (170884660..170893780, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene proteasome 20S subunit beta 1 Neighboring gene TATA-box binding protein repeat instability region Neighboring gene TATA-box binding protein Neighboring gene putative hydro-lyase KRH_21160 Neighboring gene uncharacterized LOC107986678

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC12347

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
programmed cell death protein 2
Names
zinc finger MYND domain-containing protein 7
zinc finger protein Rp-8

NCBI Reference Sequences (RefSeq)

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_001199461.2NP_001186390.1  programmed cell death protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' coding region and UTR, compared to variant 1. The resulting protein (isoform 3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AJ420535, AL031259, AW966881
    Consensus CDS
    CCDS75557.1
    UniProtKB/TrEMBL
    A0A087WYJ3
    Related
    ENSP00000481860.1, ENST00000614056.4
    Conserved Domains (1) summary
    pfam01753
    Location:135172
    zf-MYND; MYND finger
  2. NM_001199462.2NP_001186391.1  programmed cell death protein 2 isoform 4

    See identical proteins and their annotated locations for NP_001186391.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting protein (isoform 4) is shorter, compared to isoform 1.
    Source sequence(s)
    AK055180, AL031259, AY948416, DC351104
    Consensus CDS
    CCDS56461.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000375940.2, ENST00000392090.6
    Conserved Domains (2) summary
    pfam01753
    Location:102139
    zf-MYND; MYND finger
    pfam04194
    Location:193306
    PDCD2_C; Programmed cell death protein 2, C-terminal putative domain
  3. NM_001199463.2NP_001186392.1  programmed cell death protein 2 isoform 5

    See identical proteins and their annotated locations for NP_001186392.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region and differs in the 3' coding region and UTR, compared to variant 1. The resulting protein (isoform 5) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AJ420535, AK297343, AL031259
    Consensus CDS
    CCDS56460.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000397272.2, ENST00000443345.2
    Conserved Domains (1) summary
    pfam01753
    Location:102139
    zf-MYND; MYND finger
  4. NM_001199464.2NP_001186393.1  programmed cell death protein 2 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate in-frame splice site in the 5' coding region and differs in the 3' coding region and UTR, compared to variant 1. The resulting protein (isoform 6) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AJ420535, AK297343, AL031259, BX385363
    Consensus CDS
    CCDS56462.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000440572.1, ENST00000537445.5
    Conserved Domains (1) summary
    pfam01753
    Location:102139
    zf-MYND; MYND finger
  5. NM_001363655.2NP_001350584.1  programmed cell death protein 2 isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (7) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL031259
    Consensus CDS
    CCDS87471.1
    Related
    ENSP00000439914.1, ENST00000542896.5
    Conserved Domains (2) summary
    pfam01753
    Location:135172
    zf-MYND; MYND finger
    pfam04194
    Location:226292
    PDCD2_C; Programmed cell death protein 2, C-terminal putative domain
  6. NM_002598.4NP_002589.2  programmed cell death protein 2 isoform 1

    See identical proteins and their annotated locations for NP_002589.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK055180, AL031259, BC008378
    Consensus CDS
    CCDS5316.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000439467.1, ENST00000541970.6
    Conserved Domains (2) summary
    pfam01753
    Location:135172
    zf-MYND; MYND finger
    pfam04194
    Location:226339
    PDCD2_C; Programmed cell death protein 2, C-terminal putative domain
  7. NM_144781.3NP_659005.1  programmed cell death protein 2 isoform 2

    See identical proteins and their annotated locations for NP_659005.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and UTR, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AJ420535, AL031259
    Consensus CDS
    CCDS47521.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000402524.2, ENST00000453163.6
    Conserved Domains (1) summary
    pfam01753
    Location:135172
    zf-MYND; MYND finger

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    170575295..170584655 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001743458.1 RNA Sequence

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