This gene encodes a component of the TREX-2 complex (transcription and export complex 2), which regulates mRNA export from the nucleus. This protein regulates expression of Mad2 mitotic arrest deficient-like 1, a cell division checkpoint protein. This protein also interacts with and stabilizes Brca2 (breast cancer 2) protein. Alternative splicing results in multiple transcript ... See more...

Aliases for PCID2 Gene

Aliases for PCID2 Gene

  • PCI Domain Containing 2 2 3 5
  • PCI Domain-Containing Protein 2 3 4
  • CSN12-Like Protein 3 4
  • FLJ11305 2
  • PCID2 5
  • F10 3

External Ids for PCID2 Gene

Previous GeneCards Identifiers for PCID2 Gene

  • GC13M112881
  • GC13M113831
  • GC13M094270

Summaries for PCID2 Gene

Entrez Gene Summary for PCID2 Gene

  • This gene encodes a component of the TREX-2 complex (transcription and export complex 2), which regulates mRNA export from the nucleus. This protein regulates expression of Mad2 mitotic arrest deficient-like 1, a cell division checkpoint protein. This protein also interacts with and stabilizes Brca2 (breast cancer 2) protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

GeneCards Summary for PCID2 Gene

PCID2 (PCI Domain Containing 2) is a Protein Coding gene.

UniProtKB/Swiss-Prot Summary for PCID2 Gene

  • Required for B-cell survival through the regulation of the expression of cell-cycle checkpoint MAD2L1 protein during B cell differentiation (By similarity). As a component of the TREX-2 complex, involved in the export of mRNAs to the cytoplasm through the nuclear pores (PubMed:22307388) (Probable). Binds and stabilizes BRCA2 and is thus involved in the control of R-loop-associated DNA damage and transcription-associated genomic instability. R-loop accumulation does not increase in PCID2-depleted cells (PubMed:24896180).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCID2 Gene

Genomics for PCID2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCID2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCID2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCID2

Top Transcription factor binding sites by QIAGEN in the PCID2 gene promoter:
  • Arnt
  • c-Myb
  • c-Myc
  • C/EBPalpha
  • CREB
  • CUTL1
  • deltaCREB
  • En-1
  • HEN1
  • Max1

Genomic Locations for PCID2 Gene

Genomic Locations for PCID2 Gene
chr13:113,165,002-113,209,467
(GRCh38/hg38)
Size:
44,466 bases
Orientation:
Minus strand
chr13:113,831,891-113,863,029
(GRCh37/hg19)
Size:
31,139 bases
Orientation:
Minus strand

Genomic View for PCID2 Gene

Genes around PCID2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCID2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCID2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCID2 Gene

Proteins for PCID2 Gene

  • Protein details for PCID2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5JVF3-PCID2_HUMAN
    Recommended name:
    PCI domain-containing protein 2
    Protein Accession:
    Q5JVF3
    Secondary Accessions:
    • A6NK09
    • Q3ZCX1
    • Q5TC57
    • Q5TC58
    • Q9H7K1
    • Q9HBZ7
    • Q9NUK6
    • Q9NVY1
    • Q9NW44
    • Q9NWH3

    Protein attributes for PCID2 Gene

    Size:
    399 amino acids
    Molecular mass:
    46030 Da
    Quaternary structure:
    • Component of the nuclear pore complex (NPC)-associated TREX-2 complex (transcription and export complex 2), composed of at least GANP, 2 copies of ENY2, PCID2, SEM1/DSS1, and either centrin CETN2 or centrin CETN3. The TREX-2 complex also associates with ALYREF/ALY and with the nucleoporin NUP153 (PubMed:22307388, PubMed:23591820). Interacts with BRCA2 (PubMed:24896180).
    SequenceCaution:
    • Sequence=AAG09695.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAB15768.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCID2 Gene

    Alternative splice isoforms for PCID2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCID2 Gene

Post-translational modifications for PCID2 Gene

  • Ubiquitination at Lys128, Lys201, and Lys213
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PCID2 Gene

Domains & Families for PCID2 Gene

Gene Families for PCID2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PCID2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PCID2 Gene

GenScript: Design optimal peptide antigens:
  • CSN12-like protein (PCID2_HUMAN)
  • PCID2 protein (Q96H21_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5JVF3

UniProtKB/Swiss-Prot:

PCID2_HUMAN :
  • Belongs to the CSN12 family.
Family:
  • Belongs to the CSN12 family.
genes like me logo Genes that share domains with PCID2: view

Function for PCID2 Gene

Molecular function for PCID2 Gene

UniProtKB/Swiss-Prot Function:
Required for B-cell survival through the regulation of the expression of cell-cycle checkpoint MAD2L1 protein during B cell differentiation (By similarity). As a component of the TREX-2 complex, involved in the export of mRNAs to the cytoplasm through the nuclear pores (PubMed:22307388) (Probable). Binds and stabilizes BRCA2 and is thus involved in the control of R-loop-associated DNA damage and transcription-associated genomic instability. R-loop accumulation does not increase in PCID2-depleted cells (PubMed:24896180).

Phenotypes From GWAS Catalog for PCID2 Gene

Gene Ontology (GO) - Molecular Function for PCID2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003690 double-stranded DNA binding IBA 21873635
GO:0003723 RNA binding IBA 21873635
GO:0005515 protein binding IPI 23591820
genes like me logo Genes that share ontologies with PCID2: view
genes like me logo Genes that share phenotypes with PCID2: view

Animal Models for PCID2 Gene

MGI Knock Outs for PCID2:

Animal Model Products

CRISPR Products

miRNA for PCID2 Gene

miRTarBase miRNAs that target PCID2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCID2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PCID2 Gene

Localization for PCID2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCID2 Gene

Cytoplasm. Nucleus, nuclear pore complex.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PCID2 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCID2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 23591820
GO:0005643 nuclear pore IEA --
GO:0005737 cytoplasm IEA,IDA 23591820
GO:0044615 nuclear pore nuclear basket IDA 23591820
GO:0070390 transcription export complex 2 IBA,IDA 23591820
genes like me logo Genes that share ontologies with PCID2: view

Pathways & Interactions for PCID2 Gene

PathCards logo

SuperPathways for PCID2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCID2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000973 posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery IBA 21873635
GO:0006368 transcription elongation from RNA polymerase II promoter IBA 21873635
GO:0015031 protein transport IEA --
GO:0016973 poly(A)+ mRNA export from nucleus IBA 21873635
GO:0043066 negative regulation of apoptotic process IEA,IMP 20870947
genes like me logo Genes that share ontologies with PCID2: view

No data available for Pathways by source and SIGNOR curated interactions for PCID2 Gene

Drugs & Compounds for PCID2 Gene

No Compound Related Data Available

Transcripts for PCID2 Gene

mRNA/cDNA for PCID2 Gene

15 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCID2

Alternative Splicing Database (ASD) splice patterns (SP) for PCID2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15a · 15b ^
SP1: - - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - - - - - -
SP4: - - - - - - -
SP5: - - - - - - - - -
SP6: - - - - - - -
SP7: - - - - - - -
SP8: -
SP9: - - - - -
SP10: -
SP11: - - - -
SP12: -
SP13:
SP14:

ExUns: 16a · 16b ^ 17a · 17b · 17c · 17d
SP1: - -
SP2: - -
SP3: -
SP4: -
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for PCID2 Gene

GeneLoc Exon Structure for
PCID2

Expression for PCID2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCID2 Gene

Protein differential expression in normal tissues from HIPED for PCID2 Gene

This gene is overexpressed in Bone (10.4), Stomach (7.1), and Peripheral blood mononuclear cells (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCID2 Gene



Protein tissue co-expression partners for PCID2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCID2

SOURCE GeneReport for Unigene cluster for PCID2 Gene:

Hs.508769

Evidence on tissue expression from TISSUES for PCID2 Gene

  • Nervous system(4.7)
  • Spleen(4.3)
  • Eye(4.1)
  • Liver(2.3)
genes like me logo Genes that share expression patterns with PCID2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCID2 Gene

Orthologs for PCID2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PCID2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PCID2 30 31
  • 99.66 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PCID2 31
  • 97 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PCID2 31
  • 93 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pcid2 30
  • 87.39 (n)
Mouse
(Mus musculus)
Mammalia Pcid2 30 17 31
  • 87.22 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PCID2 30 31
  • 86.88 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PCID2 30 31
  • 84.63 (n)
OneToOne
Chicken
(Gallus gallus)
Aves PCID2 31
  • 82 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PCID2 31
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pcid2 30
  • 75.94 (n)
Str.1726 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.5526 30
Zebrafish
(Danio rerio)
Actinopterygii pcid2 30 31
  • 76.21 (n)
OneToOne
wufa11f03 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10068 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008498 30
  • 57.8 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta PCID2 30 31
  • 54.33 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea C27F2.10 30 31
  • 51.95 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 31
  • 21 (a)
OneToOne
THP1 33 33
Thale Cress
(Arabidopsis thaliana)
eudicotyledons EER5 30
  • 49.96 (n)
Rice
(Oryza sativa)
Liliopsida Os09g0386400 30
  • 48.05 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.973 31
  • 58 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU08388 30
  • 47.77 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC1B3.08 30
  • 44.48 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.11106 30
Species where no ortholog for PCID2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PCID2 Gene

ENSEMBL:
Gene Tree for PCID2 (if available)
TreeFam:
Gene Tree for PCID2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCID2: view image

Paralogs for PCID2 Gene

No data available for Paralogs for PCID2 Gene

Variants for PCID2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCID2 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
722302 Benign: not provided 113,171,773(-) C/T MISSENSE_VARIANT
732181 Benign: not provided 113,178,291(-) C/T INTRON_VARIANT
734834 Benign: not provided 113,171,850(-) G/A SYNONYMOUS_VARIANT
734849 Benign: not provided 113,190,934(-) C/A SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
736963 Likely Benign: not provided 113,170,509(-) AG/A FRAMESHIFT_VARIANT

Additional dbSNP identifiers (rs#s) for PCID2 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCID2 Gene

Variant ID Type Subtype PubMed ID
dgv3434n54 CNV gain 21841781
dgv3435n54 CNV loss 21841781
dgv3436n54 CNV gain+loss 21841781
dgv3437n54 CNV loss 21841781
esv25141 CNV loss 19812545
nsv1046663 CNV gain 25217958
nsv1048814 CNV gain 25217958
nsv1051556 CNV gain 25217958
nsv518044 CNV gain 19592680
nsv563302 CNV loss 21841781
nsv563305 CNV gain 21841781
nsv563314 CNV gain 21841781

Variation tolerance for PCID2 Gene

Residual Variation Intolerance Score: 34.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.77; 16.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCID2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCID2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCID2 Gene

Disorders for PCID2 Gene

No disorders were found for PCID2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCID2 Gene

Publications for PCID2 Gene

  1. BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. (PMID: 24896180) Bhatia V … Aguilera A (Nature 2014) 2 3 4
  2. The human TREX-2 complex is stably associated with the nuclear pore basket. (PMID: 23591820) Umlauf D … Tora L (Journal of cell science 2013) 3 4
  3. Functional and structural characterization of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export. (PMID: 22307388) Jani D … Wickramasinghe VO (Nucleic acids research 2012) 3 4
  4. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A … Ross MT (Nature 2004) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for PCID2 Gene

  • Signalway Proteins for PCID2

Sources for PCID2 Gene