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Aliases for PCID2 Gene

Aliases for PCID2 Gene

  • PCI Domain Containing 2 2 3 5
  • CSN12-Like Protein 3 4
  • PCI Domain-Containing Protein 2 3
  • 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. Diseases associated with PCID2 include Noonan Syndrome 1.

UniProtKB/Swiss-Prot 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). Component of the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, SEM1, and either centrin CETN2 or CETN3 (PubMed:22307388). The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. 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.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCID2 Gene

Genomics for PCID2 Gene

Regulatory Elements for PCID2 Gene

Enhancers for PCID2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13G113175 1.3 Ensembl ENCODE dbSUPER 21.5 +31.0 30994 5.7 PKNOX1 JUN SIN3A ZIC2 ZFHX2 POLR2A FOS MAFK NFE2L2 EGR2 PROZ PCID2 CUL4A F10-AS1 KARSP2 F10 F7 GRTP1 GRTP1-AS1 ENSG00000269356
GH13G113182 1.6 Ensembl ENCODE dbSUPER 11.9 +23.2 23226 6.5 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 SLC30A9 PROZ PCID2 CUL4A KARSP2 F10-AS1 F10 GRTP1 F7 LAMP1 ENSG00000269356
GH13G113272 1.5 FANTOM5 Ensembl ENCODE 10.8 -64.7 -64738 3.3 NFIB RAD21 RARA CHAMP1 RFX5 YY1 FOS ZNF263 SMARCC1 ZNF362 LAMP1 PROZ CUL4A GRTP1 PCID2 DCUN1D2-AS DCUN1D2 LDHBP1 LOC105370377
GH13G113393 1.5 Ensembl ENCODE dbSUPER 10.5 -184.5 -184467 1.5 HDGF WRNIP1 SIN3A DMAP1 GLI4 ZNF2 ZNF48 GLIS2 ZNF143 ZNF207 GRTP1 GRTP1-AS1 PCID2 CUL4A DCUN1D2-AS DCUN1D2 RASA3 PIR34234
GH13G113206 1.4 ENCODE dbSUPER 9.5 +0.6 625 5.0 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 SP3 TUBGCP3 PROZ GAS6-AS1 LAMP1 PCID2 CUL4A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCID2 on UCSC Golden Path with GeneCards custom track

Promoters for PCID2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000066105 166 3001 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 SP3

Genomic Location for PCID2 Gene

Chromosome:
13
Start:
113,177,539 bp from pter
End:
113,209,466 bp from pter
Size:
31,928 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:
    • Belongs to the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, SEM1, and either centrin CETN2 or CETN3 (PubMed:22307388). Interacts with BRCA2.
    SequenceCaution:
    • Sequence=AAG09695.1; Type=Frameshift; Positions=48; 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

Protein Domains for PCID2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PCID2 Gene

GenScript: Design optimal peptide antigens:

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). Component of the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, SEM1, and either centrin CETN2 or CETN3 (PubMed:22307388). The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. 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.

Gene Ontology (GO) - Molecular Function for PCID2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003690 double-stranded DNA binding IBA --
GO:0003723 RNA binding IBA --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with PCID2: view
genes like me logo Genes that share phenotypes with PCID2: view

Animal Model Products

miRNA for PCID2 Gene

miRTarBase miRNAs that target PCID2

Inhibitory RNA Products

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

Localization for PCID2 Gene

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 4
cytosol 3

Gene Ontology (GO) - Cellular Components for PCID2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005643 colocalizes_with nuclear pore IBA --
GO:0035327 colocalizes_with transcriptionally active chromatin IBA --
GO:0070390 transcription export complex 2 IBA --
genes like me logo Genes that share ontologies with PCID2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PCID2 Gene

Pathways & Interactions for PCID2 Gene

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 --
GO:0006368 transcription elongation from RNA polymerase II promoter IBA --
GO:0016973 poly(A)+ mRNA export from nucleus IBA --
GO:0043066 negative regulation of apoptotic process IMP 20870947
GO:0043488 regulation of mRNA stability 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

Unigene Clusters for PCID2 Gene

PCI domain containing 2:
Representative Sequences:

Inhibitory RNA Products

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
ECgene alternative splicing isoforms for
PCID2

Expression for PCID2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for PCID2 Gene



Protein tissue co-expression partners for PCID2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCID2 Gene:

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(4.2)
  • Eye(4.1)
  • Liver(2)
genes like me logo Genes that share expression patterns with PCID2: view

Primer Products

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 34 35
  • 99.66 (n)
oppossum
(Monodelphis domestica)
Mammalia PCID2 35
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PCID2 35
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pcid2 34
  • 87.39 (n)
mouse
(Mus musculus)
Mammalia Pcid2 34 16 35
  • 87.22 (n)
dog
(Canis familiaris)
Mammalia PCID2 34 35
  • 86.88 (n)
cow
(Bos Taurus)
Mammalia PCID2 34 35
  • 84.63 (n)
chicken
(Gallus gallus)
Aves PCID2 35
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PCID2 35
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pcid2 34
  • 75.94 (n)
Str.1726 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.5526 34
zebrafish
(Danio rerio)
Actinopterygii pcid2 34 35
  • 76.21 (n)
wufa11f03 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10068 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008498 34
  • 57.8 (n)
fruit fly
(Drosophila melanogaster)
Insecta PCID2 34 35
  • 54.33 (n)
worm
(Caenorhabditis elegans)
Secernentea C27F2.10 34 35
  • 51.95 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 35
  • 21 (a)
OneToOne
THP1 37
thale cress
(Arabidopsis thaliana)
eudicotyledons EER5 34
  • 49.96 (n)
rice
(Oryza sativa)
Liliopsida Os09g0386400 34
  • 48.05 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.973 35
  • 58 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU08388 34
  • 47.77 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC1B3.08 34
  • 44.48 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11106 34
Species where no ortholog for PCID2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for PCID2 Gene

No data available for Paralogs for PCID2 Gene

Variants for PCID2 Gene

Sequence variations from dbSNP and Humsavar for PCID2 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs1000010267 -- 113,168,752(+) GAGAC(C/T)GGGTC intron-variant, nc-transcript-variant
rs1000055134 -- 113,173,047(+) TCTCC(C/T)ATACG intron-variant
rs1000108535 -- 113,172,870(+) CAGCA(A/C)CTCAC intron-variant, downstream-variant-500B
rs1000120386 -- 113,178,083(+) AAAAG(C/T)GCCTC intron-variant, utr-variant-3-prime
rs1000141513 -- 113,207,608(+) CATAC(A/G)TCCAT intron-variant, upstream-variant-2KB

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)

Relevant External Links for PCID2 Gene

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

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

Disorders for PCID2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCID2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
noonan syndrome 1
  • ns1
- elite association - COSMIC cancer census association via MalaCards
Search PCID2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PCID2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCID2
genes like me logo Genes that share disorders with PCID2: view

No data available for 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) 3 4 64
  2. Functional and structural characterization of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export. (PMID: 22307388) Jani D. … Wickramasinghe V.O. (Nucleic Acids Res. 2012) 3 4 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A. … Ross M.T. (Nature 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for PCID2 Gene

Sources for PCID2 Gene

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