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PCID2 PCI domain containing 2 [ Homo sapiens (human) ]

Gene ID: 55795, updated on 2-Nov-2024

Summary

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Official Symbol
PCID2provided by HGNC
Official Full Name
PCI domain containing 2provided by HGNC
Primary source
HGNC:HGNC:25653
See related
Ensembl:ENSG00000126226 MIM:613713; AllianceGenome:HGNC:25653
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
F10
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 6.6), ovary (RPKM 4.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See PCID2 in Genome Data Viewer
Location:
13q34
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (113165002..113208669, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (112427103..112461015, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (113831850..113862983, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene WAS/WASL-interacting protein family member 2-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5538 Neighboring gene uncharacterized LOC124903216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113812445-113813022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113813599-113814176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113825981-113826504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113827099-113827599 Neighboring gene protein Z, vitamin K dependent plasma glycoprotein Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:113841395-113842594 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113862038-113862688 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113862689-113863338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5541 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113874723-113875286 Neighboring gene cullin 4A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113876707-113877556 Neighboring gene microRNA 8075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113928297-113928796 Neighboring gene Sharpr-MPRA regulatory region 2925 Neighboring gene lactate dehydrogenase B pseudogene 1

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. [PCID2 is highly expressed in gastric cancer and affects the prognosis by regulating cancer cell cycle and proliferation]. Zhang N, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2024 Feb 20. PMID 38501418, Free PMC Article
  2. Conformational stability of PCID2 upon DSS1 binding with molecular dynamics simulation. Liu Q, et al. J Mol Model, 2015 May. PMID 25914122
  3. Human TREX2 components PCID2 and centrin 2, but not ENY2, have distinct functions in protein export and co-localize to the centrosome. Cunningham CN, et al. Exp Cell Res, 2014 Jan 15. PMID 24291146
  4. Increased chemosensitivity via BRCA2-independent DNA damage in DSS1- and PCID2-depleted breast carcinomas. Gondo N, et al. Lab Invest, 2021 Aug. PMID 34031538
  5. Functional and structural characterization of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export. Jani D, et al. Nucleic Acids Res, 2012 May. PMID 22307388, Free PMC Article

See all (98) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [PCID2 is highly expressed in gastric cancer and affects the prognosis by regulating cancer cell cycle and proliferation].
    Title: [PCID2 is highly expressed in gastric cancer and affects the prognosis by regulating cancer cell cycle and proliferation].
  2. A novel amplification gene PCI domain containing 2 (PCID2) promotes colorectal cancer through directly degrading a tumor suppressor promyelocytic leukemia (PML).
    Title: A novel amplification gene PCI domain containing 2 (PCID2) promotes colorectal cancer through directly degrading a tumor suppressor promyelocytic leukemia (PML).
  3. Increased chemosensitivity via BRCA2-independent DNA damage in DSS1- and PCID2-depleted breast carcinomas.
    Title: Increased chemosensitivity via BRCA2-independent DNA damage in DSS1- and PCID2-depleted breast carcinomas.
  4. Distinct effects on mRNA export factor GANP underlie neurological disease phenotypes and alter gene expression depending on intron content.
    Title: Distinct effects on mRNA export factor GANP underlie neurological disease phenotypes and alter gene expression depending on intron content.
  5. Data show that PCI domain-containing protein 2 (Pcid2) controls lymphoid lineage commitment through the regulation of Snf2-related CREBBP activator protein (SRCAP) remodelling activity.
    Title: Suppression of SRCAP chromatin remodelling complex and restriction of lymphoid lineage commitment by Pcid2.
  6. Pcid2 is present in the CBP/p300-EID1 complex to control the switch balance of mouse and human embryonic stem cells through modulation of EID1 degradation.
    Title: Pcid2 inactivates developmental genes in human and mouse embryonic stem cells to sustain their pluripotency by modulation of EID1 stability.
  7. First discovery of specific novel functions for PCID2 other than mRNA export and components of the TREX-2 complex serve alternative shared roles in the regulation of nuclear transport and cell cycle progression.
    Title: Human TREX2 components PCID2 and centrin 2, but not ENY2, have distinct functions in protein export and co-localize to the centrosome.
  8. validated occurrence of an unusual TG 3' splice site in intron 2
    Title: Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns.
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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11305, FLJ39706, FLJ99362, MGC16774, DKFZp686C20226

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in heterochromatin organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cysteine-type endopeptidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of lymphoid progenitor cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of transcription initiation by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in poly(A)+ mRNA export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of B cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of mitotic cell cycle spindle assembly checkpoint IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of mRNA stability IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in spleen development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in transcription elongation by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
part_of nuclear pore nuclear basket IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription export complex 2 IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription export complex 2 IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
PCI domain-containing protein 2
Names
CSN12-like protein

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_001127202.4 → NP_001120674.1  PCI domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001120674.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AA779868, AI272719, AK001185, AL137002
    Consensus CDS
    CCDS9532.2
    UniProtKB/Swiss-Prot
    A6NK09, Q3ZCX1, Q5JVF3, Q5TC57, Q5TC58, Q9H7K1, Q9HBZ7, Q9NUK6, Q9NVY1, Q9NW44, Q9NWH3
    UniProtKB/TrEMBL
    A8K097
    Related
    ENSP00000337405.4, ENST00000337344.9
    Conserved Domains (1) summary
    cl02111
    Location:80 → 393
    PCI; PCI domain

  2. NM_001127203.4 → NP_001120675.1  PCI domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001120675.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a segment in the 3' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AA779868, AI272719, AL137002, BC016614, HY174088
    Consensus CDS
    CCDS9532.2
    UniProtKB/Swiss-Prot
    A6NK09, Q3ZCX1, Q5JVF3, Q5TC57, Q5TC58, Q9H7K1, Q9HBZ7, Q9NUK6, Q9NVY1, Q9NW44, Q9NWH3
    UniProtKB/TrEMBL
    A8K097
    Related
    ENSP00000364626.1, ENST00000375477.5
    Conserved Domains (1) summary
    cl02111
    Location:80 → 393
    PCI; PCI domain

  3. NM_001258213.3 → NP_001245142.1  PCI domain-containing protein 2 isoform 3

    See identical proteins and their annotated locations for NP_001245142.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (3) has a shorter, distinct N-terminus compared to isoform 1. Variants 5 and 6 encode the same isoform (3).
    Source sequence(s)
    AA779868, AI272719, AL136221, AL137002, BC031246, BM932149, DA058550
    Consensus CDS
    CCDS58301.1
    UniProtKB/TrEMBL
    A8K097
    Related
    ENSP00000364606.2, ENST00000375457.2
    Conserved Domains (1) summary
    cl02111
    Location:78 → 391
    PCI; PCI domain

  4. NM_001320655.2 → NP_001307584.1  PCI domain-containing protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' and 3' UTRs, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (3) has a shorter, distinct N-terminus compared to isoform 1. Variants 5 and 6 encode the same isoform (3).
    Source sequence(s)
    AA779868, AI272719, AK098706, AL136221, AL137002, BC031246, BM932149, DA058550
    Consensus CDS
    CCDS58301.1
    UniProtKB/TrEMBL
    A8K097
    Related
    ENSP00000364608.1, ENST00000375459.5
    Conserved Domains (1) summary
    cl02111
    Location:78 → 391
    PCI; PCI domain

  5. NM_001320656.2 → NP_001307585.1  PCI domain-containing protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses two alternate splice sites, but maintains the reading frame, and lacks a segment in the 3' UTR, compared to variant 1. The encoded isoform (2) is longer than isoform 1.
    Source sequence(s)
    AA779868, AI272719, AK002167, AL137002, BC016614, BC031246
    Consensus CDS
    CCDS58302.1
    UniProtKB/TrEMBL
    A8K097
    Related
    ENSP00000246505.5, ENST00000246505.9
    Conserved Domains (1) summary
    cl02111
    Location:190 → 447
    PCI; PCI domain

  6. NM_001320657.2 → NP_001307586.1  PCI domain-containing protein 2 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (4) has a longer, distinct C-terminus than isoform 1.
    Source sequence(s)
    AA779868, AI272719, AK001185, AK002167, AL137002, AL546858, BI763234
    UniProtKB/TrEMBL
    A8K097
    Conserved Domains (1) summary
    cl02111
    Location:80 → 368
    PCI; PCI domain

  7. NM_001320659.2 → NP_001307588.1  PCI domain-containing protein 2 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) uses an alternate splice site and lacks a segment in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (5) has a longer, distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL136221, AL137002
    UniProtKB/TrEMBL
    A8K097
    Conserved Domains (1) summary
    cl02111
    Location:80 → 368
    PCI; PCI domain

  8. NM_001320660.2 → NP_001307589.1  PCI domain-containing protein 2 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses an alternate splice site in the 3' coding region, compared to variant 1. It initiates translation at an alternate start codon. The encoded isoform (6) has distinct N- and C-termini and is longer than isoform 1.
    Source sequence(s)
    AA779868, AI272719, AK001185, AL136221, AL137002, BC031246, BI763234, BM932149, DA058550
    UniProtKB/TrEMBL
    A8K097
    Conserved Domains (1) summary
    cl02111
    Location:78 → 366
    PCI; PCI domain

  9. NM_001353091.2 → NP_001340020.1  PCI domain-containing protein 2 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL136221, AL137002
    UniProtKB/TrEMBL
    A8K097
    Conserved Domains (1) summary
    cl02111
    Location:38 → 351
    PCI; PCI domain

  10. NM_001353092.2 → NP_001340021.1  PCI domain-containing protein 2 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL136221, AL137002
    Consensus CDS
    CCDS58301.1
    UniProtKB/TrEMBL
    A8K097
    Conserved Domains (1) summary
    cl02111
    Location:78 → 391
    PCI; PCI domain

  11. NM_001353093.2 → NP_001340022.1  PCI domain-containing protein 2 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL136221, AL137002
    UniProtKB/TrEMBL
    A8K097
    Conserved Domains (1) summary
    cl02111
    Location:38 → 351
    PCI; PCI domain

  12. NM_001353094.2 → NP_001340023.1  PCI domain-containing protein 2 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL136221, AL137002
    UniProtKB/TrEMBL
    A8K097
    Conserved Domains (1) summary
    cl02111
    Location:38 → 351
    PCI; PCI domain

  13. NM_001353095.2 → NP_001340024.1  PCI domain-containing protein 2 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AL136221, AL137002
    Conserved Domains (1) summary
    cl02111
    Location:2 → 226
    PCI; PCI domain

  14. NM_018386.5 → NP_060856.2  PCI domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_060856.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks a segment in the 3' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AA779868, AI272719, AK023313, AL137002, HY174088
    Consensus CDS
    CCDS9532.2
    UniProtKB/Swiss-Prot
    A6NK09, Q3ZCX1, Q5JVF3, Q5TC57, Q5TC58, Q9H7K1, Q9HBZ7, Q9NUK6, Q9NVY1, Q9NW44, Q9NWH3
    UniProtKB/TrEMBL
    A8K097
    Related
    ENSP00000364628.2, ENST00000375479.6
    Conserved Domains (1) summary
    cl02111
    Location:80 → 393
    PCI; PCI 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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    113165002..113208669 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047430477.1 → XP_047286433.1  PCI domain-containing protein 2 isoform X1

  2. XM_047430478.1 → XP_047286434.1  PCI domain-containing protein 2 isoform X2

  3. XM_047430479.1 → XP_047286435.1  PCI domain-containing protein 2 isoform X3

  4. XM_047430480.1 → XP_047286436.1  PCI domain-containing protein 2 isoform X4

  5. XM_005268325.5 → XP_005268382.1  PCI domain-containing protein 2 isoform X5

    Conserved Domains (1) summary
    cl02111
    Location:80 → 228
    PCI; PCI domain

  6. XM_047430481.1 → XP_047286437.1  PCI domain-containing protein 2 isoform X6

RNA

  1. XR_001749631.2 RNA Sequence

  2. XR_007063692.1 RNA Sequence

  3. XR_007063691.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    112427103..112461015 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374745.1 → XP_054230720.1  PCI domain-containing protein 2 isoform X7

  2. XM_054374744.1 → XP_054230719.1  PCI domain-containing protein 2 isoform X1

  3. XM_054374746.1 → XP_054230721.1  PCI domain-containing protein 2 isoform X2

  4. XM_054374747.1 → XP_054230722.1  PCI domain-containing protein 2 isoform X8

  5. XM_054374748.1 → XP_054230723.1  PCI domain-containing protein 2 isoform X5

  6. XM_054374749.1 → XP_054230724.1  PCI domain-containing protein 2 isoform X6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001258212.1: Suppressed sequence

    Description
    NM_001258212.1: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5JVF3.2 GenPept UniProtKB/Swiss-Prot:Q5JVF3

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