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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

    Gene LinkOut

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

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