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

Summary

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

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_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[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].
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).
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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)

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
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
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
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
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
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
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
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
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
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
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
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
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
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

NC_000013.11 Reference GRCh38.p14 Primary Assembly

Range

113165002..113208669 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047430477.1 → XP_047286433.1 PCI domain-containing protein 2 isoform X1
XM_047430478.1 → XP_047286434.1 PCI domain-containing protein 2 isoform X2
XM_047430479.1 → XP_047286435.1 PCI domain-containing protein 2 isoform X3
XM_047430480.1 → XP_047286436.1 PCI domain-containing protein 2 isoform X4
XM_005268325.5 → XP_005268382.1 PCI domain-containing protein 2 isoform X5

Conserved Domains (1) summary

cl02111
Location:80 → 228

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

RNA

XR_001749631.2 RNA Sequence
XR_007063692.1 RNA Sequence
XR_007063691.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060937.1 Alternate T2T-CHM13v2.0

Range

112427103..112461015 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054374745.1 → XP_054230720.1 PCI domain-containing protein 2 isoform X7
XM_054374744.1 → XP_054230719.1 PCI domain-containing protein 2 isoform X1
XM_054374746.1 → XP_054230721.1 PCI domain-containing protein 2 isoform X2
XM_054374747.1 → XP_054230722.1 PCI domain-containing protein 2 isoform X8
XM_054374748.1 → XP_054230723.1 PCI domain-containing protein 2 isoform X5
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

NM_001258212.1: Suppressed sequence

Description

NM_001258212.1: This RefSeq was removed because currently there is insufficient support for the transcript.