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Protein

PCI domain-containing protein 2

Gene

PCID2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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, DSS1, 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.By similarity2 Publications

GO - Molecular functioni

GO - Biological processi

  • negative regulation of apoptotic process Source: UniProtKB
  • negative regulation of cysteine-type endopeptidase activity Source: UniProtKB
  • nuclear retention of pre-mRNA at the site of transcription Source: GO_Central
  • poly(A)+ mRNA export from nucleus Source: GO_Central
  • positive regulation of B cell differentiation Source: Ensembl
  • positive regulation of mitotic cell cycle spindle assembly checkpoint Source: UniProtKB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery Source: GO_Central
  • regulation of mRNA stability Source: UniProtKB
  • spleen development Source: UniProtKB
  • transcription elongation from RNA polymerase II promoter Source: GO_Central
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
PCI domain-containing protein 2
Alternative name(s):
CSN12-like protein
Gene namesi
Name:PCID2
ORF Names:HT004
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 13

Organism-specific databases

HGNCiHGNC:25653. PCID2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

DisGeNETi55795.
OpenTargetsiENSG00000126226.
PharmGKBiPA144596397.

Polymorphism and mutation databases

BioMutaiPCID2.
DMDMi85681034.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001210292 – 399PCI domain-containing protein 2Add BLAST398

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanine1 Publication1
Modified residuei45PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ5JVF3.
MaxQBiQ5JVF3.
PaxDbiQ5JVF3.
PeptideAtlasiQ5JVF3.
PRIDEiQ5JVF3.

PTM databases

iPTMnetiQ5JVF3.
PhosphoSitePlusiQ5JVF3.

Expressioni

Gene expression databases

BgeeiENSG00000126226.
CleanExiHS_PCID2.
ExpressionAtlasiQ5JVF3. baseline and differential.
GenevisibleiQ5JVF3. HS.

Organism-specific databases

HPAiHPA069107.
HPA073074.

Interactioni

Subunit structurei

Belongs to the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, DSS1, and either centrin CETN2 or CETN3 (PubMed:22307388). Interacts with BRCA2.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
IKZF3Q9UKT93EBI-1051701,EBI-747204

Protein-protein interaction databases

BioGridi120908. 28 interactors.
DIPiDIP-50497N.
IntActiQ5JVF3. 12 interactors.
STRINGi9606.ENSP00000337405.

Structurei

Secondary structure

1399
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi206 – 222Combined sources17
Helixi226 – 239Combined sources14
Helixi245 – 261Combined sources17
Helixi268 – 273Combined sources6
Helixi277 – 279Combined sources3
Helixi280 – 288Combined sources9
Helixi291 – 300Combined sources10
Helixi302 – 307Combined sources6
Helixi311 – 315Combined sources5
Helixi317 – 333Combined sources17
Beta strandi336 – 339Combined sources4
Helixi340 – 349Combined sources10
Helixi357 – 369Combined sources13
Beta strandi375 – 378Combined sources4
Turni379 – 382Combined sources4
Beta strandi383 – 386Combined sources4
Helixi395 – 397Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3T5XX-ray2.12A201-399[»]
ProteinModelPortaliQ5JVF3.
SMRiQ5JVF3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini277 – 388PCIAdd BLAST112

Sequence similaritiesi

Belongs to the CSN12 family.Curated
Contains 1 PCI domain.Curated

Phylogenomic databases

eggNOGiKOG2688. Eukaryota.
COG5600. LUCA.
GeneTreeiENSGT00390000001101.
HOVERGENiHBG055800.
InParanoidiQ5JVF3.
OMAiCRGFTPG.
PhylomeDBiQ5JVF3.
TreeFamiTF106136.

Family and domain databases

InterProiIPR000717. PCI_dom.
[Graphical view]
PfamiPF01399. PCI. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q5JVF3-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAHITINQYL QQVYEAIDSR DGASCAELVS FKHPHVANPR LQMASPEEKC
60 70 80 90 100
QQVLEPPYDE MFAAHLRCTY AVGNHDFIEA YKCQTVIVQS FLRAFQAHKE
110 120 130 140 150
ENWALPVMYA VALDLRVFAN NADQQLVKKG KSKVGDMLEK AAELLMSCFR
160 170 180 190 200
VCASDTRAGI EDSKKWGMLF LVNQLFKIYF KINKLHLCKP LIRAIDSSNL
210 220 230 240 250
KDDYSTAQRV TYKYYVGRKA MFDSDFKQAE EYLSFAFEHC HRSSQKNKRM
260 270 280 290 300
ILIYLLPVKM LLGHMPTVEL LKKYHLMQFA EVTRAVSEGN LLLLHEALAK
310 320 330 340 350
HEAFFIRCGI FLILEKLKII TYRNLFKKVY LLLKTHQLSL DAFLVALKFM
360 370 380 390
QVEDVDIDEV QCILANLIYM GHVKGYISHQ HQKLVVSKQN PFPPLSTVC
Length:399
Mass (Da):46,030
Last modified:January 10, 2006 - v2
Checksum:i8D23273361F00E18
GO
Isoform 2 (identifier: Q5JVF3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-12: MAHITINQYLQQ → MRLTDVVQQL

Note: No experimental confirmation available.
Show »
Length:397
Mass (Da):45,773
Checksum:i785FD46B5D72AF70
GO
Isoform 3 (identifier: Q5JVF3-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     92-114: Missing.

Note: No experimental confirmation available.
Show »
Length:376
Mass (Da):43,375
Checksum:i039E8F8B8192F3C1
GO
Isoform 4 (identifier: Q5JVF3-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     89-89: Q → QYPLSFMAAVPHRTHAVDYLGLETRKHWASCSFLQLERNDSVLEQKLVSALSLGT

Note: No experimental confirmation available.
Show »
Length:453
Mass (Da):52,100
Checksum:i57BB6C3A1E85A059
GO

Sequence cautioni

The sequence AAG09695 differs from that shown. Reason: Frameshift at position 48.Curated
The sequence BAB15768 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti74N → D in AAH31246 (PubMed:15489334).Curated1
Sequence conflicti87I → L in BAA91407 (PubMed:14702039).Curated1
Sequence conflicti106P → L in AAG09695 (Ref. 2) Curated1
Sequence conflicti129K → E in AAG09695 (Ref. 2) Curated1
Sequence conflicti145L → M in BAA91407 (PubMed:14702039).Curated1
Sequence conflicti180F → I in BAA91611 (PubMed:14702039).Curated1
Sequence conflicti313I → T in BAA92118 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0168431 – 12MAHIT…QYLQQ → MRLTDVVQQL in isoform 2. 1 PublicationAdd BLAST12
Alternative sequenceiVSP_01684489Q → QYPLSFMAAVPHRTHAVDYL GLETRKHWASCSFLQLERND SVLEQKLVSALSLGT in isoform 4. 1 Publication1
Alternative sequenceiVSP_01684592 – 114Missing in isoform 3. 1 PublicationAdd BLAST23

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000888 mRNA. Translation: BAA91407.1.
AK001185 mRNA. Translation: BAA91542.1.
AK001302 mRNA. Translation: BAA91611.1.
AK002167 mRNA. Translation: BAA92118.1.
AK023313 mRNA. Translation: BAB14521.1.
AK024478 mRNA. Translation: BAB15768.1. Different initiation.
AF183426 mRNA. Translation: AAG09695.1. Frameshift.
AL137002 Genomic DNA. Translation: CAI41391.1.
AL136221, AL137002 Genomic DNA. Translation: CAI13794.1.
AL137002, AL136221 Genomic DNA. Translation: CAI41378.1.
AL136221, AL137002 Genomic DNA. Translation: CAI13793.1.
AL137002, AL136221 Genomic DNA. Translation: CAI41377.1.
AL136221, AL137002 Genomic DNA. Translation: CAI13792.1.
AL137002, AL136221 Genomic DNA. Translation: CAI41379.1.
BC016614 mRNA. Translation: AAH16614.1.
BC031246 mRNA. Translation: AAH31246.1.
CCDSiCCDS58301.1. [Q5JVF3-2]
CCDS58302.1. [Q5JVF3-4]
CCDS9532.2. [Q5JVF3-1]
RefSeqiNP_001120674.1. NM_001127202.3. [Q5JVF3-1]
NP_001120675.1. NM_001127203.3. [Q5JVF3-1]
NP_001245142.1. NM_001258213.2. [Q5JVF3-2]
NP_001307584.1. NM_001320655.1. [Q5JVF3-2]
NP_001307585.1. NM_001320656.1. [Q5JVF3-4]
NP_001307586.1. NM_001320657.1.
NP_001307589.1. NM_001320660.1.
NP_060856.2. NM_018386.4. [Q5JVF3-1]
XP_016876153.1. XM_017020664.1. [Q5JVF3-2]
UniGeneiHs.508769.

Genome annotation databases

EnsembliENST00000246505; ENSP00000246505; ENSG00000126226. [Q5JVF3-4]
ENST00000337344; ENSP00000337405; ENSG00000126226. [Q5JVF3-1]
ENST00000375457; ENSP00000364606; ENSG00000126226. [Q5JVF3-2]
ENST00000375459; ENSP00000364608; ENSG00000126226. [Q5JVF3-2]
ENST00000375477; ENSP00000364626; ENSG00000126226. [Q5JVF3-1]
ENST00000375479; ENSP00000364628; ENSG00000126226. [Q5JVF3-1]
ENST00000622406; ENSP00000479494; ENSG00000126226. [Q5JVF3-4]
GeneIDi55795.
KEGGihsa:55795.
UCSCiuc058ylr.1. human. [Q5JVF3-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000888 mRNA. Translation: BAA91407.1.
AK001185 mRNA. Translation: BAA91542.1.
AK001302 mRNA. Translation: BAA91611.1.
AK002167 mRNA. Translation: BAA92118.1.
AK023313 mRNA. Translation: BAB14521.1.
AK024478 mRNA. Translation: BAB15768.1. Different initiation.
AF183426 mRNA. Translation: AAG09695.1. Frameshift.
AL137002 Genomic DNA. Translation: CAI41391.1.
AL136221, AL137002 Genomic DNA. Translation: CAI13794.1.
AL137002, AL136221 Genomic DNA. Translation: CAI41378.1.
AL136221, AL137002 Genomic DNA. Translation: CAI13793.1.
AL137002, AL136221 Genomic DNA. Translation: CAI41377.1.
AL136221, AL137002 Genomic DNA. Translation: CAI13792.1.
AL137002, AL136221 Genomic DNA. Translation: CAI41379.1.
BC016614 mRNA. Translation: AAH16614.1.
BC031246 mRNA. Translation: AAH31246.1.
CCDSiCCDS58301.1. [Q5JVF3-2]
CCDS58302.1. [Q5JVF3-4]
CCDS9532.2. [Q5JVF3-1]
RefSeqiNP_001120674.1. NM_001127202.3. [Q5JVF3-1]
NP_001120675.1. NM_001127203.3. [Q5JVF3-1]
NP_001245142.1. NM_001258213.2. [Q5JVF3-2]
NP_001307584.1. NM_001320655.1. [Q5JVF3-2]
NP_001307585.1. NM_001320656.1. [Q5JVF3-4]
NP_001307586.1. NM_001320657.1.
NP_001307589.1. NM_001320660.1.
NP_060856.2. NM_018386.4. [Q5JVF3-1]
XP_016876153.1. XM_017020664.1. [Q5JVF3-2]
UniGeneiHs.508769.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3T5XX-ray2.12A201-399[»]
ProteinModelPortaliQ5JVF3.
SMRiQ5JVF3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120908. 28 interactors.
DIPiDIP-50497N.
IntActiQ5JVF3. 12 interactors.
STRINGi9606.ENSP00000337405.

PTM databases

iPTMnetiQ5JVF3.
PhosphoSitePlusiQ5JVF3.

Polymorphism and mutation databases

BioMutaiPCID2.
DMDMi85681034.

Proteomic databases

EPDiQ5JVF3.
MaxQBiQ5JVF3.
PaxDbiQ5JVF3.
PeptideAtlasiQ5JVF3.
PRIDEiQ5JVF3.

Protocols and materials databases

DNASUi55795.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000246505; ENSP00000246505; ENSG00000126226. [Q5JVF3-4]
ENST00000337344; ENSP00000337405; ENSG00000126226. [Q5JVF3-1]
ENST00000375457; ENSP00000364606; ENSG00000126226. [Q5JVF3-2]
ENST00000375459; ENSP00000364608; ENSG00000126226. [Q5JVF3-2]
ENST00000375477; ENSP00000364626; ENSG00000126226. [Q5JVF3-1]
ENST00000375479; ENSP00000364628; ENSG00000126226. [Q5JVF3-1]
ENST00000622406; ENSP00000479494; ENSG00000126226. [Q5JVF3-4]
GeneIDi55795.
KEGGihsa:55795.
UCSCiuc058ylr.1. human. [Q5JVF3-1]

Organism-specific databases

CTDi55795.
DisGeNETi55795.
GeneCardsiPCID2.
H-InvDBHIX0130585.
HGNCiHGNC:25653. PCID2.
HPAiHPA069107.
HPA073074.
MIMi613713. gene.
neXtProtiNX_Q5JVF3.
OpenTargetsiENSG00000126226.
PharmGKBiPA144596397.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2688. Eukaryota.
COG5600. LUCA.
GeneTreeiENSGT00390000001101.
HOVERGENiHBG055800.
InParanoidiQ5JVF3.
OMAiCRGFTPG.
PhylomeDBiQ5JVF3.
TreeFamiTF106136.

Miscellaneous databases

ChiTaRSiPCID2. human.
GenomeRNAii55795.
PROiQ5JVF3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000126226.
CleanExiHS_PCID2.
ExpressionAtlasiQ5JVF3. baseline and differential.
GenevisibleiQ5JVF3. HS.

Family and domain databases

InterProiIPR000717. PCI_dom.
[Graphical view]
PfamiPF01399. PCI. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPCID2_HUMAN
AccessioniPrimary (citable) accession number: Q5JVF3
Secondary accession number(s): A6NK09
, Q3ZCX1, Q5TC57, Q5TC58, Q9H7K1, Q9HBZ7, Q9NUK6, Q9NVY1, Q9NW44, Q9NWH3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: January 10, 2006
Last modified: November 30, 2016
This is version 119 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 13
    Human chromosome 13: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.