Human Gene PCID2 (ENST00000337344.9_8) from GENCODE V47lift37
  Description: PCI domain containing 2, transcript variant 3 (from RefSeq NM_018386.5)
Gencode Transcript: ENST00000337344.9_8
Gencode Gene: ENSG00000126226.22_13
Transcript (Including UTRs)
   Position: hg19 chr13:113,831,850-113,862,983 Size: 31,134 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr13:113,832,512-113,862,948 Size: 30,437 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:113,831,850-113,862,983)mRNA (may differ from genome)Protein (399 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCID2_HUMAN
DESCRIPTION: RecName: Full=PCI domain-containing protein 2; AltName: Full=CSN12-like protein;
FUNCTION: Required for B-cell survival through the regulation of the expression of cell-cycle checkpoint MAD2L1 protein during B cell differentiation (By similarity).
SIMILARITY: Belongs to the CSN12 family.
SIMILARITY: Contains 1 PCI domain.
SEQUENCE CAUTION: Sequence=AAG09695.1; Type=Frameshift; Positions=48; Sequence=BAB15768.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PCID2
Diseases sorted by gene-association score: noonan syndrome 1 (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.02 RPKM in Testis
Total median expression: 446.44 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -19.1035-0.546 Picture PostScript Text
3' UTR -159.30662-0.241 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013143 - PAM
IPR000717 - PCI_dom

Pfam Domains:
PF01399 - PCI domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3T5X - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q5JVF3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003690 double-stranded DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000973 posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0016973 poly(A)+ mRNA export from nucleus
GO:0043066 negative regulation of apoptotic process
GO:0043488 regulation of mRNA stability
GO:0045579 positive regulation of B cell differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0048536 spleen development
GO:0071033 nuclear retention of pre-mRNA at the site of transcription
GO:0090267 positive regulation of mitotic cell cycle spindle assembly checkpoint
GO:2000117 negative regulation of cysteine-type endopeptidase activity

Cellular Component:
GO:0005575 cellular_component
GO:0070390 transcription export complex 2
GO:0005643 nuclear pore
GO:0035327 transcriptionally active chromatin


-  Descriptions from all associated GenBank mRNAs
  AK001185 - Homo sapiens cDNA FLJ10323 fis, clone NT2RM2000540.
BC016614 - Homo sapiens PCI domain containing 2, mRNA (cDNA clone MGC:8832 IMAGE:3869275), complete cds.
LF384332 - JP 2014500723-A/191835: Polycomb-Associated Non-Coding RNAs.
AK024478 - Homo sapiens mRNA for FLJ00071 protein, partial cds.
AK098706 - Homo sapiens cDNA FLJ25840 fis, clone TST08629, highly similar to Homo sapiens HT004 protein mRNA.
AK002167 - Homo sapiens cDNA FLJ11305 fis, clone PLACE1010023.
AK000888 - Homo sapiens cDNA FLJ10026 fis, clone HEMBA1000686.
AK023313 - Homo sapiens cDNA FLJ13251 fis, clone OVARC1000730.
AF183426 - Homo sapiens HT004 protein mRNA, complete cds.
AK001302 - Homo sapiens cDNA FLJ10440 fis, clone NT2RP1000695.
BC031246 - Homo sapiens PCI domain containing 2, mRNA (cDNA clone MGC:39643 IMAGE:5266649), complete cds.
AK289462 - Homo sapiens cDNA FLJ78373 complete cds, highly similar to Homo sapiens PCI domain containing 2, mRNA.
JD389733 - Sequence 370757 from Patent EP1572962.
KJ899195 - Synthetic construct Homo sapiens clone ccsbBroadEn_08589 PCID2 gene, encodes complete protein.
AK097025 - Homo sapiens cDNA FLJ39706 fis, clone SMINT2012501.
CU677649 - Synthetic construct Homo sapiens gateway clone IMAGE:100017188 5' read PCID2 mRNA.
LF371281 - JP 2014500723-A/178784: Polycomb-Associated Non-Coding RNAs.
LF371282 - JP 2014500723-A/178785: Polycomb-Associated Non-Coding RNAs.
AK309321 - Homo sapiens cDNA, FLJ99362.
MA619909 - JP 2018138019-A/191835: Polycomb-Associated Non-Coding RNAs.
MA606858 - JP 2018138019-A/178784: Polycomb-Associated Non-Coding RNAs.
MA606859 - JP 2018138019-A/178785: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NK09, ENST00000337344.1, ENST00000337344.2, ENST00000337344.3, ENST00000337344.4, ENST00000337344.5, ENST00000337344.6, ENST00000337344.7, ENST00000337344.8, HT004, NM_018386, PCID2_HUMAN, Q3ZCX1, Q5JVF3, Q5TC57, Q5TC58, Q9H7K1, Q9HBZ7, Q9NUK6, Q9NVY1, Q9NW44, Q9NWH3, uc317uta.1, uc317uta.2
UCSC ID: ENST00000337344.9_8
RefSeq Accession: NM_001127202.4
Protein: Q5JVF3 (aka PCID2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.