Human Gene PCYT1B (ENST00000379145.5) from GENCODE V44
  Description: Homo sapiens phosphate cytidylyltransferase 1, choline, beta (PCYT1B), transcript variant 2, mRNA. (from RefSeq NM_001163264)
RefSeq Summary (NM_001163264): The protein encoded by this gene belongs to the cytidylyltransferase family. It is involved in the regulation of phosphatidylcholine biosynthesis. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009].
Gencode Transcript: ENST00000379145.5
Gencode Gene: ENSG00000102230.14
Transcript (Including UTRs)
   Position: hg38 chrX:24,558,087-24,672,677 Size: 114,591 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg38 chrX:24,562,293-24,672,632 Size: 110,340 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:24,558,087-24,672,677)mRNA (may differ from genome)Protein (351 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCY1B_HUMAN
DESCRIPTION: RecName: Full=Choline-phosphate cytidylyltransferase B; EC=2.7.7.15; AltName: Full=CCT-beta; AltName: Full=CTP:phosphocholine cytidylyltransferase B; Short=CCT B; Short=CT B; AltName: Full=Phosphorylcholine transferase B;
FUNCTION: Controls phosphatidylcholine synthesis.
CATALYTIC ACTIVITY: CTP + phosphocholine = diphosphate + CDP- choline.
PATHWAY: Phospholipid metabolism; phosphatidylcholine biosynthesis; phosphatidylcholine from phosphocholine: step 1/2.
SUBCELLULAR LOCATION: Endoplasmic reticulum.
TISSUE SPECIFICITY: Highly expressed in testis, placenta, brain, ovary and fetus.
PTM: Extensively phosphorylated. The beta-1 isoform seems to be much less phosphorylated.
SIMILARITY: Belongs to the cytidylyltransferase family.
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/pcyt1b/";

-  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


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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.60 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 83.23 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 -4.0045-0.089 Picture PostScript Text
3' UTR -1364.404206-0.324 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
IPR004821 - Cyt_trans-like
IPR004820 - Cytidylyltransf
IPR014729 - Rossmann-like_a/b/a_fold

Pfam Domains:
PF01467 - Cytidylyltransferase-like

ModBase Predicted Comparative 3D Structure on Q9Y5K3
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004105 choline-phosphate cytidylyltransferase activity
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity

Biological Process:
GO:0001541 ovarian follicle development
GO:0006629 lipid metabolic process
GO:0006656 phosphatidylcholine biosynthetic process
GO:0006657 CDP-choline pathway
GO:0007283 spermatogenesis
GO:0008654 phospholipid biosynthetic process
GO:0009058 biosynthetic process

Cellular Component:
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane


-  Descriptions from all associated GenBank mRNAs
  BC045634 - Homo sapiens phosphate cytidylyltransferase 1, choline, beta, mRNA (cDNA clone MGC:39750 IMAGE:5285137), complete cds.
AK226121 - Homo sapiens mRNA for PCYT1B protein variant, clone: hh13530.
AF148464 - Homo sapiens CTP:phosphocholine cytidylyltransferase CCTB2 isoform (PCYT1B) mRNA, complete cds.
AF052510 - Homo sapiens CTP:phosphocholine cytidylyltransferase b (CTB) mRNA, complete cds.
AK296333 - Homo sapiens cDNA FLJ50783 complete cds, highly similar to Choline-phosphate cytidylyltransferase B (EC2.7.7.15).
AK315323 - Homo sapiens cDNA, FLJ96359, Homo sapiens phosphate cytidylyltransferase 1, choline, betaisoform (PCYT1B), mRNA.
KJ898027 - Synthetic construct Homo sapiens clone ccsbBroadEn_07421 PCYT1B gene, encodes complete protein.
AK022741 - Homo sapiens cDNA FLJ12679 fis, clone NT2RM4002420.
JD218813 - Sequence 199837 from Patent EP1572962.
JD258672 - Sequence 239696 from Patent EP1572962.
JD320142 - Sequence 301166 from Patent EP1572962.
JD214699 - Sequence 195723 from Patent EP1572962.
JD492488 - Sequence 473512 from Patent EP1572962.
JD074395 - Sequence 55419 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00564 - Glycerophospholipid metabolism
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q9Y5K3 (Reactome details) participates in the following event(s):

R-HSA-1483081 PCho and CTP are condensed to CDP-Cho by PCYT1 dimer
R-HSA-1483191 Synthesis of PC
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-1483257 Phospholipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: A8IX00, B2RCX8, CCTB, ENST00000379145.1, ENST00000379145.2, ENST00000379145.3, ENST00000379145.4, NM_001163264, O60621, PCY1B_HUMAN, Q86XC9, Q9Y5K3, uc004dbj.1, uc004dbj.2, uc004dbj.3, uc004dbj.4
UCSC ID: ENST00000379145.5
RefSeq Accession: NM_001163264
Protein: Q9Y5K3 (aka PCY1B_HUMAN or CTPU_HUMAN)
CCDS: CCDS55392.1

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