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PCYT1B phosphate cytidylyltransferase 1B, choline [ Homo sapiens (human) ]

Gene ID: 9468, updated on 27-Nov-2024

Summary

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Official Symbol
PCYT1Bprovided by HGNC
Official Full Name
phosphate cytidylyltransferase 1B, cholineprovided by HGNC
Primary source
HGNC:HGNC:8755
See related
Ensembl:ENSG00000102230 MIM:300948; AllianceGenome:HGNC:8755
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
CTB; CCTB
Summary
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]
Expression
Biased expression in brain (RPKM 6.6), testis (RPKM 2.8) and 7 other tissues See more
Orthologs
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Genomic context

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See PCYT1B in Genome Data Viewer
Location:
Xp22.11
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (24558087..24672887, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (24142375..24257164, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (24576204..24691004, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S26 pseudogene 58 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20719 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:24509351-24510314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29505 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:24546061-24546668 Neighboring gene pyruvate dehydrogenase kinase 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:24546669-24547275 Neighboring gene SNRPE pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29506 Neighboring gene uncharacterized LOC124905262 Neighboring gene PCYT1B antisense RNA 1 Neighboring gene ribosomal protein L23 pseudogene Neighboring gene H2B histone pseudogene 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:24710004-24710504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29507 Neighboring gene DNA polymerase alpha 1, catalytic subunit Neighboring gene small Cajal body-specific RNA 23

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
  • 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. Cloning and characterization of a second human CTP:phosphocholine cytidylyltransferase. Lykidis A, et al. J Biol Chem, 1998 May 29. PMID 9593753
  2. Mass spectrometric identification of human phosphate cytidylyltransferase 1 as a novel calcium oxalate crystal growth inhibitor purified from human renal stone matrix. Priyadarshini, et al. Clin Chim Acta, 2009 Oct. PMID 19595683
  3. Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets. Yue L, et al. Mol Biol Cell, 2020 May 1. PMID 32186954, Free PMC Article
  4. CTP:phosphocholine cytidylyltransferase: Function, regulation, and structure of an amphitropic enzyme required for membrane biogenesis. Cornell RB, et al. Prog Lipid Res, 2015 Jul. PMID 26165797
  5. Neurokinin 3 receptor and phosphocholine transferase: missing factors for pathogenesis of C-reactive protein in preeclampsia. Parchim NF, et al. Hypertension, 2015 Feb. PMID 25452470, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets.
    Title: Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets.
  2. Genetic Polymorphisms of LPCAT1, CHPT1 and PCYT1B and Risk of Neonatal Respiratory Distress Syndrome among a Chinese Han Population.
    Title: Genetic Polymorphisms of LPCAT1, CHPT1 and PCYT1B and Risk of Neonatal Respiratory Distress Syndrome among a Chinese Han Population.
  3. CCT contributes to phospholipid compositional homeostasis. [Review]
    Title: CTP:phosphocholine cytidylyltransferase: Function, regulation, and structure of an amphitropic enzyme required for membrane biogenesis.
  4. PCYT1B, a placental-specific enzyme post-translationally modifying neurokinin B, is essential for the pathogenic role of CRP in preeclampsia through activation of the neurokinin 3 receptor.
    Title: Neurokinin 3 receptor and phosphocholine transferase: missing factors for pathogenesis of C-reactive protein in preeclampsia.
  5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  7. Human phosphate cytidylyltransferase 1, choline, beta is a novel CaOx crystal growth inhibitor.
    Title: Mass spectrometric identification of human phosphate cytidylyltransferase 1 as a novel calcium oxalate crystal growth inhibitor purified from human renal stone matrix.
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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables choline-phosphate cytidylyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables choline-phosphate cytidylyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables phosphatidylcholine 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 CDP-choline pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in ovarian follicle development IEA
Inferred from Electronic Annotation
more info
  
involved_in phosphatidylcholine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm TAS
Traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
choline-phosphate cytidylyltransferase B
Names
CCT B
CCT-beta
CT B
CTP:phosphocholine cytidylyltransferase b
CTP:phosphocholine cytidylyltransferase-beta
choline-phosphate cytidylyltransferase beta
phosphate cytidylyltransferase 1, choline, beta
phosphorylcholine transferase B
phosphorylcholine transferase beta
NP_001156736.1
NP_001156737.1
NP_004836.2
XP_016885466.1
XP_054184152.1

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.

Genomic

  1. NG_013253.1 RefSeqGene

    Range
    30516..119776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001163264.2 → NP_001156736.1  choline-phosphate cytidylyltransferase B isoform 2

    See identical proteins and their annotated locations for NP_001156736.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to variant 1. This results in the use of a different start codon, and a shorter isoform (2) with a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC079168, AK226121, BC045634
    Consensus CDS
    CCDS55392.1
    UniProtKB/Swiss-Prot
    Q9Y5K3
    Related
    ENSP00000368440.1, ENST00000379145.5
    Conserved Domains (1) summary
    PLN02413
    Location:54 → 296
    PLN02413; choline-phosphate cytidylyltransferase

  2. NM_001163265.2 → NP_001156737.1  choline-phosphate cytidylyltransferase B isoform 3

    See identical proteins and their annotated locations for NP_001156737.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is alternatively spliced at the 3' end compared to variant 1, resulting in a frameshift and a shorter isoform (3) with a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC079168, AF052510, AK226121, AK315323, BC045634
    Consensus CDS
    CCDS55391.1
    UniProtKB/Swiss-Prot
    Q9Y5K3
    Related
    ENSP00000349211.4, ENST00000356768.8
    Conserved Domains (1) summary
    cd02174
    Location:75 → 224
    CCT; CTP:phosphocholine cytidylyltransferase

  3. NM_004845.5 → NP_004836.2  choline-phosphate cytidylyltransferase B isoform 1

    See identical proteins and their annotated locations for NP_004836.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.
    Source sequence(s)
    AC079168, AK226121, AK315323, BC045634
    Consensus CDS
    CCDS14213.1
    UniProtKB/Swiss-Prot
    A8IX00, B2RCX8, B4DK10, E9PD84, O60621, Q86XC9, Q9Y5K3
    Related
    ENSP00000368439.2, ENST00000379144.7
    Conserved Domains (1) summary
    PLN02413
    Location:72 → 314
    PLN02413; choline-phosphate cytidylyltransferase

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    24558087..24672887 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029977.2 → XP_016885466.1  choline-phosphate cytidylyltransferase B isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    24142375..24257164 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328177.1 → XP_054184152.1  choline-phosphate cytidylyltransferase B isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y5K3.1 GenPept UniProtKB/Swiss-Prot:Q9Y5K3

Gene LinkOut

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