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    PCYT1A phosphate cytidylyltransferase 1A, choline [ Homo sapiens (human) ]

    Gene ID: 5130, updated on 5-Mar-2024

    Summary

    Official Symbol
    PCYT1Aprovided by HGNC
    Official Full Name
    phosphate cytidylyltransferase 1A, cholineprovided by HGNC
    Primary source
    HGNC:HGNC:8754
    See related
    Ensembl:ENSG00000161217 MIM:123695; AllianceGenome:HGNC:8754
    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
    CT; CTA; CCTA; CGL5; CTPCT; PCYT1; SMDCRD; CCTalpha
    Summary
    This gene belongs to the cytidylyltransferase family and is involved in the regulation of phosphatidylcholine biosynthesis. Mutations in this gene are associated with spondylometaphyseal dysplasia with cone-rod dystrophy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]
    Expression
    Ubiquitous expression in duodenum (RPKM 22.3), small intestine (RPKM 20.1) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PCYT1A in Genome Data Viewer
    Location:
    3q29
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (196234368..196287726, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (198953844..199007214, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (195961239..196014597, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909479 Neighboring gene uncharacterized LOC105374304 Neighboring gene Sharpr-MPRA regulatory region 7098 Neighboring gene solute carrier family 51 member A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21081 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21082 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:195973646-195974845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195990064-195990615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195990616-195991166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195999955-196000454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21083 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196005871-196006483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196013420-196014080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196014081-196014740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21086 Neighboring gene dynein light chain Tctex-type 2B Neighboring gene TM4SF19-DYNLT2B readthrough (NMD candidate) Neighboring gene uncharacterized LOC107986031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21087 Neighboring gene TM4SF19 antisense RNA 1 Neighboring gene transmembrane 4 L six family member 19

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calmodulin binding IEA
    Inferred from Electronic Annotation
    more info
     
    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 choline-phosphate cytidylyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables molecular function inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylcholine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in CDP-choline pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in CDP-choline pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phosphatidylcholine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in phosphatidylcholine biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in glycogen granule ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear envelope IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    choline-phosphate cytidylyltransferase A
    Names
    CCT A
    CCT-alpha
    CT A
    CTP:phosphocholine cytidylyltransferase A
    CTP:phosphocholine cytidylyltransferase-alpha
    choline-phosphate cytidylyltransferase alpha
    phosphate cytidylyltransferase 1, choline, alpha
    phosphorylcholine transferase A
    phosphorylcholine transferase alpha
    NP_001299602.1
    NP_005008.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_042817.2 RefSeqGene

      Range
      5000..58358
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001312673.2NP_001299602.1  choline-phosphate cytidylyltransferase A

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a 5' non-coding exon, thus has a shorter 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC069257, AK304534, AK309073, DB223595, L28957
      Consensus CDS
      CCDS3315.1
      UniProtKB/Swiss-Prot
      A9LYK9, D3DXB1, P49585, Q86Y88
      UniProtKB/TrEMBL
      B2R8P1
      Related
      ENSP00000394617.1, ENST00000431016.6
      Conserved Domains (1) summary
      cd02174
      Location:75224
      CCT; CTP:phosphocholine cytidylyltransferase
    2. NM_005017.4NP_005008.2  choline-phosphate cytidylyltransferase A

      See identical proteins and their annotated locations for NP_005008.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC069257, AK309073, BC046355, DB223595
      Consensus CDS
      CCDS3315.1
      UniProtKB/Swiss-Prot
      A9LYK9, D3DXB1, P49585, Q86Y88
      UniProtKB/TrEMBL
      B2R8P1
      Related
      ENSP00000292823.2, ENST00000292823.6
      Conserved Domains (1) summary
      cd02174
      Location:75224
      CCT; CTP:phosphocholine cytidylyltransferase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      196234368..196287726 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      198953844..199007214 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)