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    GDPD5 glycerophosphodiester phosphodiesterase domain containing 5 [ Homo sapiens (human) ]

    Gene ID: 81544, updated on 28-Oct-2024

    Summary

    Official Symbol
    GDPD5provided by HGNC
    Official Full Name
    glycerophosphodiester phosphodiesterase domain containing 5provided by HGNC
    Primary source
    HGNC:HGNC:28804
    See related
    Ensembl:ENSG00000158555 MIM:609632; AllianceGenome:HGNC:28804
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GDE2; PP1665
    Summary
    Predicted to enable glycerophosphodiester phosphodiesterase activity. Predicted to be involved in negative regulation of Notch signaling pathway; positive regulation of cell cycle; and positive regulation of neuron differentiation. Predicted to act upstream of or within neuron differentiation and regulation of timing of cell differentiation. Predicted to be located in axon; neuronal cell body; and perinuclear endoplasmic reticulum. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in spleen (RPKM 16.9), fat (RPKM 8.6) and 14 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See GDPD5 in Genome Data Viewer
    Location:
    11q13.4-q13.5
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (75434640..75525941, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (75364149..75455494, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (75145685..75236986, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory regions 4651 and 6526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75118535-75119034 Neighboring gene small nucleolar RNA, C/D box 15B Neighboring gene Sharpr-MPRA regulatory regions 6111 and 12908 Neighboring gene ribosomal protein S3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75142886-75143772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75151983-75152545 Neighboring gene kelch like family member 35 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75167384-75167982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75171856-75172358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75177195-75177867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75178136-75178783 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75178784-75179430 Neighboring gene uncharacterized LOC105369389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75236337-75236837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3767 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75242693-75243509 Neighboring gene CRISPRi-validated cis-regulatory element chr11.4348 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:75248027-75248527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75254283-75254784 Neighboring gene VISTA enhancer hs1748 Neighboring gene CRISPRi-validated cis-regulatory element chr11.4355 Neighboring gene CRISPRi-validated cis-regulatory element chr11.4356 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75272978-75273517 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75273518-75274058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:75274059-75274597 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75276989-75277604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75277605-75278219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75279454-75279954 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:75287552-75288052 Neighboring gene serpin family H member 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:75289175-75289343 Neighboring gene uncharacterized LOC105369391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75295275-75295854 Neighboring gene microtubule associated protein 6

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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 glycerophosphocholine phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables glycerophosphodiester phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables phosphatidylinositol phospholipase C activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in endomembrane system IEA
    Inferred from Electronic Annotation
    more info
     
    located_in growth cone IEA
    Inferred from Electronic Annotation
    more info
     
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    glycerophosphodiester phosphodiesterase domain-containing protein 5
    Names
    glycerophosphocholine phosphodiesterase GDPD5
    glycerophosphodiester phosphodiesterase 2
    phosphoinositide phospholipase C GDPD5
    NP_001338096.1
    NP_001338097.1
    NP_110419.5
    XP_006718760.1
    XP_011543578.1
    XP_011543579.1
    XP_011543580.1
    XP_011543582.1
    XP_011543583.1
    XP_011543588.1
    XP_047283601.1
    XP_047283602.1
    XP_047283603.1
    XP_047283604.1
    XP_047283605.1
    XP_047283606.1
    XP_047283607.1
    XP_047283608.1
    XP_047283609.1
    XP_047283610.1
    XP_054226036.1
    XP_054226037.1
    XP_054226038.1
    XP_054226039.1
    XP_054226040.1
    XP_054226041.1
    XP_054226042.1
    XP_054226043.1
    XP_054226044.1
    XP_054226045.1
    XP_054226046.1
    XP_054226047.1
    XP_054226048.1
    XP_054226049.1
    XP_054226050.1

    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.

    mRNA and Protein(s)

    1. NM_001351167.2NP_001338096.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' structure, resulting in a novel 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AP002815
      Consensus CDS
      CCDS86230.1
      Related
      ENSP00000434050.1, ENST00000526177.5
      Conserved Domains (1) summary
      cd08608
      Location:89438
      GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
    2. NM_001351168.1NP_001338097.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate exon, resulting in a novel 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AF318351, AP002815
      Consensus CDS
      CCDS86229.1
      Related
      ENSP00000435196.1, ENST00000533805.5
      Conserved Domains (1) summary
      cl14615
      Location:1331
      PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
    3. NM_030792.8NP_110419.5  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 1

      See identical proteins and their annotated locations for NP_110419.5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AP002815
      Consensus CDS
      CCDS8238.1
      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
      Related
      ENSP00000337972.3, ENST00000336898.8
      Conserved Domains (2) summary
      cd08608
      Location:227576
      GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
      COG0584
      Location:227468
      UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      75434640..75525941 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427654.1XP_047283610.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    2. XM_047427645.1XP_047283601.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    3. XM_047427653.1XP_047283609.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    4. XM_011545276.3XP_011543578.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011543578.1

      Conserved Domains (2) summary
      cd08608
      Location:227577
      GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
      COG0584
      Location:227468
      UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
    5. XM_047427649.1XP_047283605.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    6. XM_047427646.1XP_047283602.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    7. XM_006718697.4XP_006718760.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      See identical proteins and their annotated locations for XP_006718760.1

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
      Conserved Domains (2) summary
      cd08608
      Location:227576
      GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
      COG0584
      Location:227468
      UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
    8. XM_047427652.1XP_047283608.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    9. XM_011545278.3XP_011543580.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011543580.1

      Conserved Domains (2) summary
      cd08608
      Location:227577
      GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
      COG0584
      Location:227468
      UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
    10. XM_011545277.3XP_011543579.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011543579.1

      Conserved Domains (2) summary
      cd08608
      Location:227577
      GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
      COG0584
      Location:227468
      UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
    11. XM_047427648.1XP_047283604.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    12. XM_047427650.1XP_047283606.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
      Related
      ENSP00000433214.1, ENST00000529721.5
    13. XM_047427651.1XP_047283607.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    14. XM_047427647.1XP_047283603.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    15. XM_011545280.2XP_011543582.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X3

      Conserved Domains (2) summary
      cd08608
      Location:170520
      GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
      COG0584
      Location:170411
      UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
    16. XM_011545281.3XP_011543583.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X4

      See identical proteins and their annotated locations for XP_011543583.1

      Related
      ENSP00000437049.1, ENST00000533784.5
      Conserved Domains (2) summary
      cd08608
      Location:89439
      GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
      COG0584
      Location:89330
      UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
    17. XM_011545286.2XP_011543588.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X5

      Conserved Domains (1) summary
      cl14615
      Location:1332
      PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      75364149..75455494 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370070.1XP_054226045.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    2. XM_054370072.1XP_054226047.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    3. XM_054370071.1XP_054226046.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    4. XM_054370068.1XP_054226043.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    5. XM_054370062.1XP_054226037.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    6. XM_054370065.1XP_054226040.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    7. XM_054370064.1XP_054226039.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    8. XM_054370063.1XP_054226038.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    9. XM_054370061.1XP_054226036.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

    10. XM_054370066.1XP_054226041.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    11. XM_054370067.1XP_054226042.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    12. XM_054370069.1XP_054226044.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

      UniProtKB/Swiss-Prot
      Q49AQ5, Q6UX76, Q7Z4S0, Q8N781, Q8NCB7, Q8TB77, Q8WTR4
    13. XM_054370073.1XP_054226048.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X3

    14. XM_054370074.1XP_054226049.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X4

    15. XM_054370075.1XP_054226050.1  glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X5