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    PHLDB3 pleckstrin homology like domain family B member 3 [ Homo sapiens (human) ]

    Gene ID: 653583, updated on 18-Dec-2024

    Summary

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    Official Symbol
    PHLDB3provided by HGNC
    Official Full Name
    pleckstrin homology like domain family B member 3provided by HGNC
    Primary source
    HGNC:HGNC:30499
    See related
    Ensembl:ENSG00000176531 MIM:621041; AllianceGenome:HGNC:30499
    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
    Summary
    Enables enzyme binding activity. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in testis (RPKM 4.9), skin (RPKM 3.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHLDB3 in Genome Data Viewer
    Location:
    19q13.31
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (43475103..43504746, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (46295450..46325619, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (43979255..44008898, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene testis expressed 101 Neighboring gene RNA, 28S ribosomal pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr19:43917243-43917429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:43967981-43968512 Neighboring gene LY6/PLAUR domain containing 3 Neighboring gene Sharpr-MPRA regulatory region 2471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44008034-44008556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44017305-44017805 Neighboring gene ETHE1 persulfide dioxygenase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44029999-44030504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44030505-44031009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10721 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:44035307-44035478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10722 Neighboring gene zinc finger protein 575

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Pleckstrin homology domain-containing protein PHLDB3 supports cancer growth via a negative feedback loop involving p53. Chao T, et al. Nat Commun, 2016 Dec 23. PMID 28008906, Free PMC Article
    2. Purification of CpG islands using a methylated DNA binding column. Cross SH, et al. Nat Genet, 1994 Mar. PMID 8012384
    3. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Armour SM, et al. Mol Cell Biol, 2013 Apr. PMID 23382074, Free PMC Article
    4. Viral immune modulators perturb the human molecular network by common and unique strategies. Pichlmair A, et al. Nature, 2012 Jul 26. PMID 22810585
    5. The DNA sequence and biology of human chromosome 19. Grimwood J, et al. Nature, 2004 Apr 1. PMID 15057824

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHLDB3 promotes tumour growth by inactivating p53 in a negative feedback fashion.
      Title: Pleckstrin homology domain-containing protein PHLDB3 supports cancer growth via a negative feedback loop involving p53.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ40193, MGC87511

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pleckstrin homology-like domain family B member 3

    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.

    mRNA and Protein(s)

    1. NM_198850.4 → NP_942147.3  pleckstrin homology-like domain family B member 3

      See identical proteins and their annotated locations for NP_942147.3

      Status: VALIDATED

      Source sequence(s)
      AA621318, BC007947, BC029299, BG403419, BU858992, CA502903, CB850627
      Consensus CDS
      CCDS12621.2
      UniProtKB/Swiss-Prot
      Q6NSJ2, Q8N7Z4
      Related
      ENSP00000292140.5, ENST00000292140.10
      Conserved Domains (2) summary
      cd14673
      Location:535 → 635
      PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
      pfam00169
      Location:535 → 630
      PH; PH domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      43475103..43504746 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005259170.5 → XP_005259227.1  pleckstrin homology-like domain family B member 3 isoform X2

      Conserved Domains (2) summary
      cd14673
      Location:496 → 596
      PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
      pfam00169
      Location:496 → 591
      PH; PH domain

    2. XM_005259169.5 → XP_005259226.1  pleckstrin homology-like domain family B member 3 isoform X1

      See identical proteins and their annotated locations for XP_005259226.1

      Conserved Domains (2) summary
      cd14673
      Location:530 → 630
      PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
      pfam00169
      Location:530 → 625
      PH; PH domain

    3. XM_047439241.1 → XP_047295197.1  pleckstrin homology-like domain family B member 3 isoform X2

    4. XM_047439240.1 → XP_047295196.1  pleckstrin homology-like domain family B member 3 isoform X1

    5. XM_005259171.5 → XP_005259228.1  pleckstrin homology-like domain family B member 3 isoform X3

      Conserved Domains (1) summary
      TIGR02168
      Location:111 → 319
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    6. XM_047439242.1 → XP_047295198.1  pleckstrin homology-like domain family B member 3 isoform X4

      Related
      ENSP00000469372.2, ENST00000596141.2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      46295450..46325619 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321808.1 → XP_054177783.1  pleckstrin homology-like domain family B member 3 isoform X1

    2. XM_054321809.1 → XP_054177784.1  pleckstrin homology-like domain family B member 3 isoform X2

    3. XM_054321807.1 → XP_054177782.1  pleckstrin homology-like domain family B member 3 isoform X1

    4. XM_054321810.1 → XP_054177785.1  pleckstrin homology-like domain family B member 3 isoform X2

    5. XM_054321811.1 → XP_054177786.1  pleckstrin homology-like domain family B member 3 isoform X3

    6. XM_054321812.1 → XP_054177787.1  pleckstrin homology-like domain family B member 3 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NSJ2.3 GenPept UniProtKB/Swiss-Prot:Q6NSJ2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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