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

Gene ID: 653583, updated on 5-Mar-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 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, Apr 2022]
Expression
Broad expression in testis (RPKM 4.9), skin (RPKM 3.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19q13.31
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (43475103..43504746, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (46295450..46325619, complement)
105.20220307 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: 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. 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 (26) 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)

Genotypes

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 

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_2023_10

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

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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