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PHF24 PHD finger protein 24 [ Homo sapiens (human) ]

Gene ID: 23349, updated on 2-Nov-2024

Summary

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Official Symbol
PHF24provided by HGNC
Official Full Name
PHD finger protein 24provided by HGNC
Primary source
HGNC:HGNC:29180
See related
Ensembl:ENSG00000122733 MIM:619928; AllianceGenome:HGNC:29180
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
GINIP
Summary
Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. Predicted to be active in glutamatergic synapse; nucleus; and synaptic vesicle membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in brain (RPKM 19.5) and testis (RPKM 9.9) See more
Orthologs
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Genomic context

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See PHF24 in Genome Data Viewer
Location:
9p13.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (34665607..34982544)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (34684209..35001725)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (34957484..34982541)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:34654819-34655434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:34659625-34660126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19855 Neighboring gene uncharacterized LOC124902146 Neighboring gene uncharacterized LOC730098 Neighboring gene interleukin 11 receptor subunit alpha Neighboring gene galactose-1-phosphate uridylyltransferase Neighboring gene C-C motif chemokine ligand 27 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19856 Neighboring gene C-C motif chemokine ligand 19 Neighboring gene SPATA31 subfamily F member 1 Neighboring gene C-C motif chemokine ligand 21 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34766948-34767450 Neighboring gene SPATA31 subfamily F member 2, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr9:34870473-34870974 Neighboring gene SPATA31 subfamily F member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34926275-34926796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34926797-34927317 Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta pseudogene 6 Neighboring gene glutamate-ammonia ligase pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34989927-34990856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34990857-34991786 Neighboring gene Sharpr-MPRA regulatory region 8519 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34992717-34993646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34994577-34995506 Neighboring gene DNAJB5 divergent transcript Neighboring gene DnaJ heat shock protein family (Hsp40) member B5

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 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. Solution structure of the PHD finger from the human KIAA1045 protein. Miyamoto K, et al. Protein Sci, 2018 May. PMID 29430827, Free PMC Article
  2. Fine-tuning GPCR-mediated neuromodulation by biasing signaling through different G protein subunits. Park JC, et al. Mol Cell, 2023 Jul 20. PMID 37390816, Free PMC Article
  3. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Kikuno R, et al. DNA Res, 1999 Jun 30. PMID 10470851
  4. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article
  5. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

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

  • KIAA1045, DKFZp434I2112

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in detection of mechanical stimulus involved in sensory perception of pain IEA
Inferred from Electronic Annotation
more info
  
involved_in gamma-aminobutyric acid signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of G protein-coupled receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of synaptic transmission, GABAergic IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
PHD finger protein 24
Names
Galpha inhibitory interacting protein

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_052851.2 RefSeqGene

    Range
    297680..321939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001304333.3 → NP_001291262.1  PHD finger protein 24 isoform 1

    See identical proteins and their annotated locations for NP_001291262.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 5. The encoded isoform (1) is shorter than isoform 2. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AK294342, AL355377, BC041169
    Consensus CDS
    CCDS43796.1
    UniProtKB/Swiss-Prot
    B7Z253, Q58FE9, Q5T662, Q9UPV7
    Conserved Domains (1) summary
    pfam16744
    Location:126 → 198
    Zf_RING; KIAA1045 RING finger

  2. NM_001347982.1 → NP_001334911.1  PHD finger protein 24 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) represents the longest transcript and encodes the longest isoform (2). Variants 5 and 6 both encode the same isoform (2).
    Source sequence(s)
    AL355377

  3. NM_001347983.2 → NP_001334912.1  PHD finger protein 24 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 5. Variants 5 and 6 encode the same isoform (2).
    Source sequence(s)
    AL355377

  4. NM_001395369.1 → NP_001382298.1  PHD finger protein 24 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL355377

  5. NM_001395370.1 → NP_001382299.1  PHD finger protein 24 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL355377

  6. NM_001395371.1 → NP_001382300.1  PHD finger protein 24 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AL355377

  7. NM_001395372.1 → NP_001382301.1  PHD finger protein 24 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AL355377

  8. NM_015297.3 → NP_056112.1  PHD finger protein 24 isoform 1

    See identical proteins and their annotated locations for NP_056112.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 5. The encoded isoform (1) is shorter than isoform 2. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AB028968, AL355377, BC041169
    Consensus CDS
    CCDS43796.1
    UniProtKB/Swiss-Prot
    B7Z253, Q58FE9, Q5T662, Q9UPV7
    Related
    ENSP00000242315.3, ENST00000242315.4
    Conserved Domains (1) summary
    pfam16744
    Location:126 → 198
    Zf_RING; KIAA1045 RING finger

RNA

  1. NR_136307.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AK294342, AL355377, BC041169

  2. NR_136308.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL355377, BC041169

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    34665607..34982544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423102.1 → XP_047279058.1  PHD finger protein 24 isoform X1

  2. XM_047423103.1 → XP_047279059.1  PHD finger protein 24 isoform X2

  3. XM_017014554.2 → XP_016870043.1  PHD finger protein 24 isoform X3

    Conserved Domains (1) summary
    pfam16744
    Location:132 → 203
    Zf_RING; KIAA1045 RING finger

  4. XM_017014555.2 → XP_016870044.1  PHD finger protein 24 isoform X3

    Conserved Domains (1) summary
    pfam16744
    Location:132 → 203
    Zf_RING; KIAA1045 RING finger

  5. XM_017014553.3 → XP_016870042.1  PHD finger protein 24 isoform X3

    Conserved Domains (1) summary
    pfam16744
    Location:132 → 203
    Zf_RING; KIAA1045 RING finger

  6. XM_017014556.2 → XP_016870045.1  PHD finger protein 24 isoform X3

    Conserved Domains (1) summary
    pfam16744
    Location:132 → 203
    Zf_RING; KIAA1045 RING finger

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    34684209..35001725
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362539.1 → XP_054218514.1  PHD finger protein 24 isoform X1

  2. XM_054362541.1 → XP_054218516.1  PHD finger protein 24 isoform X2

  3. XM_054362538.1 → XP_054218513.1  PHD finger protein 24 isoform X5

  4. XM_054362540.1 → XP_054218515.1  PHD finger protein 24 isoform X6

  5. XM_054362537.1 → XP_054218512.1  PHD finger protein 24 isoform X4

RNA

  1. XR_008487970.1 RNA Sequence

  2. XR_008487971.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UPV7.2 GenPept UniProtKB/Swiss-Prot:Q9UPV7

Gene LinkOut

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