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

    Gene ID: 23349, updated on 10-Dec-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, Dec 2024]
    Expression
    Biased expression in brain (RPKM 19.5) and testis (RPKM 9.9) See more
    Orthologs
    mouse all
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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: 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. 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

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

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