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PHF3 PHD finger protein 3 [ Homo sapiens (human) ]

Gene ID: 23469, updated on 4-Nov-2018

Summary

Official Symbol
PHF3provided by HGNC
Official Full Name
PHD finger protein 3provided by HGNC
Primary source
HGNC:HGNC:8921
See related
Ensembl:ENSG00000118482 MIM:607789; Vega:OTTHUMG00000014952
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
Expression
Ubiquitous expression in testis (RPKM 15.6), thyroid (RPKM 14.4) and 25 other tissues See more
Orthologs

Genomic context

See PHF3 in Genome Data Viewer
Location:
6q12
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (63635802..63715522)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (64345707..64424407)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene lengsin, lens protein with glutamine synthetase domain Neighboring gene ribosomal protein L7a pseudogene 34 Neighboring gene protein tyrosine phosphatase type IVA, member 1 Neighboring gene ribosomal protein L9 pseudogene 18 Neighboring gene platelet activating factor acetylhydrolase 1b regulatory subunit 1 pseudogene Neighboring gene eyes shut homolog Neighboring gene glucosaminyl (N-acetyl) transferase 1 pseudogene 4

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of PHD finger protein 3 (PHF3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0244, MGC142210, MGC142212

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
multicellular organism development NAS
Non-traceable Author Statement
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 

NCBI Reference Sequences (RefSeq)

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_034034.1 RefSeqGene

    Range
    5001..84721
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001290259.1NP_001277188.1  PHD finger protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001277188.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AF091622, AK055678, AL354719, BX648268, CR737498
    UniProtKB/Swiss-Prot
    Q92576
    UniProtKB/TrEMBL
    B3KP41
    Conserved Domains (4) summary
    cd15638
    Location:631681
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam07500
    Location:837947
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:11211227
    SPOC; SPOC domain
    pfam12871
    Location:18441938
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
  2. NM_001290260.1NP_001277189.1  PHD finger protein 3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 3' structure, compared to variant 1. The encoded protein (isoform 3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL513043, BC040583, BC113650
    Consensus CDS
    CCDS78155.1
    UniProtKB/Swiss-Prot
    Q92576
    UniProtKB/TrEMBL
    D6R9X2
    Related
    ENSP00000422841.1, OTTHUMP00000217899, ENST00000509330.5, OTTHUMT00000359965
  3. NM_015153.3NP_055968.1  PHD finger protein 3 isoform 1

    See identical proteins and their annotated locations for NP_055968.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF091622, AL354719, CR737498
    Consensus CDS
    CCDS4966.1
    UniProtKB/Swiss-Prot
    Q92576
    Related
    ENSP00000377048.1, ENST00000393387.5
    Conserved Domains (5) summary
    cd15638
    Location:719769
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam07500
    Location:9251035
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:12091315
    SPOC; SPOC domain
    pfam08648
    Location:19452039
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:19322026
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    63635802..63715522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248702.3XP_005248759.1  PHD finger protein 3 isoform X3

    See identical proteins and their annotated locations for XP_005248759.1

    UniProtKB/Swiss-Prot
    Q92576
    Conserved Domains (4) summary
    cd15638
    Location:631681
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam07500
    Location:837947
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:11211227
    SPOC; SPOC domain
    pfam12871
    Location:18441938
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
  2. XM_017010626.1XP_016866115.1  PHD finger protein 3 isoform X4

    Conserved Domains (3) summary
    pfam07500
    Location:194304
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:478584
    SPOC; SPOC domain
    cl22851
    Location:138
    PHD_SF; PHD finger superfamily
  3. XM_005248703.4XP_005248760.1  PHD finger protein 3 isoform X4

    Conserved Domains (3) summary
    pfam07500
    Location:194304
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:478584
    SPOC; SPOC domain
    cl22851
    Location:138
    PHD_SF; PHD finger superfamily
  4. XM_005248701.4XP_005248758.1  PHD finger protein 3 isoform X2

    See identical proteins and their annotated locations for XP_005248758.1

    UniProtKB/Swiss-Prot
    Q92576
    Related
    ENSP00000262043.3, OTTHUMP00000016677, ENST00000262043.7
    Conserved Domains (5) summary
    cd15638
    Location:719769
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam07500
    Location:9251035
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:12091315
    SPOC; SPOC domain
    pfam08648
    Location:19452039
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:19322026
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
  5. XM_006715426.3XP_006715489.1  PHD finger protein 3 isoform X2

    See identical proteins and their annotated locations for XP_006715489.1

    UniProtKB/Swiss-Prot
    Q92576
    Conserved Domains (5) summary
    cd15638
    Location:719769
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam07500
    Location:9251035
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:12091315
    SPOC; SPOC domain
    pfam08648
    Location:19452039
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:19322026
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
  6. XM_011535648.3XP_011533950.1  PHD finger protein 3 isoform X1

    Conserved Domains (5) summary
    cd15638
    Location:728778
    PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
    pfam07500
    Location:9341044
    TFIIS_M; Transcription factor S-II (TFIIS), central domain
    pfam07744
    Location:12181324
    SPOC; SPOC domain
    pfam08648
    Location:19542048
    DUF1777; Protein of unknown function (DUF1777)
    pfam12871
    Location:19412035
    PRP38_assoc; Pre-mRNA-splicing factor 38-associated hydrophilic C-term
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