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PHF11 PHD finger protein 11 [ Homo sapiens (human) ]

Gene ID: 51131, updated on 7-Jun-2020

Summary

Official Symbol
PHF11provided by HGNC
Official Full Name
PHD finger protein 11provided by HGNC
Primary source
HGNC:HGNC:17024
See related
Ensembl:ENSG00000136147 MIM:607796
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
Also known as
APY; BCAP; IGEL; IGER; IGHER; NYREN34; NY-REN-34
Summary
This gene encodes a protein containing a PHD (plant homeodomain) type zinc finger. This gene has been identified in some studies as a candidate gene for asthma. Naturally-occurring readthrough transcription may occur from the upstream SETDB2 (SET domain bifurcated 2) gene to this locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
Expression
Ubiquitous expression in lymph node (RPKM 13.0), spleen (RPKM 12.7) and 25 other tissues See more
Orthologs

Genomic context

See PHF11 in Genome Data Viewer
Location:
13q14.2
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (49495953..49528992)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50069746..50103123)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene calcium binding protein 39 like Neighboring gene SETDB2-PHF11 readthrough Neighboring gene SET domain bifurcated histone lysine methyltransferase 2 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 14 Neighboring gene RCC1 and BTB domain containing protein 1 Neighboring gene uncharacterized LOC105370204

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Hypertrophy-associated polymorphisms ascertained in a founder cohort applied to heart failure risk and mortality.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough SETDB2-PHF11

Readthrough gene: SETDB2-PHF11, Included gene: SETDB2

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear membrane IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
PHD finger protein 11
Names
BRCA1 C-terminus-associated protein
IgE responsiveness (atopic)
renal carcinoma antigen NY-REN-34

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.

mRNA and Protein(s)

  1. NM_001040443.3NP_001035533.1  PHD finger protein 11 isoform a

    See identical proteins and their annotated locations for NP_001035533.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AK026228, DA652444
    Consensus CDS
    CCDS31975.1
    UniProtKB/Swiss-Prot
    Q9UIL8
    UniProtKB/TrEMBL
    B4DDL5
    Related
    ENSP00000367570.3, ENST00000378319.8
    Conserved Domains (1) summary
    cd15712
    Location:45159
    ePHD_PHF11; Extended PHD finger found in PHD finger protein 11 (PHF11)
  2. NM_001040444.2NP_001035534.1  PHD finger protein 11 isoform b

    See identical proteins and their annotated locations for NP_001035534.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AA765949, AK026228, DB050568
    Consensus CDS
    CCDS41887.1
    UniProtKB/Swiss-Prot
    Q9UIL8
    Related
    ENSP00000417539.1, ENST00000488958.5
    Conserved Domains (1) summary
    cl22851
    Location:6120
    PHD_SF; PHD finger superfamily

RNA

  1. NR_135322.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK026228, AK293242, BX461254
  2. NR_135323.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks the 5' terminal exon, contains two alternate 5' exons, and contains an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK026228, AK225986, DB050568
    Related
    ENST00000465045.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    49495953..49528992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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