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PHF19 PHD finger protein 19 [ Homo sapiens (human) ]

Gene ID: 26147, updated on 7-Oct-2018

Summary

Official Symbol
PHF19provided by HGNC
Official Full Name
PHD finger protein 19provided by HGNC
Primary source
HGNC:HGNC:24566
See related
Ensembl:ENSG00000119403 MIM:609740; Vega:OTTHUMG00000020577
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
PCL3; MTF2L1; TDRD19B
Expression
Ubiquitous expression in lymph node (RPKM 8.7), ovary (RPKM 6.6) and 24 other tissues See more
Orthologs

Genomic context

See PHF19 in Genome Data Viewer
Location:
9q33.2
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (120855651..120902160, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (123617929..123657168, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, non-ATPase 5 Neighboring gene Sharpr-MPRA regulatory regions 2033 and 13781 Neighboring gene cutA divalent cation tolerance homolog-like, pseudogene Neighboring gene TNF receptor associated factor 1 Neighboring gene C5 3'UTR overlapping transcript 1 Neighboring gene complement C5

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
NHGRI GWA Catalog
Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans.
NHGRI GWA Catalog
REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis.
NHGRI GWA Catalog

Pathways from BioSystems

  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • PRC2 methylates histones and DNA, organism-specific biosystem (from REACTOME)
    PRC2 methylates histones and DNA, organism-specific biosystemPolycomb group proteins are responsible for the heritable repression of genes during development (Lee et al. 2006, Ku et al. 2008, reviewed in Simon and Kingston 2009, Margueron and Reinberg 2011, Di...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC23929, MGC131698, MGC149712, MGC149713

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to nucleosome binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
negative regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
positive regulation of histone H3-K27 methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of histone H3-K27 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with ESC/E(Z) complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with ESC/E(Z) complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
PHD finger protein 19
Names
polycomb like 3
polycomb-like protein 3
tudor domain containing 19B

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_001009936.2NP_001009936.1  PHD finger protein 19 isoform b

    See identical proteins and their annotated locations for NP_001009936.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains alternate exon structure in both the 5' and 3' regions, and it thus differs in both UTRs, initiates translation from a downstream in-frame start codon, and includes an alternate 3' coding region, compared to variant 3. The encoded isoform (b, also known as hPCL3S) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform c.
    Source sequence(s)
    AI369987, BC022374, BM784783
    Consensus CDS
    CCDS35117.1
    UniProtKB/Swiss-Prot
    Q5T6S3
    Related
    ENSP00000310372.6, OTTHUMP00000021998, ENST00000312189.10, OTTHUMT00000053840
    Conserved Domains (2) summary
    smart00333
    Location:3887
    TUDOR; Tudor domain
    cd15579
    Location:98150
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
  2. NM_001286840.1NP_001273769.1  PHD finger protein 19 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).
    Source sequence(s)
    AI193743, AK303433, BC044224, BU632411, BX640713
    Consensus CDS
    CCDS75889.1
    UniProtKB/Swiss-Prot
    Q5T6S3
    UniProtKB/TrEMBL
    A0A087X169, B7Z8H3
    Related
    ENSP00000483946.1, ENST00000616568.5
    Conserved Domains (4) summary
    smart00333
    Location:57106
    TUDOR; Tudor domain
    cd15579
    Location:117169
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
    cd15581
    Location:216267
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:550596
    Mtf2_C; Polycomb-like MTF2 factor 2
  3. NM_001286842.1NP_001273771.1  PHD finger protein 19 isoform d

    See identical proteins and their annotated locations for NP_001273771.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks several 5' exons but includes an alternate 5' terminal exon, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 3. The encoded isoform (d) is shorter at the N-terminus, compared to isoform c.
    Source sequence(s)
    AI193743, AK302996, BC044224, BU632411, HY013521
    Consensus CDS
    CCDS69648.1
    UniProtKB/TrEMBL
    B7Z887, F5H8K3
    Related
    ENSP00000407433.1, ENST00000419155.5
    Conserved Domains (2) summary
    pfam14061
    Location:322368
    Mtf2_C; Polycomb-like MTF2 factor 2
    cl22851
    Location:139
    PHD_SF; PHD finger superfamily
  4. NM_001286843.1NP_001273772.1  PHD finger protein 19 isoform e

    See identical proteins and their annotated locations for NP_001273772.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains alternate exon structure in both the 5' and 3' regions, and it thus differs in both UTRs, initiates translation from a downstream in-frame start codon, and includes an alternate 3' coding region, compared to variant 3. The encoded isoform (e) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform c.
    Source sequence(s)
    AI369987, BC022374, BC108663, BM784783
    UniProtKB/Swiss-Prot
    Q5T6S3
    Related
    ENSP00000397935.1, OTTHUMP00000021999, ENST00000456291.1, OTTHUMT00000053842
    Conserved Domains (2) summary
    smart00333
    Location:3887
    TUDOR; Tudor domain
    cl22851
    Location:98124
    PHD_SF; PHD finger superfamily
  5. NM_015651.2NP_056466.1  PHD finger protein 19 isoform a

    See identical proteins and their annotated locations for NP_056466.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) uses an alternate 5' terminal exon and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 3. The encoded isoform (a, also known as hPCL3L) is shorter at the N-terminus, compared to isoform c.
    Source sequence(s)
    AI193743, BC044224, BC125076, BM784783, BU632411
    Consensus CDS
    CCDS35116.1
    UniProtKB/Swiss-Prot
    Q5T6S3
    Related
    ENSP00000363003.3, OTTHUMP00000021996, ENST00000373896.7, OTTHUMT00000053838
    Conserved Domains (4) summary
    smart00333
    Location:3887
    TUDOR; Tudor domain
    cd15579
    Location:98150
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
    cd15581
    Location:197248
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:531577
    Mtf2_C; Polycomb-like MTF2 factor 2

RNA

  1. NR_104601.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks several 5' exons but includes an alternate 5' terminal exon, and it also lacks an alternate exon in the 3' region, compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI193743, BC044224, BU632411, HY013521

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_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    120855651..120902160 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447505.1XP_024303273.1  PHD finger protein 19 isoform X4

    Conserved Domains (2) summary
    cd15581
    Location:53104
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:387433
    Mtf2_C; Polycomb-like MTF2 factor 2
  2. XM_024447504.1XP_024303272.1  PHD finger protein 19 isoform X4

    Conserved Domains (2) summary
    cd15581
    Location:53104
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:387433
    Mtf2_C; Polycomb-like MTF2 factor 2
  3. XM_024447507.1XP_024303275.1  PHD finger protein 19 isoform X6

    Conserved Domains (2) summary
    cd15581
    Location:2475
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:358404
    Mtf2_C; Polycomb-like MTF2 factor 2
  4. XM_005251906.3XP_005251963.1  PHD finger protein 19 isoform X1

    See identical proteins and their annotated locations for XP_005251963.1

    UniProtKB/Swiss-Prot
    Q5T6S3
    Conserved Domains (4) summary
    smart00333
    Location:3887
    TUDOR; Tudor domain
    cd15579
    Location:98150
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
    cd15581
    Location:197248
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:531577
    Mtf2_C; Polycomb-like MTF2 factor 2
  5. XM_024447506.1XP_024303274.1  PHD finger protein 19 isoform X4

    Conserved Domains (2) summary
    cd15581
    Location:53104
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:387433
    Mtf2_C; Polycomb-like MTF2 factor 2
  6. XM_017014612.2XP_016870101.1  PHD finger protein 19 isoform X1

    UniProtKB/Swiss-Prot
    Q5T6S3
    Conserved Domains (4) summary
    smart00333
    Location:3887
    TUDOR; Tudor domain
    cd15579
    Location:98150
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
    cd15581
    Location:197248
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:531577
    Mtf2_C; Polycomb-like MTF2 factor 2
  7. XM_011518509.3XP_011516811.1  PHD finger protein 19 isoform X1

    See identical proteins and their annotated locations for XP_011516811.1

    UniProtKB/Swiss-Prot
    Q5T6S3
    Conserved Domains (4) summary
    smart00333
    Location:3887
    TUDOR; Tudor domain
    cd15579
    Location:98150
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
    cd15581
    Location:197248
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:531577
    Mtf2_C; Polycomb-like MTF2 factor 2
  8. XM_011518511.2XP_011516813.1  PHD finger protein 19 isoform X2

    Conserved Domains (3) summary
    smart00333
    Location:57106
    TUDOR; Tudor domain
    cd15579
    Location:117169
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
    cd15581
    Location:216267
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
  9. XM_011518515.2XP_011516817.1  PHD finger protein 19 isoform X5

    Conserved Domains (3) summary
    smart00333
    Location:57106
    TUDOR; Tudor domain
    cd15579
    Location:117169
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
    cd15581
    Location:216267
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
  10. XM_017014613.1XP_016870102.1  PHD finger protein 19 isoform X3

  11. XM_011518516.2XP_011516818.1  PHD finger protein 19 isoform X7

    Conserved Domains (3) summary
    smart00333
    Location:57106
    TUDOR; Tudor domain
    cd15579
    Location:117169
    PHD1_PHF19; PHD finger 1 found in PHD finger protein 19 (PHF19)
    cd15581
    Location:216267
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)

RNA

  1. XR_929758.3 RNA Sequence

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