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

Gene ID: 26147, updated on 17-Jun-2024

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; AllianceGenome:HGNC:24566
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
Summary
Enables methylated histone binding activity. Involved in positive regulation of histone H3-K27 methylation. Colocalizes with ESC/E(Z) complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 8.7), ovary (RPKM 6.6) and 24 other tissues See more
Orthologs
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Genomic context

See PHF19 in Genome Data Viewer
Location:
9q33.2
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (120855651..120904128, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (133051794..133091037, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (123617929..123657174, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr9:123587005-123587204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123595637-123596180 Neighboring gene proteasome 26S subunit, non-ATPase 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123603211-123603712 Neighboring gene Sharpr-MPRA regulatory regions 2033 and 13781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123618013-123618514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123618515-123619014 Neighboring gene cutA divalent cation tolerance like, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20224 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:123635243-123635866 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:123635867-123636492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:123638303-123638894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28901 Neighboring gene CRISPRi-validated cis-regulatory element chr9.2278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123675790-123676294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:123687703-123688226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28909 Neighboring gene TNF receptor associated factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28912 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:123725569-123725752 Neighboring gene C5 3' UTR overlapping transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28913 Neighboring gene complement C5 Neighboring gene uncharacterized LOC124902261

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

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC23929, MGC131698, MGC149712, MGC149713

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in negative regulation of gene expression, epigenetic IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in stem cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of ESC/E(Z) complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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)

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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.

mRNA and Protein(s)

  1. NM_001009936.3NP_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
    Consensus CDS
    CCDS35117.1
    UniProtKB/Swiss-Prot
    Q5T6S3
    Related
    ENSP00000310372.6, ENST00000312189.10
    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/TrEMBL
    A0A087X169, B3KV88
    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:322369
    Mtf2_C; Polycomb-like MTF2 factor 2
    cl22851
    Location:139
    PHD_SF; PHD finger superfamily
  4. NM_001286843.2NP_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
    UniProtKB/TrEMBL
    X6RER8
    Related
    ENSP00000397935.1, ENST00000456291.1
    Conserved Domains (2) summary
    smart00333
    Location:3887
    TUDOR; Tudor domain
    cl22851
    Location:98124
    PHD_SF; PHD finger superfamily
  5. NM_015651.3NP_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
    Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
    UniProtKB/TrEMBL
    B3KV88
    Related
    ENSP00000363003.3, ENST00000373896.8
    Conserved Domains (4) summary
    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:531578
    Mtf2_C; Polycomb-like MTF2 factor 2
    cd20451
    Location:3995
    Tudor_PHF19; Tudor domain found in PHD finger protein1 (PHF19) and similar proteins

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: GCF_000001405.40-RS_2023_10

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
    120855651..120904128 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014612.3XP_016870101.1  PHD finger protein 19 isoform X2

    UniProtKB/Swiss-Prot
    Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
    UniProtKB/TrEMBL
    B3KV88
    Conserved Domains (4) summary
    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:531578
    Mtf2_C; Polycomb-like MTF2 factor 2
    cd20451
    Location:3995
    Tudor_PHF19; Tudor domain found in PHD finger protein1 (PHF19) and similar proteins
  2. XM_005251906.4XP_005251963.2  PHD finger protein 19 isoform X1

    UniProtKB/TrEMBL
    B3KV88
  3. XM_011518509.4XP_011516811.1  PHD finger protein 19 isoform X2

    See identical proteins and their annotated locations for XP_011516811.1

    UniProtKB/Swiss-Prot
    Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
    UniProtKB/TrEMBL
    B3KV88
    Conserved Domains (4) summary
    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:531578
    Mtf2_C; Polycomb-like MTF2 factor 2
    cd20451
    Location:3995
    Tudor_PHF19; Tudor domain found in PHD finger protein1 (PHF19) and similar proteins
  4. XM_047423211.1XP_047279167.1  PHD finger protein 19 isoform X5

    UniProtKB/TrEMBL
    B7Z887
  5. XM_024447507.2XP_024303275.1  PHD finger protein 19 isoform X5

    UniProtKB/TrEMBL
    B7Z887
    Conserved Domains (2) summary
    cd15581
    Location:2475
    PHD2_PHF19; PHD finger 2 found in PHD finger protein 19 (PHF19)
    pfam14061
    Location:358405
    Mtf2_C; Polycomb-like MTF2 factor 2
  6. XM_047423210.1XP_047279166.1  PHD finger protein 19 isoform X3

  7. XM_011518515.3XP_011516817.1  PHD finger protein 19 isoform X4

    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)
  8. XM_011518516.3XP_011516818.1  PHD finger protein 19 isoform X6

    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)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    133051794..133091037 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362697.1XP_054218672.1  PHD finger protein 19 isoform X2

    UniProtKB/Swiss-Prot
    Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
    UniProtKB/TrEMBL
    B3KV88
  2. XM_054362698.1XP_054218673.1  PHD finger protein 19 isoform X2

    UniProtKB/Swiss-Prot
    Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
    UniProtKB/TrEMBL
    B3KV88
  3. XM_054362701.1XP_054218676.1  PHD finger protein 19 isoform X5

    UniProtKB/TrEMBL
    B7Z887
  4. XM_054362702.1XP_054218677.1  PHD finger protein 19 isoform X5

    UniProtKB/TrEMBL
    B7Z887
  5. XM_054362699.1XP_054218674.1  PHD finger protein 19 isoform X3

  6. XM_054362700.1XP_054218675.1  PHD finger protein 19 isoform X4

  7. XM_054362703.1XP_054218678.1  PHD finger protein 19 isoform X6