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

    Gene ID: 26147, updated on 3-Jun-2018
    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
    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

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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
    • 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...
    Products Interactant Other Gene Complex Source Pubs Description

    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 
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    Preferred Names
    PHD finger protein 19
    Names
    polycomb like 3
    polycomb-like protein 3
    tudor domain containing 19B

    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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