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    PRDM7 PR/SET domain 7 [ Homo sapiens (human) ]

    Gene ID: 11105, updated on 17-Jun-2024

    Summary

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    Official Symbol
    PRDM7provided by HGNC
    Official Full Name
    PR/SET domain 7provided by HGNC
    Primary source
    HGNC:HGNC:9351
    See related
    Ensembl:ENSG00000126856 MIM:609759; AllianceGenome:HGNC:9351
    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
    PFM4; ZNF910
    Summary
    This gene encodes a member of a family of proteins that may have roles in transcription and other nuclear processes. The encoded protein contains a KRAB (Kruppel-associated box) domain -A box and a SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain and may function as a histone methyltransferase. [provided by RefSeq, Aug 2013]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See PRDM7 in Genome Data Viewer
    Location:
    16q24.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (90056566..90077331, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (96142849..96163610, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (90122974..90143739, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene growth arrest specific 8 Neighboring gene GAS8 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:90112831-90113344 Neighboring gene urate (hydroxyiso-) hydrolase, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:90123853-90125052 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:90148312-90148967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:90148968-90149622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:90159897-90160670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:90160671-90161443 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:90164228-90164378 Neighboring gene tubulin beta 8 class VIII pseudogene 7 Neighboring gene uncharacterized LOC105376786

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. PR Domain-containing Protein 7 (PRDM7) Is a Histone 3 Lysine 4 Trimethyltransferase. Blazer LL, et al. J Biol Chem, 2016 Jun 24. PMID 27129774, Free PMC Article
    2. Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. Fumasoni I, et al. BMC Evol Biol, 2007 Oct 4. PMID 17916234, Free PMC Article
    3. The yin-yang of PR-domain family genes in tumorigenesis. Jiang GL, et al. Histol Histopathol, 2000 Jan. PMID 10668202
    4. SET domains and histone methylation. Xiao B, et al. Curr Opin Struct Biol, 2003 Dec. PMID 14675547
    5. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. Sun XJ, et al. PLoS One, 2008 Jan 30. PMID 18231586, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of PR domain containing 7 (PRDM7) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC129525

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H3K36 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables recombination hotspot binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of reciprocal meiotic recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase PRDM7
    Names
    PR domain 7
    PR domain containing 7
    PR domain zinc finger protein 7
    PR-domain family protein 4
    [histone H3]-lysine4 N-methyltransferase PRDM7
    probable histone-lysine N-methyltransferase PRDM7
    NP_001091643.1
    XP_011521131.1
    XP_011521133.1
    XP_016878371.1
    XP_016878372.1
    XP_016878373.1
    XP_054235407.1
    XP_054235408.1
    XP_054235409.1
    XP_054235410.1
    XP_054235411.1

    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_001098173.2 → NP_001091643.1  histone-lysine N-methyltransferase PRDM7

      See identical proteins and their annotated locations for NP_001091643.1

      Status: REVIEWED

      Source sequence(s)
      AC133919, AF274348, AM690991
      Consensus CDS
      CCDS45557.1
      UniProtKB/Swiss-Prot
      A4Q9G8, Q08EM4, Q9NQW4, Q9NQW5
      Related
      ENSP00000396732.2, ENST00000449207.8
      Conserved Domains (4) summary
      smart00317
      Location:246 → 364
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00349
      Location:27 → 85
      KRAB; krueppel associated box
      pfam01352
      Location:27 → 64
      KRAB; KRAB box
      pfam09514
      Location:171 → 201
      SSXRD; SSXRD motif

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      90056566..90077331 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017022883.2 → XP_016878372.1  histone-lysine N-methyltransferase PRDM7 isoform X1

    2. XM_011522829.2 → XP_011521131.1  histone-lysine N-methyltransferase PRDM7 isoform X2

      See identical proteins and their annotated locations for XP_011521131.1

      Conserved Domains (3) summary
      smart00349
      Location:27 → 85
      KRAB; krueppel associated box
      pfam01352
      Location:27 → 64
      KRAB; KRAB box
      pfam09514
      Location:171 → 201
      SSXRD; SSXRD motif

    3. XM_017022882.2 → XP_016878371.1  histone-lysine N-methyltransferase PRDM7 isoform X1

    4. XM_017022884.2 → XP_016878373.1  histone-lysine N-methyltransferase PRDM7 isoform X3

    5. XM_011522831.4 → XP_011521133.1  histone-lysine N-methyltransferase PRDM7 isoform X4

      UniProtKB/TrEMBL
      A4Q9G9
      Related
      ENSP00000455390.1, ENST00000568473.5
      Conserved Domains (2) summary
      smart00349
      Location:27 → 85
      KRAB; krueppel associated box
      pfam01352
      Location:27 → 64
      KRAB; KRAB box

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      96142849..96163610 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379433.1 → XP_054235408.1  histone-lysine N-methyltransferase PRDM7 isoform X1

    2. XM_054379434.1 → XP_054235409.1  histone-lysine N-methyltransferase PRDM7 isoform X2

    3. XM_054379432.1 → XP_054235407.1  histone-lysine N-methyltransferase PRDM7 isoform X1

    4. XM_054379435.1 → XP_054235410.1  histone-lysine N-methyltransferase PRDM7 isoform X3

    5. XM_054379436.1 → XP_054235411.1  histone-lysine N-methyltransferase PRDM7 isoform X4

      UniProtKB/TrEMBL
      A4Q9G9

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_052996.2: Suppressed sequence

      Description
      NM_052996.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQW5.2 GenPept UniProtKB/Swiss-Prot:Q9NQW5

    Gene LinkOut

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