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

Gene ID: 11105, updated on 3-Apr-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

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

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