U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    PRDM11 PR/SET domain 11 [ Homo sapiens (human) ]

    Gene ID: 56981, updated on 10-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    PRDM11provided by HGNC
    Official Full Name
    PR/SET domain 11provided by HGNC
    Primary source
    HGNC:HGNC:13996
    See related
    Ensembl:ENSG00000019485 MIM:616347; AllianceGenome:HGNC:13996
    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
    PFM8
    Summary
    Predicted to enable chromatin binding activity. Involved in several processes, including negative regulation of cell growth; positive regulation of fibroblast apoptotic process; and regulation of DNA-templated transcription. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 2.3), ovary (RPKM 1.9) and 24 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See PRDM11 in Genome Data Viewer
    Location:
    11p11.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (45094159..45235109)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (45251156..45392625)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45115710..45256660)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44996027-44996672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44997901-44998858 Neighboring gene long intergenic non-protein coding RNA 2685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45011181-45012070 Neighboring gene uncharacterized LOC105376650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45062883-45063384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45070929-45071428 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:45072318-45072505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45096169-45096784 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:45096785-45097399 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3283 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45103805-45104682 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45104683-45105558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45108817-45109553 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45122734-45123274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45123275-45123813 Neighboring gene Sharpr-MPRA regulatory region 3485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3284 Neighboring gene uncharacterized LOC105376652 Neighboring gene Sharpr-MPRA regulatory region 15340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45149168-45149668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45149669-45150169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45203073-45203804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45230951-45231698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45231699-45232446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45232447-45233193 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45233771-45234633 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45234634-45235495 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45240557-45241118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45241119-45241678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45265182-45265682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45288476-45288976 Neighboring gene synaptotagmin 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45307287-45308073 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:45320242-45320786 Neighboring gene Sharpr-MPRA regulatory region 11350 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:45368824-45369362 Neighboring gene long intergenic non-protein coding RNA 2696

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Loss of PRDM11 promotes MYC-driven lymphomagenesis. Fog CK, et al. Blood, 2015 Feb 19. PMID 25499759
    2. Genome-wide association analysis identifies six new loci associated with forced vital capacity. Loth DW, et al. Nat Genet, 2014 Jul. PMID 24929828, 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. A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function. Porcu E, et al. PLoS Genet, 2013. PMID 23408906, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

    Go to the top of the page Help

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

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
    EBI GWAS Catalog
    Genome-wide association analysis identifies six new loci associated with forced vital capacity.
    EBI GWAS Catalog

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • FLJ14242

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell fate commitment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell growth IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of fibroblast apoptotic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of MAPK cascade IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    PR domain-containing protein 11
    Names
    PR-domain containing protein 11

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001256695.2 → NP_001243624.1  PR domain-containing protein 11 isoform 1

      See identical proteins and their annotated locations for NP_001243624.1

      Status: VALIDATED

      Source sequence(s)
      AC103681
      Consensus CDS
      CCDS73277.1
      UniProtKB/TrEMBL
      A0A087WWZ6
      Related
      ENSP00000480626.1, ENST00000622142.5
      Conserved Domains (1) summary
      cd19195
      Location:109 → 235
      PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins

    2. NM_001256696.2 → NP_001243625.1  PR domain-containing protein 11 isoform 2

      See identical proteins and their annotated locations for NP_001243625.1

      Status: VALIDATED

      Source sequence(s)
      AC103681
      Consensus CDS
      CCDS58130.1
      UniProtKB/Swiss-Prot
      Q8N9F1, Q9NQV5
      Related
      ENSP00000394314.2, ENST00000424263.6
      Conserved Domains (1) summary
      cd19195
      Location:109 → 235
      PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins

    3. NM_001359633.2 → NP_001346562.2  PR domain-containing protein 11 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC103681, AC103682
      Consensus CDS
      CCDS58130.1
      UniProtKB/Swiss-Prot
      Q8N9F1, Q9NQV5
      Related
      ENSP00000435976.2, ENST00000530656.5
      Conserved Domains (1) summary
      cd19195
      Location:109 → 235
      PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins

    4. NM_001384648.1 → NP_001371577.1  PR domain-containing protein 11 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC103681
      Consensus CDS
      CCDS73277.1
      UniProtKB/TrEMBL
      A0A087WWZ6
      Related
      ENSP00000507575.1, ENST00000683152.1
      Conserved Domains (1) summary
      cd19195
      Location:109 → 235
      PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins

    5. NM_001384649.1 → NP_001371578.1  PR domain-containing protein 11 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC103681
      Consensus CDS
      CCDS91463.1
      UniProtKB/TrEMBL
      H3BSZ2
      Related
      ENSP00000456942.2, ENST00000534751.3
      Conserved Domains (2) summary
      PHA03247
      Location:334 → 404
      PHA03247; large tegument protein UL36; Provisional
      cl40432
      Location:109 → 235
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    6. NM_001384650.1 → NP_001371579.1  PR domain-containing protein 11 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC103681
      Consensus CDS
      CCDS91463.1
      UniProtKB/TrEMBL
      H3BSZ2
      Conserved Domains (2) summary
      PHA03247
      Location:334 → 404
      PHA03247; large tegument protein UL36; Provisional
      cl40432
      Location:109 → 235
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    7. NM_001384651.1 → NP_001371580.1  PR domain-containing protein 11 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC103681
      Consensus CDS
      CCDS91463.1
      UniProtKB/TrEMBL
      H3BSZ2
      Conserved Domains (2) summary
      PHA03247
      Location:334 → 404
      PHA03247; large tegument protein UL36; Provisional
      cl40432
      Location:109 → 235
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      45094159..45235109
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520225.3 → XP_011518527.1  PR domain-containing protein 11 isoform X1

      See identical proteins and their annotated locations for XP_011518527.1

      UniProtKB/TrEMBL
      A0A087WWZ6
      Conserved Domains (1) summary
      cd19195
      Location:109 → 235
      PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins

    2. XM_011520222.3 → XP_011518524.1  PR domain-containing protein 11 isoform X1

      See identical proteins and their annotated locations for XP_011518524.1

      UniProtKB/TrEMBL
      A0A087WWZ6
      Conserved Domains (1) summary
      cd19195
      Location:109 → 235
      PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins

    3. XM_011520228.4 → XP_011518530.1  PR domain-containing protein 11 isoform X3

      Conserved Domains (1) summary
      smart00317
      Location:129 → 230
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

    4. XM_011520224.4 → XP_011518526.1  PR domain-containing protein 11 isoform X1

      See identical proteins and their annotated locations for XP_011518526.1

      UniProtKB/TrEMBL
      A0A087WWZ6
      Conserved Domains (1) summary
      cd19195
      Location:109 → 235
      PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins

    5. XM_047427314.1 → XP_047283270.1  PR domain-containing protein 11 isoform X5

      UniProtKB/Swiss-Prot
      Q8N9F1, Q9NQV5

    6. XM_047427313.1 → XP_047283269.1  PR domain-containing protein 11 isoform X4

      UniProtKB/TrEMBL
      H3BSZ2

    7. XM_011520226.3 → XP_011518528.1  PR domain-containing protein 11 isoform X2

      See identical proteins and their annotated locations for XP_011518528.1

      Conserved Domains (2) summary
      pfam09306
      Location:195 → 327
      Phage-scaffold; Bacteriophage, scaffolding protein
      cl02566
      Location:1 → 47
      SET; SET domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      45251156..45392625
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369438.1 → XP_054225413.1  PR domain-containing protein 11 isoform X1

      UniProtKB/TrEMBL
      A0A087WWZ6

    2. XM_054369436.1 → XP_054225411.1  PR domain-containing protein 11 isoform X1

      UniProtKB/TrEMBL
      A0A087WWZ6

    3. XM_054369440.1 → XP_054225415.1  PR domain-containing protein 11 isoform X3

    4. XM_054369437.1 → XP_054225412.1  PR domain-containing protein 11 isoform X1

      UniProtKB/TrEMBL
      A0A087WWZ6

    5. XM_054369442.1 → XP_054225417.1  PR domain-containing protein 11 isoform X5

      UniProtKB/Swiss-Prot
      Q8N9F1, Q9NQV5

    6. XM_054369441.1 → XP_054225416.1  PR domain-containing protein 11 isoform X4

    7. XM_054369439.1 → XP_054225414.1  PR domain-containing protein 11 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQV5.2 GenPept UniProtKB/Swiss-Prot:Q9NQV5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools