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

Gene ID: 56981, updated on 17-Sep-2024

Summary

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 transcription, DNA-templated. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 2.3), ovary (RPKM 1.9) and 24 other tissues See more
Orthologs
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Genomic context

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

Expression

  • Project title: HPA RNA-seq normal tissues 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

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ14242

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 
Component Evidence Code Pubs
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

Preferred Names
PR domain-containing protein 11
Names
PR-domain containing protein 11

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_001256695.2NP_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:109235
    PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
  2. NM_001256696.2NP_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:109235
    PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
  3. NM_001359633.2NP_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:109235
    PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
  4. NM_001384648.1NP_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:109235
    PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
  5. NM_001384649.1NP_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:334404
    PHA03247; large tegument protein UL36; Provisional
    cl40432
    Location:109235
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  6. NM_001384650.1NP_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:334404
    PHA03247; large tegument protein UL36; Provisional
    cl40432
    Location:109235
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  7. NM_001384651.1NP_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:334404
    PHA03247; large tegument protein UL36; Provisional
    cl40432
    Location:109235
    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_011520225.3XP_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:109235
    PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
  2. XM_011520222.3XP_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:109235
    PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
  3. XM_011520228.4XP_011518530.1  PR domain-containing protein 11 isoform X3

    Conserved Domains (1) summary
    smart00317
    Location:129230
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  4. XM_011520224.4XP_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:109235
    PR-SET_PRDM11; PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins
  5. XM_047427314.1XP_047283270.1  PR domain-containing protein 11 isoform X5

    UniProtKB/Swiss-Prot
    Q8N9F1, Q9NQV5
  6. XM_047427313.1XP_047283269.1  PR domain-containing protein 11 isoform X4

    UniProtKB/TrEMBL
    H3BSZ2
  7. XM_011520226.3XP_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:195327
    Phage-scaffold; Bacteriophage, scaffolding protein
    cl02566
    Location:147
    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_054369438.1XP_054225413.1  PR domain-containing protein 11 isoform X1

    UniProtKB/TrEMBL
    A0A087WWZ6
  2. XM_054369436.1XP_054225411.1  PR domain-containing protein 11 isoform X1

    UniProtKB/TrEMBL
    A0A087WWZ6
  3. XM_054369440.1XP_054225415.1  PR domain-containing protein 11 isoform X3

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

    UniProtKB/TrEMBL
    A0A087WWZ6
  5. XM_054369442.1XP_054225417.1  PR domain-containing protein 11 isoform X5

    UniProtKB/Swiss-Prot
    Q8N9F1, Q9NQV5
  6. XM_054369441.1XP_054225416.1  PR domain-containing protein 11 isoform X4

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