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

Gene ID: 56981, updated on 12-Oct-2019

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
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
Expression
Ubiquitous expression in thyroid (RPKM 2.3), ovary (RPKM 1.9) and 24 other tissues See more
Orthologs

Genomic context

See PRDM11 in Genome Data Viewer
Location:
11p11.2
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (45094013..45235124)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45115564..45256675)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376649 Neighboring gene long intergenic non-protein coding RNA 2685 Neighboring gene uncharacterized LOC105376650 Neighboring gene uncharacterized LOC105376652 Neighboring gene uncharacterized LOC101060179 Neighboring gene synaptotagmin 13 Neighboring gene Sharpr-MPRA regulatory region 11350

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ14242

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
core promoter binding IDA
Inferred from Direct Assay
more info
PubMed 
methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell growth IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of fibroblast apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of MAPK cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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

    See identical proteins and their annotated locations for NP_001243624.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). There are currently no full-length transcripts representing the exon combination of this variant; the extended 3' end is predicted based on partial human and homologous transcript alignments, on RNA-Seq data, and on bioinformatics analysis in http://genomewiki.ucsc.edu/index.php/PRDM11:_giant_missing_exon.
    Source sequence(s)
    AC103681, AK094792, AW665411, DR731303
    Consensus CDS
    CCDS73277.1
    UniProtKB/Swiss-Prot
    Q9NQV5
    UniProtKB/TrEMBL
    A0A087WWZ6
    Related
    ENSP00000480626.1, ENST00000622142.5
    Conserved Domains (2) summary
    smart00317
    Location:129230
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam09306
    Location:378510
    Phage-scaffold; Bacteriophage, scaffolding protein
  2. NM_001256696.1NP_001243625.1  PR domain-containing protein 11 isoform 2

    See identical proteins and their annotated locations for NP_001243625.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate terminal exon and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AA468074, AC103681, AK094792
    Consensus CDS
    CCDS58130.1
    UniProtKB/Swiss-Prot
    Q9NQV5
    Related
    ENSP00000394314.2, ENST00000424263.6
    Conserved Domains (1) summary
    smart00317
    Location:129230
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  3. NM_001359633.1NP_001346562.1  PR domain-containing protein 11 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AA468074, AC103681, AF275818
    Consensus CDS
    CCDS7912.1
    Related
    ENSP00000435976.1, ENST00000530656.5
    Conserved Domains (1) summary
    smart00317
    Location:163264
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    45094013..45235124
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520223.2XP_011518525.1  PR domain-containing protein 11 isoform X1

    See identical proteins and their annotated locations for XP_011518525.1

    UniProtKB/TrEMBL
    A0A087WWZ6
    Conserved Domains (2) summary
    smart00317
    Location:129230
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam09306
    Location:378510
    Phage-scaffold; Bacteriophage, scaffolding protein
  2. XM_011520225.2XP_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 (2) summary
    smart00317
    Location:129230
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam09306
    Location:378510
    Phage-scaffold; Bacteriophage, scaffolding protein
  3. XM_011520224.3XP_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 (2) summary
    smart00317
    Location:129230
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam09306
    Location:378510
    Phage-scaffold; Bacteriophage, scaffolding protein
  4. XM_011520222.2XP_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 (2) summary
    smart00317
    Location:129230
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam09306
    Location:378510
    Phage-scaffold; Bacteriophage, scaffolding protein
  5. XM_011520228.3XP_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
  6. XM_011520226.2XP_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
  7. XM_011520227.2XP_011518529.1  PR domain-containing protein 11 isoform X2

    See identical proteins and their annotated locations for XP_011518529.1

    Conserved Domains (2) summary
    pfam09306
    Location:195327
    Phage-scaffold; Bacteriophage, scaffolding protein
    cl02566
    Location:147
    SET; SET domain
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