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PRDM5 PR/SET domain 5 [ Homo sapiens (human) ]

Gene ID: 11107, updated on 18-Nov-2018

Summary

Official Symbol
PRDM5provided by HGNC
Official Full Name
PR/SET domain 5provided by HGNC
Primary source
HGNC:HGNC:9349
See related
Ensembl:ENSG00000138738 MIM:614161; Vega:OTTHUMG00000132970
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
BCS2; PFM2
Summary
The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in ovary (RPKM 2.4), endometrium (RPKM 1.5) and 24 other tissues See more
Orthologs

Genomic context

See PRDM5 in Genome Data Viewer
Location:
4q27
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (120684906..120922866, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (121613070..121844013, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene LTV1 ribosome biogenesis factor pseudogene 1 Neighboring gene secretion associated Ras related GTPase 1A pseudogene 3 Neighboring gene RNA, U6 small nuclear 550, pseudogene Neighboring gene uncharacterized LOC105377399 Neighboring gene SET pseudogene 12 Neighboring gene RNA, 7SK small nuclear pseudogene 137 Neighboring gene neuron derived neurotrophic factor

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Brittle cornea syndrome 2
MedGen: C3280011 OMIM: 614170 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients.
NHGRI GWA Catalog
Genome-wide association with diabetes-related traits in the Framingham Heart Study.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of PR domain containing 5 (PRDM5) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
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 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
repressing transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
repressing transcription factor binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
histone H3-K9 methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K9 methylation IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
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 zinc finger protein 5
Names
PR domain 5
PR domain containing 5
NP_001287752.1
NP_001287753.1
NP_061169.2
XP_005262765.1
XP_011529864.1
XP_011529865.1
XP_011529866.1
XP_011529867.1
XP_011529868.1
XP_011529869.1
XP_011529870.1
XP_011529871.1
XP_011529872.1
XP_016863157.1
XP_016863158.1
XP_016863159.1
XP_016863160.1
XP_024309647.1

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.

Genomic

  1. NG_031862.2 RefSeqGene

    Range
    4993..235946
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001300823.1NP_001287752.1  PR domain zinc finger protein 5 isoform 2

    See identical proteins and their annotated locations for NP_001287752.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AC025741, AF272897, BC066942, BC121037
    Consensus CDS
    CCDS75188.1
    UniProtKB/Swiss-Prot
    Q9NQX1
    Related
    ENSP00000404832.2, OTTHUMP00000219784, ENST00000428209.6, OTTHUMT00000363931
    Conserved Domains (3) summary
    smart00317
    Location:20130
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:174589
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:460480
    ZF_C2H2; C2H2 Zn finger [structural motif]
  2. NM_001300824.1NP_001287753.1  PR domain zinc finger protein 5 isoform 3

    See identical proteins and their annotated locations for NP_001287753.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two exons in the central coding region, one of which results in a frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC025741, BC066942, BC121038
    Consensus CDS
    CCDS75187.1
    UniProtKB/Swiss-Prot
    Q9NQX1
    Related
    ENSP00000422309.1, OTTHUMP00000219783, ENST00000515109.5, OTTHUMT00000363930
    Conserved Domains (4) summary
    COG5048
    Location:145337
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:319339
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
    pfam13465
    Location:304328
    zf-H2C2_2; Zinc-finger double domain
  3. NM_018699.3NP_061169.2  PR domain zinc finger protein 5 isoform 1

    See identical proteins and their annotated locations for NP_061169.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC025741, AF272897, AK314293, BC066942, BC121037
    Consensus CDS
    CCDS3716.1
    UniProtKB/Swiss-Prot
    Q9NQX1
    Related
    ENSP00000264808.3, OTTHUMP00000163922, ENST00000264808.7, OTTHUMT00000256528
    Conserved Domains (4) summary
    COG5048
    Location:262620
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:491511
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
    pfam13465
    Location:532556
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    120684906..120922866 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011531569.3XP_011529871.1  PR domain zinc finger protein 5 isoform X7

    See identical proteins and their annotated locations for XP_011529871.1

    Conserved Domains (3) summary
    COG5048
    Location:225463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:361381
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
  2. XM_011531566.3XP_011529868.1  PR domain zinc finger protein 5 isoform X5

    Conserved Domains (4) summary
    COG5048
    Location:225463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:502522
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
    pfam13465
    Location:543567
    zf-H2C2_2; Zinc-finger double domain
  3. XM_011531563.2XP_011529865.1  PR domain zinc finger protein 5 isoform X3

    Conserved Domains (4) summary
    COG5048
    Location:174600
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:471491
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
    pfam13465
    Location:512536
    zf-H2C2_2; Zinc-finger double domain
  4. XM_011531564.2XP_011529866.1  PR domain zinc finger protein 5 isoform X4

    Conserved Domains (5) summary
    COG5048
    Location:225463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:474494
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:553571
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
    pfam13465
    Location:515538
    zf-H2C2_2; Zinc-finger double domain
  5. XM_011531562.2XP_011529864.1  PR domain zinc finger protein 5 isoform X1

    Conserved Domains (4) summary
    COG5048
    Location:262631
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:502522
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
    pfam13465
    Location:543567
    zf-H2C2_2; Zinc-finger double domain
  6. XM_024453879.1XP_024309647.1  PR domain zinc finger protein 5 isoform X10

    Conserved Domains (3) summary
    COG5048
    Location:221382
    COG5048; FOG: Zn-finger [General function prediction only]
    COG5189
    Location:87161
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:253273
    ZF_C2H2; C2H2 Zn finger [structural motif]
  7. XM_011531570.3XP_011529872.1  PR domain zinc finger protein 5 isoform X9

    Conserved Domains (3) summary
    COG5048
    Location:232393
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:264284
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:305329
    zf-H2C2_2; Zinc-finger double domain
  8. XM_017007668.2XP_016863157.1  PR domain zinc finger protein 5 isoform X2

  9. XM_017007671.1XP_016863160.1  PR domain zinc finger protein 5 isoform X12

  10. XM_017007669.1XP_016863158.1  PR domain zinc finger protein 5 isoform X8

  11. XM_011531567.2XP_011529869.1  PR domain zinc finger protein 5 isoform X7

    See identical proteins and their annotated locations for XP_011529869.1

    Conserved Domains (3) summary
    COG5048
    Location:225463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:361381
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
  12. XM_017007670.1XP_016863159.1  PR domain zinc finger protein 5 isoform X8

  13. XM_011531565.2XP_011529867.1  PR domain zinc finger protein 5 isoform X6

    Conserved Domains (4) summary
    COG5048
    Location:225463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:502522
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
    pfam13465
    Location:543567
    zf-H2C2_2; Zinc-finger double domain
  14. XM_011531568.2XP_011529870.1  PR domain zinc finger protein 5 isoform X7

    See identical proteins and their annotated locations for XP_011529870.1

    Conserved Domains (3) summary
    COG5048
    Location:225463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:361381
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain
  15. XM_005262708.3XP_005262765.1  PR domain zinc finger protein 5 isoform X11

    Conserved Domains (3) summary
    COG5048
    Location:145338
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:269287
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20123
    SET; SET domain

RNA

  1. XR_938677.3 RNA Sequence

  2. XR_938678.1 RNA Sequence

  3. XR_938679.1 RNA Sequence

  4. XR_938680.2 RNA Sequence

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