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

Gene ID: 11107, updated on 5-Mar-2024

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; AllianceGenome:HGNC:9349
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
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Genomic context

See PRDM5 in Genome Data Viewer
Location:
4q27
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (120684291..120922726, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (123965980..124226930, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (121613070..121843881, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene secretion associated Ras related GTPase 1A pseudogene 3 Neighboring gene uncharacterized LOC124900771 Neighboring gene Sharpr-MPRA regulatory region 8715 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72414 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72419 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21861 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:121655223-121655429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:121662174-121662740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:121662741-121663307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21862 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72556 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72587 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72607 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72637 Neighboring gene RNA, U6 small nuclear 550, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr4:121806618-121806798 Neighboring gene uncharacterized LOC105377399 Neighboring gene SET pseudogene 12 Neighboring gene NANOG hESC enhancer GRCh37_chr4:121885637-121886160 Neighboring gene RN7SK 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

EBI GWAS Catalog

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

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
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 zinc finger protein 5
Names
PR domain 5
PR domain containing 5
NP_001287752.1
NP_001287753.1
NP_001366033.1
NP_001366035.1
NP_061169.2
XP_005262765.1
XP_011529865.1
XP_011529866.1
XP_011529867.1
XP_011529868.1
XP_011529870.1
XP_016863157.1
XP_016863159.1
XP_016863160.1
XP_047305510.1
XP_047305511.1
XP_047305512.1
XP_047305513.1
XP_047305514.1
XP_047305515.1
XP_054204795.1
XP_054204796.1
XP_054204797.1
XP_054204798.1
XP_054204799.1
XP_054204800.1
XP_054204801.1
XP_054204802.1
XP_054204803.1
XP_054204804.1
XP_054204805.1
XP_054204806.1
XP_054204807.1
XP_054204808.1
XP_054204809.1

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.

Genomic

  1. NG_031862.3 RefSeqGene

    Range
    5000..235811
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for NP_001287752.1

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Consensus CDS
    CCDS75188.1
    UniProtKB/Swiss-Prot
    Q9NQX1
    Related
    ENSP00000404832.2, ENST00000428209.6
    Conserved Domains (3) summary
    COG5048
    Location:174589
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:460480
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
  2. NM_001300824.2NP_001287753.1  PR domain zinc finger protein 5 isoform 3

    See identical proteins and their annotated locations for NP_001287753.1

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Consensus CDS
    CCDS75187.1
    UniProtKB/Swiss-Prot
    Q9NQX1
    Related
    ENSP00000422309.1, ENST00000515109.5
    Conserved Domains (3) summary
    COG5048
    Location:145337
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:319339
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
  3. NM_001379104.1NP_001366033.1  PR domain zinc finger protein 5 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Conserved Domains (3) summary
    COG5048
    Location:262631
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:502522
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
  4. NM_001379106.1NP_001366035.1  PR domain zinc finger protein 5 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Conserved Domains (5) summary
    COG5048
    Location:145337
    COG5048; FOG: Zn-finger [General function prediction only]
    COG5189
    Location:482559
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:432452
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:511529
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
  5. NM_018699.4NP_061169.2  PR domain zinc finger protein 5 isoform 1

    See identical proteins and their annotated locations for NP_061169.2

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Consensus CDS
    CCDS3716.1
    UniProtKB/Swiss-Prot
    Q0VAI9, Q0VAJ0, Q6NXQ7, Q9NQX1
    Related
    ENSP00000264808.3, ENST00000264808.8
    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]
    cd19190
    Location:2128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
    cd20908
    Location:172220
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    120684291..120922726 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449558.1XP_047305514.1  PR domain zinc finger protein 5 isoform X12

  2. XM_047449557.1XP_047305513.1  PR domain zinc finger protein 5 isoform X10

  3. XM_011531566.4XP_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
  4. XM_011531563.3XP_011529865.1  PR domain zinc finger protein 5 isoform X2

    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
  5. XM_047449554.1XP_047305510.1  PR domain zinc finger protein 5 isoform X4

  6. XM_011531564.3XP_011529866.1  PR domain zinc finger protein 5 isoform X3

    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
  7. XM_017007668.3XP_016863157.1  PR domain zinc finger protein 5 isoform X1

  8. XM_017007671.2XP_016863160.1  PR domain zinc finger protein 5 isoform X15

  9. XM_047449555.1XP_047305511.1  PR domain zinc finger protein 5 isoform X7

  10. XM_011531565.3XP_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
  11. XM_011531568.3XP_011529870.1  PR domain zinc finger protein 5 isoform X9

    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
  12. XM_017007670.2XP_016863159.1  PR domain zinc finger protein 5 isoform X11

    Conserved Domains (4) summary
    COG5048
    Location:264423
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:350370
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
    cd20908
    Location:172220
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  13. XM_047449559.1XP_047305515.1  PR domain zinc finger protein 5 isoform X13

  14. XM_047449556.1XP_047305512.1  PR domain zinc finger protein 5 isoform X8

  15. XM_005262708.4XP_005262765.1  PR domain zinc finger protein 5 isoform X14

    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_938678.2 RNA Sequence

  2. XR_938680.3 RNA Sequence

  3. XR_938679.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    123965980..124226930 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348829.1XP_054204804.1  PR domain zinc finger protein 5 isoform X10

  2. XM_054348830.1XP_054204805.1  PR domain zinc finger protein 5 isoform X12

  3. XM_054348825.1XP_054204800.1  PR domain zinc finger protein 5 isoform X5

  4. XM_054348821.1XP_054204796.1  PR domain zinc finger protein 5 isoform X2

  5. XM_054348823.1XP_054204798.1  PR domain zinc finger protein 5 isoform X4

  6. XM_054348822.1XP_054204797.1  PR domain zinc finger protein 5 isoform X3

  7. XM_054348820.1XP_054204795.1  PR domain zinc finger protein 5 isoform X1

  8. XM_054348834.1XP_054204809.1  PR domain zinc finger protein 5 isoform X15

  9. XM_054348826.1XP_054204801.1  PR domain zinc finger protein 5 isoform X7

  10. XM_054348824.1XP_054204799.1  PR domain zinc finger protein 5 isoform X6

  11. XM_054348828.1XP_054204803.1  PR domain zinc finger protein 5 isoform X9

  12. XM_054348831.1XP_054204806.1  PR domain zinc finger protein 5 isoform X11

  13. XM_054348832.1XP_054204807.1  PR domain zinc finger protein 5 isoform X13

  14. XM_054348827.1XP_054204802.1  PR domain zinc finger protein 5 isoform X8

  15. XM_054348833.1XP_054204808.1  PR domain zinc finger protein 5 isoform X14

RNA

  1. XR_008486889.1 RNA Sequence

  2. XR_008486891.1 RNA Sequence

  3. XR_008486890.1 RNA Sequence