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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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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)

    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.

    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