U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Prdm5 PR/SET domain 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 689788, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Prdm5provided by RGD
    Official Full Name
    PR/SET domain 5provided by RGD
    Primary source
    RGD:1588700
    See related
    EnsemblRapid:ENSRNOG00000023679 AllianceGenome:RGD:1588700
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; DNA-binding transcription factor binding activity; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in mitotic cell cycle; regulation of DNA-templated transcription; and regulation of extracellular matrix organization. Predicted to act upstream of or within cellular response to leukemia inhibitory factor; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nuclear body and nucleolus. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in brittle cornea syndrome 2. Orthologous to human PRDM5 (PR/SET domain 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 111.4), Uterus (RPKM 88.2) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Prdm5 in Genome Data Viewer
    Location:
    4q31
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (96405492..96567647)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (95075736..95237921)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (96659062..96810816)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA17 Neighboring gene transfer RNA leucine (anticodon AAG) 20 Neighboring gene RSA-14-44 protein Neighboring gene U6 spliceosomal RNA

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. LncRNA DGCR5 suppresses neuronal apoptosis to improve acute spinal cord injury through targeting PRDM5. Zhang H, et al. Cell Cycle, 2018. PMID 30146926, Free PMC Article
    2. PRDM5 Expression and Essential Role After Acute Spinal Cord Injury in Adult Rat. Liu J, et al. Neurochem Res, 2016 Dec. PMID 27830494
    3. Upregulation of PRDM5 Is Associated with Astrocyte Proliferation and Neuronal Apoptosis Caused by Lipopolysaccharide. Zhang Y, et al. J Mol Neurosci, 2016 May. PMID 27074744
    4. LncRNA MALAT1 Promotes Neuronal Apoptosis During Spinal Cord Injury Through miR-199a-5p/ PRDM5 Axis. Guo X, et al. Turk Neurosurg, 2024. PMID 35253153
    5. Knockdown of lncRNA BDNF-AS suppresses neuronal cell apoptosis via downregulating miR-130b-5p target gene PRDM5 in acute spinal cord injury. Zhang H, et al. RNA Biol, 2018. PMID 29995562, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA MALAT1 Promotes Neuronal Apoptosis During Spinal Cord Injury Through miR-199a-5p/ PRDM5 Axis.
      Title: LncRNA MALAT1 Promotes Neuronal Apoptosis During Spinal Cord Injury Through miR-199a-5p/ PRDM5 Axis.
    2. DGCR5 suppresses neuronal apoptosis through directly binding and negatively regulating PRDM5.
      Title: LncRNA DGCR5 suppresses neuronal apoptosis to improve acute spinal cord injury through targeting PRDM5.
    3. High PRDM5 expression is associated with acute spinal cord injury.
      Title: Knockdown of lncRNA BDNF-AS suppresses neuronal cell apoptosis via downregulating miR-130b-5p target gene PRDM5 in acute spinal cord injury.
    4. PRDM5 might play crucial roles in CNS pathophysiology after spinal cord injury
      Title: PRDM5 Expression and Essential Role After Acute Spinal Cord Injury in Adult Rat.
    5. PRDM5 expression was increased in activated astrocytes and apoptotic neurons of the adult rat cerebral cortex after LPS injection. PRDM5 was required for astrocyte proliferation and neuronal apoptosis induced by LPS.
      Title: Upregulation of PRDM5 Is Associated with Astrocyte Proliferation and Neuronal Apoptosis Caused by Lipopolysaccharide.
    Submit: New GeneRIF Correction

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of extracellular matrix organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    PR domain zinc finger protein 5
    Names
    PR domain 5
    PR domain containing 5
    NP_001414444.1
    XP_038964623.1
    XP_038964624.1
    XP_063142791.1
    XP_063142792.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    mRNA and Protein(s)

    1. NM_001427515.1 → NP_001414444.1  PR domain zinc finger protein 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A0A8I5ZQN7, A6KF30
      Related
      ENSRNOP00000080705.2, ENSRNOT00000113591.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      96405492..96567647
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063286722.1 → XP_063142792.1  PR domain zinc finger protein 5 isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZQN7

    2. XM_063286721.1 → XP_063142791.1  PR domain zinc finger protein 5 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AMS1
      Related
      ENSRNOP00000095499.1, ENSRNOT00000095255.2

    3. XM_039108695.2 → XP_038964623.1  PR domain zinc finger protein 5 isoform X1

      UniProtKB/TrEMBL
      D3ZRZ9
      Related
      ENSRNOP00000009569.8, ENSRNOT00000009569.10
      Conserved Domains (3) summary
      COG5048
      Location:186 → 509
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:432 → 452
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19190
      Location:2 → 128
      PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins

    4. XM_039108696.2 → XP_038964624.1  PR domain zinc finger protein 5 isoform X2

      Conserved Domains (2) summary
      COG5048
      Location:47 → 451
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:321 → 341
      ZF_C2H2; C2H2 Zn finger [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools