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    Prdm15 PR domain containing 15 [ Mus musculus (house mouse) ]

    Gene ID: 114604, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Prdm15provided by MGI
    Official Full Name
    PR domain containing 15provided by MGI
    Primary source
    MGI:MGI:1930121
    See related
    Ensembl:ENSMUSG00000014039 AllianceGenome:MGI:1930121
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    ORF62; Zfp298; C21orf83; E130018M06Rik
    Summary
    Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and promoter-specific chromatin binding activity. Involved in positive regulation of transcription by RNA polymerase II; regulation of signal transduction; and regulation of stem cell division. Located in nucleus. Is expressed in several structures, including central nervous system; genitourinary system; incisor; sensory organ; and skin. Orthologous to human PRDM15 (PR/SET domain 15). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 6.0), whole brain E14.5 (RPKM 4.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Prdm15 in Genome Data Viewer
    Location:
    16 C4; 16 57.66 cM
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (97592720..97653076, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (97791467..97851875, complement)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 41513 Neighboring gene receptor-interacting serine-threonine kinase 4 Neighboring gene STARR-seq mESC enhancer starr_41639 Neighboring gene C2 calcium-dependent domain containing 2 Neighboring gene STARR-seq mESC enhancer starr_41640 Neighboring gene microRNA 6964 Neighboring gene zinc finger and BTB domain containing 21 Neighboring gene predicted gene, 53924

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. PRDM15 is a key regulator of metabolism critical to sustain B-cell lymphomagenesis. Mzoughi S, et al. Nat Commun, 2020 Jul 14. PMID 32665551, Free PMC Article
    2. PRDM15 safeguards naive pluripotency by transcriptionally regulating WNT and MAPK-ERK signaling. Mzoughi S, et al. Nat Genet, 2017 Sep. PMID 28740264
    3. Ts65Dn -- localization of the translocation breakpoint and trisomic gene content in a mouse model for Down syndrome. Akeson EC, et al. Cytogenet Cell Genet, 2001. PMID 11528125
    4. PRDM15 loss of function links NOTCH and WNT/PCP signaling to patterning defects in holoprosencephaly. Mzoughi S, et al. Sci Adv, 2020 Jan. PMID 31950080, Free PMC Article
    5. Evolutionary breakpoints on human chromosome 21. Davisson MT, et al. Genomics, 2001 Nov. PMID 11707078

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PRDM15 loss of function links NOTCH and WNT/PCP signaling to patterning defects in holoprosencephaly.
      Title: PRDM15 loss of function links NOTCH and WNT/PCP signaling to patterning defects in holoprosencephaly.
    2. Findings indicate that PR domain containing 15 protein (PRDM15) is important in both mouse and human induced pluripotent stem cells (iPSCs) reprogramming.
      Title: PRDM15 safeguards naive pluripotency by transcriptionally regulating WNT and MAPK-ERK signaling.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (5) 
    • Targeted (3)  1 citation

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables promoter-specific chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of MAPK cascade IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of stem cell division IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 nucleoplasm ISO
    Inferred from Sequence Orthology
    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 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    PR domain zinc finger protein 15
    Names
    PR domain-containing protein 15
    zinc finger protein 298

    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.

    mRNA and Protein(s)

    1. NM_001359077.2 → NP_001346006.1  PR domain zinc finger protein 15 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC121560
      Consensus CDS
      CCDS88979.1
      UniProtKB/Swiss-Prot
      E9Q6A1, E9Q8T2, Q3UML7
      Related
      ENSMUSP00000113791.2, ENSMUST00000121584.8
      Conserved Domains (4) summary
      COG5048
      Location:665 → 834
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:701 → 721
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:12 → 37
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:41 → 166
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins

    2. NM_001359078.2 → NP_001346007.1  PR domain zinc finger protein 15 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC121560
      Conserved Domains (2) summary
      COG5048
      Location:162 → 331
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:198 → 218
      ZF_C2H2; C2H2 Zn finger [structural motif]

    3. NM_001403426.1 → NP_001390355.1  PR domain zinc finger protein 15 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC121560

    4. NM_001403427.1 → NP_001390356.1  PR domain zinc finger protein 15 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC121560

    5. NM_001403428.1 → NP_001390357.1  PR domain zinc finger protein 15 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC121560

    6. NM_001403429.1 → NP_001390358.1  PR domain zinc finger protein 15 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC121560

    7. NM_001403430.1 → NP_001390359.1  PR domain zinc finger protein 15 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC121560

    8. NM_001403431.1 → NP_001390360.1  PR domain zinc finger protein 15 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC121560

    9. NM_001403432.1 → NP_001390361.1  PR domain zinc finger protein 15 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC121560

    10. NM_001403437.2 → NP_001390366.2  PR domain zinc finger protein 15 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC121560

    11. NM_001403438.2 → NP_001390367.2  PR domain zinc finger protein 15 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC121560

    12. NM_144789.3 → NP_659038.3  PR domain zinc finger protein 15 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC121560
      Consensus CDS
      CCDS49926.1
      Related
      ENSMUSP00000093533.4, ENSMUST00000095849.10

    RNA

    1. NR_175376.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC121560
      Related
      ENSMUST00000142295.8

    2. NR_175377.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC121560

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000082.7 Reference GRCm39 C57BL/6J

      Range
      97592720..97653076 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030248930.2 → XP_030104790.1  PR domain zinc finger protein 15 isoform X6

      UniProtKB/Swiss-Prot
      E9Q6A1, E9Q8T2, Q3UML7
      Conserved Domains (4) summary
      COG5048
      Location:662 → 831
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:698 → 718
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:48 → 73
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:77 → 202
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins

    2. XM_006522866.5 → XP_006522929.1  PR domain zinc finger protein 15 isoform X4

      UniProtKB/Swiss-Prot
      E9Q6A1, E9Q8T2, Q3UML7
      Conserved Domains (4) summary
      COG5048
      Location:667 → 836
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:703 → 723
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:48 → 73
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:77 → 202
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins

    3. XM_006522865.5 → XP_006522928.1  PR domain zinc finger protein 15 isoform X3

      UniProtKB/Swiss-Prot
      E9Q6A1, E9Q8T2, Q3UML7
      Conserved Domains (4) summary
      COG5048
      Location:667 → 836
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:703 → 723
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:48 → 73
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:77 → 202
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins

    4. XM_030248931.2 → XP_030104791.1  PR domain zinc finger protein 15 isoform X8

      UniProtKB/Swiss-Prot
      E9Q6A1, E9Q8T2, Q3UML7
      Conserved Domains (4) summary
      COG5048
      Location:631 → 800
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:667 → 687
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam18445
      Location:12 → 37
      zf_PR_Knuckle; PR zinc knuckle motif
      cd19199
      Location:41 → 166
      PR-SET_PRDM15; PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins

    5. XM_030248932.2 → XP_030104792.1  PR domain zinc finger protein 15 isoform X10

      UniProtKB/Swiss-Prot
      E9Q6A1, E9Q8T2, Q3UML7
      Conserved Domains (3) summary
      COG5048
      Location:549 → 718
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:585 → 605
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl40432
      Location:1 → 50
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    6. XM_036159746.1 → XP_036015639.1  PR domain zinc finger protein 15 isoform X12

      Conserved Domains (2) summary
      COG5048
      Location:193 → 362
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:229 → 249
      ZF_C2H2; C2H2 Zn finger [structural motif]

    7. XM_036159745.1 → XP_036015638.1  PR domain zinc finger protein 15 isoform X11

      UniProtKB/Swiss-Prot
      E9Q6A1, E9Q8T2, Q3UML7
      Conserved Domains (3) summary
      COG5048
      Location:510 → 679
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:546 → 566
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl40432
      Location:1 → 50
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    8. XM_006522868.5 → XP_006522931.1  PR domain zinc finger protein 15 isoform X10

      See identical proteins and their annotated locations for XP_006522931.1

      UniProtKB/Swiss-Prot
      E9Q6A1, E9Q8T2, Q3UML7
      Conserved Domains (3) summary
      COG5048
      Location:549 → 718
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:585 → 605
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cl40432
      Location:1 → 50
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily

    RNA

    1. XR_004939145.1 RNA Sequence

    2. XR_384928.5 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    E9Q8T2.1 GenPept UniProtKB/Swiss-Prot:E9Q8T2

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