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Prdm4 PR domain containing 4 [ Mus musculus (house mouse) ]

Gene ID: 72843, updated on 5-Mar-2024

Summary

Official Symbol
Prdm4provided by MGI
Official Full Name
PR domain containing 4provided by MGI
Primary source
MGI:MGI:1920093
See related
Ensembl:ENSMUSG00000035529 AllianceGenome:MGI:1920093
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
SC1; SC-1; 1700031E19Rik; 2810470D21Rik
Summary
This gene encodes a member of the PR/SET family of zinc finger proteins. This protein has been shown to bind DNA in a sequence-specific manner and has been implicated in neural stem cell proliferation and differentiation. Pseudogenes have been identified on chromosomes 14 and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
Expression
Ubiquitous expression in testis adult (RPKM 15.6), whole brain E14.5 (RPKM 14.9) and 28 other tissues See more
Orthologs
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Genomic context

Location:
10 C1; 10 41.75 cM
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (85727828..85752958, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (85891964..85917152, complement)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene uncharacterized protein C12orf73 homolog Neighboring gene PWP1 homolog, endonuclein Neighboring gene STARR-positive B cell enhancer ABC_E723 Neighboring gene achaete-scute family bHLH transcription factor 4 Neighboring gene STARR-seq mESC enhancer starr_27454 Neighboring gene RNA 2',3'-cyclic phosphate and 5'-OH ligase Neighboring gene predicted gene, 48175

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (6)  1 citation
  • Endonuclease-mediated (2) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables death receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables histone methyltransferase binding IPI
Inferred from Physical Interaction
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 sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cell growth ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of neural precursor cell proliferation ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of stem cell differentiation 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
 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
part_of histone methyltransferase complex IPI
Inferred from Physical Interaction
more info
PubMed 
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 4
Names
PR domain-containing protein 4

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_001302886.1NP_001289815.1  PR domain zinc finger protein 4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains a longer 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AK028414, BC057596, CD350319
    Consensus CDS
    CCDS88065.1
    UniProtKB/TrEMBL
    A0A1X7SB67, B7ZP41
    Related
    ENSMUSP00000041942.9, ENSMUST00000037646.9
    Conserved Domains (5) summary
    sd00017
    Location:616636
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:614636
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:628653
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:361398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401533
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
  2. NM_001302887.1NP_001289816.1  PR domain zinc finger protein 4 isoform 3

    See identical proteins and their annotated locations for NP_001289816.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    BC057596, CD350319
    UniProtKB/TrEMBL
    Q8C0V8
    Conserved Domains (5) summary
    sd00017
    Location:434454
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:432454
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:446471
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:172209
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:212351
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
  3. NM_181650.3NP_857633.2  PR domain zinc finger protein 4 isoform 1

    See identical proteins and their annotated locations for NP_857633.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC057596, BC139409, CD350319
    Consensus CDS
    CCDS24093.1
    UniProtKB/Swiss-Prot
    B2RTL4, Q80V63
    UniProtKB/TrEMBL
    B7ZP41
    Conserved Domains (4) summary
    sd00017
    Location:623643
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:361398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401540
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
    pfam13465
    Location:635660
    zf-H2C2_2; Zinc-finger double domain

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_000076.7 Reference GRCm39 C57BL/6J

    Range
    85727828..85752958 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011243582.2XP_011241884.1  PR domain zinc finger protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011241884.1

    UniProtKB/Swiss-Prot
    B2RTL4, Q80V63
    UniProtKB/TrEMBL
    B7ZP41
    Related
    ENSMUSP00000151931.2, ENSMUST00000220032.2
    Conserved Domains (4) summary
    sd00017
    Location:623643
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:361398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401540
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
    pfam13465
    Location:635660
    zf-H2C2_2; Zinc-finger double domain
  2. XM_006514194.4XP_006514257.1  PR domain zinc finger protein 4 isoform X1

    See identical proteins and their annotated locations for XP_006514257.1

    UniProtKB/Swiss-Prot
    B2RTL4, Q80V63
    UniProtKB/TrEMBL
    B7ZP41
    Conserved Domains (4) summary
    sd00017
    Location:623643
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18445
    Location:361398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401540
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
    pfam13465
    Location:635660
    zf-H2C2_2; Zinc-finger double domain
  3. XM_006514197.4XP_006514260.1  PR domain zinc finger protein 4 isoform X3

    UniProtKB/TrEMBL
    Q8R3B9
    Conserved Domains (5) summary
    sd00017
    Location:557577
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:555577
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:569594
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:295332
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:335474
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
  4. XM_030245304.1XP_030101164.1  PR domain zinc finger protein 4 isoform X2

    UniProtKB/TrEMBL
    A0A1X7SB67, B7ZP41
    Conserved Domains (5) summary
    sd00017
    Location:616636
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:614636
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:628653
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:361398
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:401533
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
  5. XM_017314116.2XP_017169605.1  PR domain zinc finger protein 4 isoform X4

    UniProtKB/TrEMBL
    Q8R3B9
    Conserved Domains (5) summary
    sd00017
    Location:550570
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:548570
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:562587
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:295332
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:335467
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins
  6. XM_011243583.4XP_011241885.1  PR domain zinc finger protein 4 isoform X5

    See identical proteins and their annotated locations for XP_011241885.1

    UniProtKB/TrEMBL
    Q8C0V8
    Conserved Domains (5) summary
    sd00017
    Location:434454
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:432454
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:446471
    zf-H2C2_2; Zinc-finger double domain
    pfam18445
    Location:172209
    zf_PR_Knuckle; PR zinc knuckle motif
    cd19189
    Location:212351
    PR-SET_PRDM4; PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins