Prdm13 PR domain containing 13 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Prdm13provided by MGI
Official Full Name: PR domain containing 13provided by MGI
Primary source: MGI:MGI:2448528
See related: Ensembl:ENSMUSG00000040478 AllianceGenome:MGI:2448528
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
Summary: Enables RNA polymerase II-specific DNA-binding transcription factor binding activity; chromatin binding activity; and histone methyltransferase activity. Involved in GABAergic neuron differentiation and hypothalamus cell differentiation. Acts upstream of or within negative regulation of transcription by RNA polymerase II and neurogenesis. Located in nucleus. Is expressed in several structures, including central nervous system and retina. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia. Orthologous to human PRDM13 (PR/SET domain 13). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: human all
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Genomic context

Location:: 4 A3; 4 8.78 cM

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (21675865..21685963, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (21675865..21685963, complement)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sleep-wake patterns are altered with age, Prdm13 signaling in the DMH, and diet restriction in mice.
Title: Sleep-wake patterns are altered with age, Prdm13 signaling in the DMH, and diet restriction in mice.
Recessive PRDM13 mutations cause fatal perinatal brainstem dysfunction with cerebellar hypoplasia and disrupt Purkinje cell differentiation.
Title: Recessive PRDM13 mutations cause fatal perinatal brainstem dysfunction with cerebellar hypoplasia and disrupt Purkinje cell differentiation.
A recessive PRDM13 mutation results in congenital hypogonadotropic hypogonadism and cerebellar hypoplasia.
Title: A recessive PRDM13 mutation results in congenital hypogonadotropic hypogonadism and cerebellar hypoplasia.
Investigation of PRDM10 and PRDM13 Expression in Developing Mouse Embryos by an Optimized PACT-Based Embryo Clearing Method.
Title: Investigation of PRDM10 and PRDM13 Expression in Developing Mouse Embryos by an Optimized PACT-Based Embryo Clearing Method.
The findings highlight the function of PRDM13 in repressing the activity of basic helix-loop-helix transcriptional activators that together are required to achieve precise neuronal specification during mouse development.
Title: Repression by PRDM13 is critical for generating precision in neuronal identity.
data show that Prdm13 is not required for amacrine fate as a class, but is essential for the formation of Ebf3+ amacrine cell subtypes. Rather than driving subtype identity, Prdm13 may act by restricting competing fate programs to maintain identity and survival.
Title: Prdm13 is required for Ebf3+ amacrine cell formation in the retina.
Findings indicate that Prdm13/Nkx2-1-mediated signaling in the DMC declines with advanced age, leading to decreased sleep quality and increased adiposity.
Title: Deficiency of Prdm13, a dorsomedial hypothalamus-enriched gene, mimics age-associated changes in sleep quality and adiposity.
Targeted deletion of Prdm13 leads to a specific reduction of amacrine cells and changes visual sensitivity.
Title: Prdm13 regulates subtype specification of retinal amacrine interneurons and modulates visual sensitivity.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (9) 1 citation
Targeted (2) 1 citation

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in GABAergic neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in hypothalamus cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neurogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
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

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Preferred Names: PR domain zinc finger protein 13

Names: PR domain-containing protein 13

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)

NM_001080771.1 → NP_001074240.1 PR domain zinc finger protein 13

See identical proteins and their annotated locations for NP_001074240.1

Status: VALIDATED

Source sequence(s)

BB665287, BC017632

Consensus CDS

CCDS38699.1

UniProtKB/Swiss-Prot

B1AV74, E9PZZ1

Related

ENSMUSP00000092761.4, ENSMUST00000095141.4

Conserved Domains (6) summary

sd00017
Location:622 → 642

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00018
Location:185 → 208

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:622 → 642

zf-C2H2; Zinc finger, C2H2 type

pfam00856
Location:62 → 159

SET; SET domain

pfam13465
Location:635 → 657

zf-H2C2_2; Zinc-finger double domain

pfam13894
Location:677 → 700

zf-C2H2_4; C2H2-type zinc finger

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

NC_000070.7 Reference GRCm39 C57BL/6J

Range

21675865..21685963 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006537807.2 → XP_006537870.1 PR domain zinc finger protein 13 isoform X1

See identical proteins and their annotated locations for XP_006537870.1

Conserved Domains (6) summary

COG5189
Location:527 → 602

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:524 → 544

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00018
Location:87 → 110

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:524 → 544

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:537 → 555

zf-H2C2_2; Zinc-finger double domain

cl40432
Location:1 → 69

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_006537806.2 → XP_006537869.1 PR domain zinc finger protein 13 isoform X1

See identical proteins and their annotated locations for XP_006537869.1

Conserved Domains (6) summary

COG5189
Location:527 → 602

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:524 → 544

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00018
Location:87 → 110

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:524 → 544

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:537 → 555

zf-H2C2_2; Zinc-finger double domain

cl40432
Location:1 → 69

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily