prdm1.S PR domain 1 S homeolog [Xenopus laevis (African clawed frog)] - Gene

Summary

Official Symbol: prdm1.S
Official Full Name: PR domain 1 S homeolog
Primary source: Xenbase:XB-GENE-853257
Locus tag: XELAEV_18029311mg
See related: EnsemblRapid:ENSXLAG00005004412 AllianceGenome:Xenbase:XB-GENE-853257
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Xenopus laevis
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus
Also known as: prdm1; blimp1; xblimp1
Summary: Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and metal ion binding activity. Predicted to act upstream of or within cell fate commitment and negative regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm and nucleus. Is expressed in musculoskeletal system; nervous system; and primary germ layer. Human ortholog(s) of this gene implicated in hepatocellular carcinoma and lung adenocarcinoma. Orthologous to human PRDM1 (PR/SET domain 1). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

Location:: chromosome: 5S

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
101	current	Xenopus_laevis_v10.1 (GCF_017654675.1)	5S	NC_054380.1 (66149933..66166711, complement)
100	previous assembly	Xenopus_laevis_v2 (GCF_001663975.1)	5S	NC_030733.1 (62019123..62035901, complement)

Chromosome 5S - NC_054380.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by Xenbase

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell fate commitment	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular developmental process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of gene expression	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: PR domain 1 S homeolog

Names: PR domain containing 1, with ZNF domain S homeolog

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_001087104.1 → NP_001080573.1 PR domain 1 S homeolog

See identical proteins and their annotated locations for NP_001080573.1

Status: PROVISIONAL

Source sequence(s)

BC044261

UniProtKB/TrEMBL

Q9PUI4

Related

ENSXLAP00005013173.1, ENSXLAT00005013353.1

Conserved Domains (5) summary

smart00317
Location:64 → 170

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

COG5048
Location:348 → 644

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:533 → 553

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:531 → 553

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:573 → 598

zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Xenopus laevis Annotation Release 101 details...

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

Reference Xenopus_laevis_v10.1 Primary Assembly

Genomic

NC_054380.1 Reference Xenopus_laevis_v10.1 Primary Assembly

Range

66149933..66166711 complement

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GenBank, FASTA, Sequence Viewer (Graphics)