spr-5 Lysine-specific histone demethylase 1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: spr-5
Official Full Name: Lysine-specific histone demethylase 1
Primary source: WormBase:WBGene00005010
Locus tag: CELE_Y40B1B.6
See related: AllianceGenome:WB:WBGene00005010
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables FAD-dependent H3K4me/H3K4me3 demethylase activity. Involved in epigenetic regulation of gene expression. Located in cytoplasm and nucleus. Is expressed in germ line. Orthologous to human KDM1A (lysine demethylase 1A). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See spr-5 in Genome Data Viewer

Location:: chromosome: I

Exon count:: 8

Sequence:: Chromosome: I; NC_003279.8 (13438058..13450216)

Chromosome I - NC_003279.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003279.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SPR-5 interacts with FNCM-1. SPR-5 absence suppresses the embryonic lethality and larval arrest observed in fncm-1 mutants.
Title: Fanconi Anemia FANCM/FNCM-1 and FANCD2/FCD-2 Are Required for Maintaining Histone Methylation Levels and Interact with the Histone Demethylase LSD1/SPR-5 in Caenorhabditis elegans.
germ cells deficient for spr-5 and let-418 mainly reprogram as neurons, suggesting that neuronal fate might be the first to be derepressed in early embryogenesis.
Title: LET-418/Mi2 and SPR-5/LSD1 cooperatively prevent somatic reprogramming of C. elegans germline stem cells.
SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state during passage through the germ line.
Title: SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state during passage through the germ line.
Studies indicate that cellular identity in is the sum of interplay between PcG and Trx-G group proteins, as well as histone modifying enzymes MES-4 and SPR-5.
Title: Epigenetics in C. elegans: facts and challenges.
Data suggest that SPR-5 may function directly in DSBR.
Title: SPR-5 is a histone H3K4 demethylase with a role in meiotic double-strand break repair.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Y40B1B.6 (e-PCR)
- UniSTS:313307

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IGI Inferred from Genetic Interaction more info	PubMed
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables flavin adenine dinucleotide binding	IBA Inferred from Biological aspect of Ancestor more info
enables flavin adenine dinucleotide binding	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in epigenetic regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in epigenetic regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay 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
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Lysine-specific histone demethylase 1

NP_493366.1

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_003279.8 Reference assembly

Range

13438058..13450216

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_060965.7 → NP_493366.1 Lysine-specific histone demethylase 1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_493366.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9XWP6

Conserved Domains (2) summary

pfam01593
Location:151 → 676

Amino_oxidase; Flavin containing amine oxidoreductase

pfam04433
Location:36 → 117

SWIRM; SWIRM domain