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protein coding gene - phf1 (SPCC4G3.07c) - PHD finger protein Phf1

Gene summary

Standard name
phf1
Systematic ID
SPCC4G3.07c
Product
PHD finger protein Phf1
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
swp1, saf50
UniProt ID
P87233
ORFeome ID
44/44D07
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome III: 459868..461914 forward strand

Annotation

GO biological process

GO:0006338 - chromatin remodeling

References:

GO:0033696 - heterochromatin boundary formation

References:

GO cellular component

GO:0000785 - chromatin

References:

GO:0033193 - Lsd1/2 complex

References:

GO:0031934 - mating-type region heterochromatin

References:

GO:0005634 - nucleus

References:

GO:0005721 - pericentric heterochromatin

References:

GO:0140720 - subtelomeric heterochromatin

References:

GO molecular function

GO:0003677 - DNA binding

References:

GO:0031491 - nucleosome binding

References:

Protein features

PBO:0111814 - human retinoblastoma binding protein 2-like family

PBO:0111780 - zf-PHD finger

PBO:0111743 - zinc finger protein

Qualitative gene expression

PomGeneEx:0000011 - RNA level increased

References:

Quantitative gene expression

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0001991 - inviable after spore germination, without cell division

References:

Genotypes:

FYPO:0002151 - inviable spore

References:

Genotypes:

FYPO:0002150 - inviable spore population

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

FYPO:0001511 - inviable vegetative cell, abnormal cell shape, normal cell size

References:

Genotypes:

FYPO:0006680 - sensitive to bisphenol A

References:

Genotypes:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0000055 - no apparent S. cerevisiae ortholog

PBO:0006222 - predominantly single copy (one to one)

Protein features

IDNameInterPro nameDB name
PF00628PHDZnf_PHD-fingerPfam
cd15502PHD_Phf1p_Phf2p_likeCDD
PS01359ZF_PHD_1Zinc_finger_PHD-type_CSPROSITE patterns
PS50016ZF_PHD_2Znf_PHD-fingerPROSITE profiles
SM00249PHDZnf_PHDSMART
G3DSA:3.30.40.10:FF:000101CATH-FunFam
G3DSA:3.30.40.10Znf_RING/FYVE/PHDCATH-Gene3D
SSF57903Znf_FYVE_PHDSUPERFAMILY
PTHR12628PANTHER
mobidb-lite-Disorderdisorder_predictionMobiDB-Disorder
mobidb-lite-Polardisorder_predictionMobiDB-Polar

Orthologs

References / Literature

PMID:30099677 - Genome-wide evidences of bisphenol a toxicity using Schizosaccharomyces pombe.
Kim DM et al. Arch Pharm Res 2018 Aug;41(8):830-837
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.
Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:12161753 - The transcriptional program of meiosis and sporulation in fission yeast.
Mata J et al. Nat Genet 2002 Sep;32(1):143-7
PMID:17371846 - Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries.
Gordon M et al. Mol Cell Biol 2007 Jun;27(11):4058-69
PMID:33313903 - Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.
Rubio A et al. Nucleic Acids Res 2021 Jan 11;49(1):383-399
PMID:28218250 - Chromatin remodeller Fun30 Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation.
Lee J et al. Nat Commun 2017 Feb 20;8:14527
PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.
Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:16990277 - Fission yeast homologs of human histone H3 lysine 4 demethylase regulate a common set of genes with diverse functions.
Nicolas E et al. J Biol Chem 2006 Nov 24;281(47):35983-8
PMID:24013502 - Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries.
Wang J et al. Genes Dev 2013 Sep 01;27(17):1886-902
PMID:17440621 - Genome-wide studies of histone demethylation catalysed by the fission yeast homologues of mammalian LSD1.
Opel M et al. PLoS One 2007 Apr 18;2(4):e386
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:40015273 - A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin.
Skribbe M et al. Mol Cell 2025 Feb 19;
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.
Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PMID:38181050 - The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe.
Liu H et al. PLoS Genet 2024 Jan 05;20(1):e1011107
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.
Hayles J et al. Open Biol 2013 May 22;3(5):130053
PMID:26771498 - A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.
Vo TV et al. Cell 2016 Jan 14;164(1-2):310-323
PMID:22681890 - Hierarchical modularity and the evolution of genetic interactomes across species.
Ryan CJ et al. Mol Cell 2012 Jun 08;46(5):691-704
PMID:17434129 - S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription.
Lan F et al. Mol Cell 2007 Apr 13;26(1):89-101