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protein coding gene - phf2 (SPAC30D11.08c) - Lsd1/2 complex PHD finger protein Phf2

Gene summary

Standard name
phf2
Systematic ID
SPAC30D11.08c
Product
Lsd1/2 complex PHD finger protein Phf2
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
swp2, saf60
UniProt ID
Q09908
ORFeome ID
34/34H08
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 1104768..1106608 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:

GO:0003713 - transcription coactivator activity

References:

Modification

MOD:00046 - O-phospho-L-serine

References:

MOD:01149 - sumoylated lysine

References:

MOD:01148 - ubiquitinylated lysine

References:

Protein features

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

PBO:0111780 - zf-PHD finger

PBO:0111743 - zinc finger protein

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0002148 - inviable after spore germination, multiple cell divisions, abnormal morphology

References:

Genotypes:

FYPO:0002150 - inviable spore population

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

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
mobidb-lite-Polyampholytedisorder_predictionMobiDB-Polyampholyte

Orthologs

References / Literature

PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
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: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:29996109 - Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe.
Swaffer MP et al. Cell Rep 2018 Jul 10;24(2):503-514
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.
Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
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: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:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).
Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.
Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
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:22540037 - Predicting the fission yeast protein interaction network.
Pancaldi V et al. G3 (Bethesda) 2012 Apr;2(4):453-67
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: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: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
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
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:26537787 - Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast.
Køhler JB et al. Nat Commun 2015 Nov 05;6:8827