phf8 PHD finger protein 8 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: phf8provided by ZNC
Official Full Name: PHD finger protein 8provided by ZNC
Primary source: ZFIN:ZDB-GENE-060419-1
See related: Ensembl:ENSDARG00000006584 AllianceGenome:ZFIN:ZDB-GENE-060419-1
Gene type: protein coding
RefSeq status: INFERRED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zPHF8
Summary: Predicted to enable chromatin binding activity; histone demethylase activity; and methylated histone binding activity. Involved in brain development and positive regulation of transcription, DNA-templated. Acts upstream of or within embryonic viscerocranium morphogenesis; primitive erythrocyte differentiation; and regulation of neuron apoptotic process. Predicted to be located in nucleolus. Is expressed in head; mandibular arch skeleton; and tail bud. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability Siderius type. Orthologous to human PHF8 (PHD finger protein 8). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 23

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	23	NC_007134.7 (27591366..27608287, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	23	NC_007134.6 (27663870..27681754, complement)

Chromosome 23 - NC_007134.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PHF8 regulates zebrafish neuronal cell survival and jaw development in part by directly regulating the expression of the homeodomain transcription factor MSX1/MSXB, which functions downstream of multiple signalling and developmental pathways
Title: Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development.

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General gene information

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Markers

fb93c06.x1 (e-PCR)
- UniSTS:203532

fc20a06.y1 (e-PCR)
- UniSTS:192968

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K27me2/H3K27me3 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K36 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K36me/H3K36me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K9me/H3K9me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K20 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in G1/S transition of mitotic cell cycle	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of rDNA heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase I	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within posterior lateral line neuromast deposition	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within primitive erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of neuron apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: histone lysine demethylase PHF8

Names: [histone H3]-dimethyl-L-lysine(36) demethylase PHF8; [histone H3]-dimethyl-L-lysine(9) demethylase PHF8

NP_001189376.1

EC 1.14.11.27

EC 1.14.11.65

XP_005162322.1

EC 1.14.11.27

EC 1.14.11.65

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_001202447.1 → NP_001189376.1 histone lysine demethylase PHF8

See identical proteins and their annotated locations for NP_001189376.1

Status: INFERRED

Source sequence(s)

CR352210

UniProtKB/Swiss-Prot

P0CH95

Related

ENSDARP00000148598.1, ENSDART00000183639.1

Conserved Domains (3) summary

smart00558
Location:203 → 266

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cd15642
Location:6 → 57

PHD_PHF8; PHD finger found in histone lysine demethylase PHF8

cl21464
Location:238 → 338

cupin_like; Conserved domain found in cupin and related proteins

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007134.7 Reference GRCz11 Primary Assembly

Range

27591366..27608287 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005162265.4 → XP_005162322.1 histone lysine demethylase PHF8 isoform X1

See identical proteins and their annotated locations for XP_005162322.1

UniProtKB/Swiss-Prot

P0CH95

Related

ENSDARP00000007140.7, ENSDART00000026314.8

Conserved Domains (3) summary

smart00558
Location:203 → 266

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cd15642
Location:6 → 57

PHD_PHF8; PHD finger found in histone lysine demethylase PHF8

cl21464
Location:238 → 338

cupin_like; Conserved domain found in cupin and related proteins