Phf1 PHD finger protein 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Phf1provided by RGD
Official Full Name: PHD finger protein 1provided by RGD
Primary source: RGD:1303205
See related: EnsemblRapid:ENSRNOG00000000480 AllianceGenome:RGD:1303205
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Tctex3
Summary: Enables chromatin binding activity. Predicted to be involved in DNA repair-dependent chromatin remodeling and negative regulation of gene expression, epigenetic. Predicted to be located in several cellular components, including centrosome; nucleoplasm; and site of double-strand break. Predicted to be part of ESC/E(Z) complex. Predicted to be active in nucleus. Orthologous to human PHF1 (PHD finger protein 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 90.9), Kidney (RPKM 85.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (5019650..5024732)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (5017765..5022872)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (5526926..5531940)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

We established that mutations that occur in the Tctex5 long transcript of the t-haplotype mice are important for normal sperm function, whereas the short transcript of Tctex5 might have a conserved function among different tissues.
Title: Mutations of t-complex testis expressed gene 5 transcripts in the testis of sterile t-haplotype mutant mouse.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone methyltransferase binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA repair-dependent chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in negative regulation of gene expression, epigenetic	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of ESC/E(Z) complex	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in site of double-strand break	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: PHD finger protein 1

Names: T-complex testis-expressed 3; polycomb-like 1

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_001414742.1 → NP_001401671.1 PHD finger protein 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000020

UniProtKB/TrEMBL

A6JJJ4, Q6MGC9
NM_212538.2 → NP_997703.1 PHD finger protein 1

See identical proteins and their annotated locations for NP_997703.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000020

UniProtKB/TrEMBL

A6JJJ4, Q6MGC9

Conserved Domains (4) summary

smart00333
Location:29 → 80

TUDOR; Tudor domain

cd15500
Location:89 → 139

PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)

cd15582
Location:188 → 239

PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)

pfam14061
Location:532 → 557

Mtf2_C; Polycomb-like MTF2 factor 2

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086038.1 Reference GRCr8

Range

5019650..5024732

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039098511.2 → XP_038954439.1 PHD finger protein 1 isoform X6

UniProtKB/TrEMBL

A6JJJ4

Conserved Domains (3) summary

cd15500
Location:153 → 203

PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)

cd15582
Location:252 → 303

PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)

cd20449
Location:94 → 146

Tudor_PHF1; Tudor domain found in PHD finger protein1 (PHF1) and similar proteins
XM_017601589.3 → XP_017457078.1 PHD finger protein 1 isoform X5

UniProtKB/TrEMBL

A6JJJ4
XM_039098510.2 → XP_038954438.1 PHD finger protein 1 isoform X2

UniProtKB/TrEMBL

A6JJJ4

Conserved Domains (4) summary

cd15500
Location:153 → 203

PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)

cd15582
Location:252 → 303

PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)

pfam14061
Location:595 → 621

Mtf2_C; Polycomb-like MTF2 factor 2

cd20449
Location:94 → 146

Tudor_PHF1; Tudor domain found in PHD finger protein1 (PHF1) and similar proteins
XM_017601587.3 → XP_017457076.1 PHD finger protein 1 isoform X1

UniProtKB/TrEMBL

A6JJJ4
XM_017601588.3 → XP_017457077.1 PHD finger protein 1 isoform X3

UniProtKB/TrEMBL

A6JJJ4, Q6MGC9

Related

ENSRNOP00000098528.2, ENSRNOT00000120945.2

Conserved Domains (4) summary

smart00333
Location:29 → 80

TUDOR; Tudor domain

cd15500
Location:89 → 139

PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)

cd15582
Location:188 → 239

PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)

pfam14061
Location:532 → 557

Mtf2_C; Polycomb-like MTF2 factor 2
XM_063279027.1 → XP_063135097.1 PHD finger protein 1 isoform X7

UniProtKB/TrEMBL

A6JJJ4
XM_063279026.1 → XP_063135096.1 PHD finger protein 1 isoform X4

UniProtKB/TrEMBL

A6JJJ4