Jade1 jade family PHD finger 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Jade1provided by RGD
Official Full Name: jade family PHD finger 1provided by RGD
Primary source: RGD:1306920
See related: EnsemblRapid:ENSRNOG00000014066 AllianceGenome:RGD:1306920
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: Phf17
Summary: Predicted to enable transcription coactivator activity. Predicted to contribute to histone acetyltransferase activity. Predicted to be involved in several processes, including negative regulation of canonical Wnt signaling pathway; regulation of cell growth; and regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within negative regulation of G1/S transition of mitotic cell cycle. Predicted to be located in several cellular components, including cytosol; microtubule organizing center; and nuclear speck. Predicted to be part of histone acetyltransferase complex. Orthologous to human JADE1 (jade family PHD finger 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 162.6), Adrenal (RPKM 124.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q26

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (126471124..126524252)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (124543233..124596361)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (128461147..128514298)

Chromosome 2 - NC_086020.1 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 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?

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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

BI294258 (e-PCR)
- UniSTS:246063

AW534015 (e-PCR)
- UniSTS:260563

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
contributes_to histone H3K14 acetyltransferase activity	ISO Inferred from Sequence Orthology more info
contributes_to histone H4K12 acetyltransferase activity	ISO Inferred from Sequence Orthology more info
NOT contributes_to histone H4K16 acetyltransferase activity	ISO Inferred from Sequence Orthology more info
contributes_to histone H4K5 acetyltransferase activity	ISO Inferred from Sequence Orthology more info
contributes_to histone H4K8 acetyltransferase activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of G1/S transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA replication	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of histone acetyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of histone acetyltransferase complex	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: protein Jade-1

Names: PHD finger protein 17

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_001415052.1 → NP_001401981.1 protein Jade-1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

D3ZM64

Related

ENSRNOP00000018872.7, ENSRNOT00000018872.8

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_086020.1 Reference GRCr8

Range

126471124..126524252

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006232303.5 → XP_006232365.1 protein Jade-1 isoform X2

See identical proteins and their annotated locations for XP_006232365.1

UniProtKB/TrEMBL

A6II53, D3ZM64

Conserved Domains (3) summary

cd15671
Location:258 → 368

ePHD_JADE; Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins

cd15679
Location:205 → 250

PHD_JADE1; PHD finger found in protein Jade-1 and similar proteins

pfam10513
Location:92 → 180

EPL1; Enhancer of polycomb-like
XM_006232304.5 → XP_006232366.1 protein Jade-1 isoform X2

See identical proteins and their annotated locations for XP_006232366.1

UniProtKB/TrEMBL

A6II53, D3ZM64

Conserved Domains (3) summary

cd15671
Location:258 → 368

ePHD_JADE; Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins

cd15679
Location:205 → 250

PHD_JADE1; PHD finger found in protein Jade-1 and similar proteins

pfam10513
Location:92 → 180

EPL1; Enhancer of polycomb-like
XM_008760928.4 → XP_008759150.2 protein Jade-1 isoform X2

UniProtKB/TrEMBL

A6II53, D3ZM64

Related

ENSRNOP00000105202.1, ENSRNOT00000172515.1

Conserved Domains (3) summary

cd15671
Location:258 → 368

ePHD_JADE; Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins

cd15679
Location:205 → 250

PHD_JADE1; PHD finger found in protein Jade-1 and similar proteins

pfam10513
Location:92 → 180

EPL1; Enhancer of polycomb-like
XM_006232301.5 → XP_006232363.1 protein Jade-1 isoform X1

UniProtKB/TrEMBL

A0A8I6AB02, A6II53

Related

ENSRNOP00000090026.1, ENSRNOT00000098865.2

Conserved Domains (3) summary

cd15679
Location:220 → 265

PHD_JADE1; PHD finger found in protein Jade-1 and similar proteins

cd15704
Location:270 → 387

ePHD_JADE1; Extended PHD finger found in protein Jade-1 and similar proteins

pfam10513
Location:107 → 195

EPL1; Enhancer of polycomb-like
XM_063281777.1 → XP_063137847.1 protein Jade-1 isoform X3
XM_039102248.2 → XP_038958176.1 protein Jade-1 isoform X3

UniProtKB/TrEMBL

A0A8I6GJ46

Conserved Domains (2) summary

COG5141
Location:32 → 367

COG5141; PHD zinc finger-containing protein [General function prediction only]

cd15704
Location:93 → 210

ePHD_JADE1; Extended PHD finger found in protein Jade-1 and similar proteins

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001107670.1: Suppressed sequence

Description

NM_001107670.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.