Kdm7a lysine demethylase 7A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Kdm7aprovided by RGD
Official Full Name: lysine demethylase 7Aprovided by RGD
Primary source: RGD:1592650
See related: EnsemblRapid:ENSRNOG00000052445 AllianceGenome:RGD:1592650
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: Jhdm1d
Summary: Predicted to enable several functions, including histone demethylase activity; methylated histone binding activity; and transition metal ion binding activity. Predicted to be involved in chromatin remodeling; positive regulation of DNA-templated transcription; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleolus and nucleoplasm. Human ortholog(s) of this gene implicated in melanoma. Orthologous to human KDM7A (lysine demethylase 7A). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Muscle (RPKM 187.9), Spleen (RPKM 150.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q23

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (68866263..68992979, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (67899407..67974264, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (66915603..66957971, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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General gene information

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Markers

D7Mit18 (e-PCR), detects polymorphism
- UniSTS:239955

BF416062 (e-PCR)
- UniSTS:249201

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 2-oxoglutarate-dependent dioxygenase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K27me2/H3K27me3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H4K20 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables iron ion binding	ISO Inferred from Sequence Orthology more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	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 membrane	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lysine demethylase 7A; lysine-specific demethylase 7A

Names: jumonji C domain containing histone demethylase 1; lysine (K)-specific demethylase 7A

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_001428919.1 → NP_001415848.1 lysine demethylase 7A

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A0A0G2K1Z1, A0A8I6AQU2

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_086022.1 Reference GRCr8

Range

68866263..68992979 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063286832.1 → XP_063142902.1 lysine-specific demethylase 7A isoform X1
XM_063286833.1 → XP_063142903.1 lysine-specific demethylase 7A isoform X2
XM_063286827.1 → XP_063142897.1 lysine-specific demethylase 7A isoform X1
XM_063286830.1 → XP_063142900.1 lysine-specific demethylase 7A isoform X1
XM_063286828.1 → XP_063142898.1 lysine-specific demethylase 7A isoform X1
XM_063286831.1 → XP_063142901.1 lysine-specific demethylase 7A isoform X1
XM_039109016.2 → XP_038964944.1 lysine-specific demethylase 7A isoform X1

Related

ENSRNOP00000096667.1, ENSRNOT00000101937.2

Conserved Domains (5) summary

TIGR00934
Location:508 → 823

2a38euk; potassium uptake protein, Trk family

smart00558
Location:234 → 297

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

cd15640
Location:39 → 88

PHD_KDM7; PHD finger found in lysine-specific demethylase 7 (KDM7)

pfam17811
Location:373 → 476

JHD; Jumonji helical domain

cl40423
Location:269 → 369

cupin_RmlC-like; RmlC-like cupin superfamily
XM_039109018.2 → XP_038964946.1 lysine-specific demethylase 7A isoform X2

UniProtKB/TrEMBL

A0A0G2K1Z1

Related

ENSRNOP00000112711.1, ENSRNOT00000145902.1

Conserved Domains (4) summary

TIGR00934
Location:415 → 730

2a38euk; potassium uptake protein, Trk family

smart00558
Location:141 → 204

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

pfam17811
Location:280 → 383

JHD; Jumonji helical domain

cl40423
Location:176 → 276

cupin_RmlC-like; RmlC-like cupin superfamily
XM_039109019.2 → XP_038964947.1 lysine-specific demethylase 7A isoform X3

Conserved Domains (4) summary

TIGR00934
Location:304 → 619

2a38euk; potassium uptake protein, Trk family

smart00558
Location:30 → 93

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

pfam17811
Location:169 → 272

JHD; Jumonji helical domain

cl40423
Location:65 → 165

cupin_RmlC-like; RmlC-like cupin superfamily