Kdm5b lysine demethylase 5B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Kdm5bprovided by RGD
Official Full Name: lysine demethylase 5Bprovided by RGD
Primary source: RGD:1565602
See related: EnsemblRapid:ENSRNOG00000060544 AllianceGenome:RGD:1565602
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Jarid1b; RGD1565602
Summary: Predicted to enable several functions, including histone H3K4me/H3K4me2/H3K4me3 demethylase activity; transcription corepressor activity; and zinc ion binding activity. Involved in cellular response to fibroblast growth factor stimulus; lens fiber cell differentiation; and response to fungicide. Predicted to be located in chromatin; cytosol; and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in autosomal recessive intellectual developmental disorder 65; breast cancer; and high grade glioma. Orthologous to human KDM5B (lysine demethylase 5B). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 315.1), Testes (RPKM 201.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q13

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (48554367..48625721)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (46001589..46073868)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (51384371..51455392)

Chromosome 13 - NC_086031.1 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?

Prenatal Iron Deficiency and Choline Supplementation Interact to Epigenetically Regulate Jarid1b and Bdnf in the Rat Hippocampus into Adulthood.
Title: Prenatal Iron Deficiency and Choline Supplementation Interact to Epigenetically Regulate Jarid1b and Bdnf in the Rat Hippocampus into Adulthood.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH132812 (e-PCR)
- UniSTS:216095

D13Mco9 (e-PCR)
- UniSTS:239841

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables histone H3K4 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within branching involved in mammary gland duct morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to fibroblast growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in lens fiber cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within mammary duct terminal end bud growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of mammary gland epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within post-embryonic development	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of estradiol secretion	ISO Inferred from Sequence Orthology more info
involved_in response to fungicide	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within single fertilization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within uterus morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor 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	IEA Inferred from Electronic Annotation 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

General protein information

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Preferred Names: lysine-specific demethylase 5B

Names: Jumonji, AT rich interactive domain 1B (RBP2-like); jumonji, AT rich interactive domain 1B (Rbp2 like); lysine (K)-specific demethylase 5B

NP_001100647.1

EC 1.14.11.67

XP_063128368.1

EC 1.14.11.67

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_001107177.1 → NP_001100647.1 lysine-specific demethylase 5B

See identical proteins and their annotated locations for NP_001100647.1

Status: PROVISIONAL

Source sequence(s)

CH473958

UniProtKB/TrEMBL

A0A0G2K6G9, A6ICC6

Conserved Domains (8) summary

smart00545
Location:31 → 72

JmjN; Small domain found in the jumonji family of transcription factors

cd15603
Location:311 → 356

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15687
Location:1486 → 1535

PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)

cd16874
Location:94 → 183

ARID_KDM5B; ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B)

pfam02373
Location:486 → 602

JmjC; JmjC domain, hydroxylase

pfam02928
Location:692 → 744

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:757 → 1086

PLU-1; PLU-1-like protein

cl22851
Location:1178 → 1221

PHD_SF; PHD finger superfamily