Kdm1a lysine demethylase 1A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Kdm1aprovided by RGD
Official Full Name: lysine demethylase 1Aprovided by RGD
Primary source: RGD:1562975
See related: Ensembl:ENSRNOG00000022372 AllianceGenome:RGD:1562975
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: Aof2; Kdm1; RGD1562975
Summary: Enables chromatin binding activity. Involved in several processes, including cellular response to cAMP; nervous system development; and response to fungicide. Located in chromatin and nucleus. Biomarker of breast cancer; diabetic retinopathy; schizophrenia; and transient cerebral ischemia. Orthologous to human KDM1A (lysine demethylase 1A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 190.0), Brain (RPKM 146.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (154066436..154121913, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (148782976..148838319, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (154909003..154965171, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Targeting lysine-specific demethylase 1A inhibits renal epithelial-mesenchymal transition and attenuates renal fibrosis.
Title: Targeting lysine-specific demethylase 1A inhibits renal epithelial-mesenchymal transition and attenuates renal fibrosis.
The regulatory correlation between KDM1A and BMP-2 offers insights into vascular remodelling and VSMC phenotypic modulation. The reported findings contribute to the development of innovative strategies against vascular disorders.
Title: Inhibition of lysine-specific demethylase 1A suppresses neointimal hyperplasia by targeting bone morphogenetic protein 2 and mediating vascular smooth muscle cell phenotype.
pharmacologic treatments that suppress LSD1 activity may be a novel therapeutic strategy that can be used to treat neurodegenerative diseases.
Title: Potential Neuroprotective Effects of an LSD1 Inhibitor in Retinal Ganglion Cells via p38 MAPK Activity.
Epigenetic regulation of ATN1 by LSD1 is required for cortical progenitor maintenance.
Title: Epigenetic regulation of Atrophin1 by lysine-specific demethylase 1 is required for cortical progenitor maintenance.
Thr369b phosphorylation is required for morphogenic activity, converting neuronal LSD1-8a in a dominant-negative isoform
Title: Phosphorylation of neuronal Lysine-Specific Demethylase 1LSD1/KDM1A impairs transcriptional repression by regulating interaction with CoREST and histone deacetylases HDAC1/2.
LSD1 in metastasized cancer cells contributed to the production of the endogenous formaldehyde
Title: Lysine-specific demethylase 1 in breast cancer cells contributes to the production of endogenous formaldehyde in the metastatic bone cancer pain model of rats.
A critical function of LSD1 in its tightly regulated distribution in the brain during ischemic insult is suggested for lysine (K)-specific demethylase 1.
Title: Distribution of lysine-specific demethylase 1 in the brain of rat and its response in transient global cerebral ischemia.

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

AA408884 (e-PCR)
- UniSTS:159310

RH128773 (e-PCR)
- UniSTS:212081

D5Uwm55 (e-PCR)
- UniSTS:240011

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables MRF binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology 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 chromatin binding	ISO Inferred from Sequence Orthology more info
enables demethylase activity	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables flavin adenine dinucleotide binding	IBA Inferred from Biological aspect of Ancestor more info
enables flavin adenine dinucleotide binding	ISO Inferred from Sequence Orthology more info
enables histone H3K4 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9me2/H3K9me3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone demethylase activity	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables lncRNA binding	ISO Inferred from Sequence Orthology more info
enables nuclear androgen receptor binding	ISO Inferred from Sequence Orthology more info
enables nuclear receptor coactivator activity	ISO Inferred from Sequence Orthology more info
enables oxidoreductase activity	IBA Inferred from Biological aspect of Ancestor more info
enables oxidoreductase activity	ISO Inferred from Sequence Orthology more info
enables p53 binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
NOT enables telomeric DNA binding	ISO Inferred from Sequence Orthology more info
enables telomeric repeat-containing RNA binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables transcription factor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA repair-dependent chromatin remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to UV	ISO Inferred from Sequence Orthology more info
involved_in cellular response to cAMP	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cellular response to gamma radiation	ISO Inferred from Sequence Orthology more info
involved_in cerebral cortex development	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in granulocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in guanine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle cell development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA damage response, signal transduction by p53 class mediator	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in neuron maturation	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within neuron projection extension	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pituitary gland development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell size	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cold-induced thermogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of megakaryocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein modification process	IEP Inferred from Expression Pattern more info	PubMed
involved_in protein modification process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA methylation-dependent heterochromatin formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of primitive erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of protein localization	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to fungicide	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of DNA repair complex	ISO Inferred from Sequence Orthology more info
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	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	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lysine-specific histone demethylase 1A

Names: amine oxidase (flavin containing) domain 2; lysine (K)-specific demethylase 1; lysine (K)-specific demethylase 1A; neuroprotective protein 3

NP_001123570.1

EC 1.14.99.66

XP_038966552.1

EC 1.14.99.66

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_001130098.1 → NP_001123570.1 lysine-specific histone demethylase 1A

See identical proteins and their annotated locations for NP_001123570.1

Status: PROVISIONAL

Source sequence(s)

EF688598

UniProtKB/TrEMBL

A6ITB7, B3STT9, F1MA31

Related

ENSRNOP00000052846.5, ENSRNOT00000055992.5

Conserved Domains (2) summary

PLN02328
Location:203 → 845

PLN02328; lysine-specific histone demethylase 1 homolog

PHA03378
Location:38 → 98

PHA03378; EBNA-3B; Provisional

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_086023.1 Reference GRCr8

Range

154066436..154121913 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039110624.2 → XP_038966552.1 lysine-specific histone demethylase 1A isoform X1

UniProtKB/TrEMBL

A0A8I6G2K8, A6ITB7

Related

ENSRNOP00000078937.1

Conserved Domains (2) summary

PLN02328
Location:183 → 825

PLN02328; lysine-specific histone demethylase 1 homolog

PHA03378
Location:38 → 98

PHA03378; EBNA-3B; Provisional