kdm1a lysine (K)-specific demethylase 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: kdm1aprovided by ZNC
Official Full Name: lysine (K)-specific demethylase 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-7828
See related: Ensembl:ENSDARG00000060679 AllianceGenome:ZFIN:ZDB-GENE-030131-7828
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: aof2; kdm1; wu:fb82e06; wu:fc51a02; wu:fj36a05; wu:fj66b06
Summary: Enables histone deacetylase activity. Acts upstream of or within nervous system development; regulation of hemopoiesis; and regulation of retinoic acid biosynthetic process. Predicted to be located in nucleus. Is expressed in brain; head; intestine; and spinal cord. Orthologous to human KDM1A (lysine demethylase 1A). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 17

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	17	NC_007128.7 (28084395..28101985, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (28067432..28085042, complement)

Chromosome 17 - NC_007128.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LSD1 promotes the egress of hematopoietic stem and progenitor cells into the bloodstream during the endothelial-to-hematopoietic transition.
Title: LSD1 promotes the egress of hematopoietic stem and progenitor cells into the bloodstream during the endothelial-to-hematopoietic transition.
Genetic and epigenetic orchestration of Gfi1aa-Lsd1-cebpa in zebrafish neutrophil development.
Title: Genetic and epigenetic orchestration of Gfi1aa-Lsd1-cebpa in zebrafish neutrophil development.
LSD1 plays a critical role in hair cell regeneration and might represent a novel biomarker and potential therapeutic approach for the treatment of hearing loss.
Title: LSD1 is Required for Hair Cell Regeneration in Zebrafish.
results suggest that the LSD1-dependent shutdown of Etv2 gene expression may be a significant event required for hemangioblasts to initiate hematopoietic differentiation
Title: LSD1/KDM1A promotes hematopoietic commitment of hemangioblasts through downregulation of Etv2.
Results indicate that LSD1 demethylase activity is required for neuromast development in zebrafish larvae.
Title: Trans-2-phenylcyclopropylamine regulates zebrafish lateral line neuromast development mediated by depression of LSD1 activity.

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General gene information

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Markers

fc51a02.x1 (e-PCR)
- UniSTS:188202

z1278 (e-PCR), detects polymorphism
- UniSTS:205123

fj66b06.x1 (e-PCR)
- UniSTS:199784

G39994 (e-PCR)
- UniSTS:13429

fb82e06.x1 (e-PCR)
- UniSTS:203474

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables FAD-dependent H3K4me/H3K4me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables flavin adenine dinucleotide binding	IBA Inferred from Biological aspect of Ancestor more info
enables flavin adenine dinucleotide binding	IEA Inferred from Electronic Annotation more info
enables histone deacetylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	IBA Inferred from Biological aspect of Ancestor more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables transcription factor binding	IBA Inferred from Biological aspect of Ancestor more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of retinoic acid biosynthetic process	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lysine-specific histone demethylase 1A

Names: amine oxidase (flavin containing) domain 2; lsd1; lysine (K)-specific demethylase 1; lysine-specific demethylase 1

NP_001229924.1

EC 1.14.99.66

XP_005158840.1

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_001242995.1 → NP_001229924.1 lysine-specific histone demethylase 1A

Status: PROVISIONAL

Source sequence(s)

BC125965

UniProtKB/TrEMBL

A0A8M1NYP3, A0JMQ3, F6NIA2

Related

ENSDARP00000080193.4, ENSDART00000085758.6

Conserved Domains (5) summary

pfam01593
Location:262 → 805

Amino_oxidase; Flavin containing amine oxidoreductase

pfam04433
Location:151 → 238

SWIRM; SWIRM domain

pfam13450
Location:257 → 315

NAD_binding_8; NAD(P)-binding Rossmann-like domain

cl09111
Location:393 → 494

Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...

cl17165
Location:371 → 441

SKA2; Spindle and kinetochore-associated protein 2

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007128.7 Reference GRCz11 Primary Assembly

Range

28084395..28101985 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005158783.4 → XP_005158840.1 lysine-specific histone demethylase 1A isoform X1

UniProtKB/TrEMBL

A0A0P0UQI8, A0JMQ3

Conserved Domains (5) summary

pfam01593
Location:259 → 802

Amino_oxidase; Flavin containing amine oxidoreductase

pfam04433
Location:148 → 235

SWIRM; SWIRM domain

pfam13450
Location:254 → 312

NAD_binding_8; NAD(P)-binding Rossmann-like domain

cl09111
Location:390 → 491

Prefoldin; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits ...

cl17165
Location:368 → 438

SKA2; Spindle and kinetochore-associated protein 2