kdm2aa lysine (K)-specific demethylase 2Aa [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: kdm2aaprovided by ZNC
Official Full Name: lysine (K)-specific demethylase 2Aaprovided by ZNC
Primary source: ZFIN:ZDB-GENE-061215-144
See related: Ensembl:ENSDARG00000059653 AllianceGenome:ZFIN:ZDB-GENE-061215-144
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: jhdm1A-b; wu:fb76b11; wu:fj11c04; zgc:158441; zgc:158606
Summary: Predicted to enable histone demethylase activity and transcription coregulator activity. Acts upstream of or within sex determination. Predicted to be located in nucleus. Used to study melanoma. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human KDM2A (lysine demethylase 2A). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 1

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	1	NC_007112.7 (44838706..44869972)
105	previous assembly	GRCz10 (GCF_000002035.5)	1	NC_007112.6 (44137403..44168669)

Chromosome 1 - NC_007112.7 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?

loss of the orthologue kdm2aa in zebrafish causes widespread transcriptional disruption and leads to spontaneous melanomas at a high frequency
Title: Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

fb76b11.x1 (e-PCR)
- UniSTS:191285

fb76b11 (e-PCR)
- UniSTS:187509

fj11c04.x1 (e-PCR)
- UniSTS:198521

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K36me/H3K36me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	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 protein demethylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sex determination	IMP Inferred from Mutant Phenotype 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 (K)-specific demethylase 2Aa; lysine (K)-specific demethylase 2B

Names: JmjC domain-containing histone demethylation protein 1B

NP_001075161.2

EC 1.14.11.27

XP_005160305.1

EC 1.14.11.27

XP_009291632.1

EC 1.14.11.27

XP_009291637.1

EC 1.14.11.27

XP_009291640.1

EC 1.14.11.27

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_001081692.2 → NP_001075161.2 lysine (K)-specific demethylase 2Aa

Status: VALIDATED

Source sequence(s)

BX901937

UniProtKB/TrEMBL

A0A0R4IH56, A0A8M1NBS2

Related

ENSDARP00000134050.1, ENSDART00000162779.2

Conserved Domains (6) summary

cd09293
Location:1093 → 1268

AMN1; Antagonist of mitotic exit network protein 1

pfam02008
Location:511 → 545

zf-CXXC; CXXC zinc finger domain

sd00034
Location:1067 → 1091

LRR_AMN1; leucine-rich repeat [structural motif]

pfam12937
Location:1033 → 1073

F-box-like; F-box-like

pfam16866
Location:550 → 606

PHD_4; PHD-finger

cl21464
Location:199 → 299

cupin_like; Conserved domain found in cupin and related proteins

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_007112.7 Reference GRCz11 Primary Assembly

Range

44838706..44869972

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009293357.3 → XP_009291632.1 lysine (K)-specific demethylase 2B isoform X2

UniProtKB/TrEMBL

A0A8M3B2Q2

Conserved Domains (6) summary

cd09293
Location:1091 → 1266

AMN1; Antagonist of mitotic exit network protein 1

pfam02008
Location:509 → 543

zf-CXXC; CXXC zinc finger domain

sd00034
Location:1065 → 1089

LRR_AMN1; leucine-rich repeat [structural motif]

pfam12937
Location:1031 → 1071

F-box-like; F-box-like

pfam16866
Location:548 → 604

PHD_4; PHD-finger

cl21464
Location:197 → 297

cupin_like; Conserved domain found in cupin and related proteins
XM_005160248.4 → XP_005160305.1 lysine (K)-specific demethylase 2B isoform X1

UniProtKB/TrEMBL

A0A8M2B724

Conserved Domains (6) summary

cd09293
Location:1116 → 1291

AMN1; Antagonist of mitotic exit network protein 1

pfam02008
Location:534 → 568

zf-CXXC; CXXC zinc finger domain

sd00034
Location:1090 → 1114

LRR_AMN1; leucine-rich repeat [structural motif]

pfam12937
Location:1056 → 1096

F-box-like; F-box-like

pfam16866
Location:573 → 629

PHD_4; PHD-finger

cl21464
Location:222 → 322

cupin_like; Conserved domain found in cupin and related proteins
XM_009293362.3 → XP_009291637.1 lysine (K)-specific demethylase 2B isoform X3

UniProtKB/TrEMBL

A0A8M3AK71

Conserved Domains (6) summary

cd09293
Location:1063 → 1238

AMN1; Antagonist of mitotic exit network protein 1

pfam02008
Location:534 → 568

zf-CXXC; CXXC zinc finger domain

sd00034
Location:1037 → 1061

LRR_AMN1; leucine-rich repeat [structural motif]

pfam12937
Location:1003 → 1043

F-box-like; F-box-like

pfam16866
Location:573 → 629

PHD_4; PHD-finger

cl21464
Location:222 → 322

cupin_like; Conserved domain found in cupin and related proteins
XM_009293365.3 → XP_009291640.1 lysine (K)-specific demethylase 2B isoform X4

UniProtKB/TrEMBL

A0A8M3AJC4

Conserved Domains (6) summary

cd09293
Location:1037 → 1212

AMN1; Antagonist of mitotic exit network protein 1

pfam02008
Location:455 → 489

zf-CXXC; CXXC zinc finger domain

sd00034
Location:1011 → 1035

LRR_AMN1; leucine-rich repeat [structural motif]

pfam12937
Location:977 → 1017

F-box-like; F-box-like

pfam16866
Location:494 → 550

PHD_4; PHD-finger

cl21464
Location:143 → 243

cupin_like; Conserved domain found in cupin and related proteins