Alkbh1 alkB homolog 1, histone H2A dioxygenase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Alkbh1provided by RGD
Official Full Name: alkB homolog 1, histone H2A dioxygenaseprovided by RGD
Primary source: RGD:1308327
See related: EnsemblRapid:ENSRNOG00000012264 AllianceGenome:RGD:1308327
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: Alkbh
Summary: Predicted to enable several functions, including 2-oxoglutarate-dependent dioxygenase activity; class I DNA-(apurinic or apyrimidinic site) endonuclease activity; and ferrous iron binding activity. Predicted to be involved in several processes, including RNA modification; positive regulation of gene expression, epigenetic; and regulation of translation. Predicted to act upstream of or within several processes, including generation of neurons; in utero embryonic development; and negative regulation of neuron apoptotic process. Predicted to be located in several cellular components, including euchromatin; mitochondrion; and nucleoplasm. Predicted to be active in cytoplasm and nucleus. Orthologous to human ALKBH1 (alkB homolog 1, histone H2A dioxygenase). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 101.0), Spleen (RPKM 87.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q31

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (112799234..112819708, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (107068301..107088784, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (111456096..111476829, complement)

Chromosome 6 - NC_086024.1 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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 2-oxoglutarate-dependent dioxygenase activity	ISO Inferred from Sequence Orthology more info
enables broad specificity oxidative DNA demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables broad specificity oxidative DNA demethylase activity	ISO Inferred from Sequence Orthology more info
enables chemoattractant activity	ISO Inferred from Sequence Orthology more info
enables class I DNA-(apurinic or apyrimidinic site) endonuclease activity	ISO Inferred from Sequence Orthology more info
enables ferrous iron binding	IBA Inferred from Biological aspect of Ancestor more info
enables ferrous iron binding	ISO Inferred from Sequence Orthology more info
enables oxidative RNA demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables oxidative RNA demethylase activity	ISO Inferred from Sequence Orthology more info
enables tRNA binding	ISO Inferred from Sequence Orthology more info
enables tRNA demethylase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA repair	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 developmental growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in oxidative RNA demethylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in oxidative RNA demethylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within placenta development	ISO Inferred from Sequence Orthology more info
involved_in positive chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitochondrial translation	ISO Inferred from Sequence Orthology more info
involved_in regulation of translational elongation	ISO Inferred from Sequence Orthology more info
involved_in regulation of translational initiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of translational initiation by tRNA modification	ISO Inferred from Sequence Orthology more info
involved_in tRNA wobble cytosine modification	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in euchromatin	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	ISO Inferred from Sequence Orthology 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

General protein information

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Preferred Names: nucleic acid dioxygenase ALKBH1

Names: DNA demethylase ALKBH1; alkB, alkylation repair homolog 1; alkylated DNA repair protein alkB homolog 1

NP_001382540.1

EC 4.2.99.18

XP_038968446.1

EC 4.2.99.18

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_001395611.2 → NP_001382540.1 nucleic acid dioxygenase ALKBH1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/TrEMBL

D3Z8W2

Related

ENSRNOP00000062185.3, ENSRNOT00000016389.8

Conserved Domains (1) summary

cl21496
Location:119 → 289

2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

RNA

NR_172646.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

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_086024.1 Reference GRCr8

Range

112799234..112819708 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039112518.2 → XP_038968446.1 nucleic acid dioxygenase ALKBH1 isoform X1

UniProtKB/TrEMBL

A6JEA5

Conserved Domains (1) summary

cl21496
Location:23 → 156

2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily