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Alkbh3 alkB homolog 3, alpha-ketoglutarate-dependent dioxygenase [ Rattus norvegicus (Norway rat) ]

Gene ID: 362169, updated on 10-Oct-2019

Summary

Official Symbol
Alkbh3provided by RGD
Official Full Name
alkB homolog 3, alpha-ketoglutarate-dependent dioxygenaseprovided by RGD
Primary source
RGD:1359731
See related
Ensembl:ENSRNOG00000021678
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
Expression
Biased expression in Heart (RPKM 461.0), Muscle (RPKM 383.7) and 9 other tissues See more
Orthologs

Genomic context

See Alkbh3 in Genome Data Viewer
Location:
3q31
Exon count:
10
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (82874242..82907467, complement)
106 current Rn_Celera (GCF_000002265.2) 3 AC_000071.1 (79141033..79172722, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 3 NC_005102.3 (89575451..89608158, complement)

Chromosome 3 - NC_005102.4Genomic Context describing neighboring genes Neighboring gene ATP synthase lipid-binding protein, mitochondrial-like Neighboring gene similar to LOC387763 protein Neighboring gene hydroxysteroid (17-beta) dehydrogenase 12 Neighboring gene mitochondrial import inner membrane translocase subunit Tim23-like Neighboring gene microRNA 129-2

Genomic regions, transcripts, and products

Expression

  • 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

General gene information

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
DNA-N1-methyladenine dioxygenase activity ISO
Inferred from Sequence Orthology
more info
PubMed 
DNA-N1-methyladenine dioxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA N1-methyladenosine dioxygenase activity ISO
Inferred from Sequence Orthology
more info
PubMed 
RNA N1-methyladenosine dioxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosine C-5 DNA demethylase activity IEA
Inferred from Electronic Annotation
more info
 
cytosine C-5 DNA demethylase activity ISO
Inferred from Sequence Orthology
more info
PubMed 
NOT endonuclease activity ISO
Inferred from Sequence Orthology
more info
PubMed 
NOT exonuclease activity ISO
Inferred from Sequence Orthology
more info
PubMed 
ferrous iron binding ISO
Inferred from Sequence Orthology
more info
PubMed 
ferrous iron binding ISS
Inferred from Sequence or Structural Similarity
more info
 
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors ISO
Inferred from Sequence Orthology
more info
PubMed 
Process Evidence Code Pubs
DNA dealkylation involved in DNA repair ISO
Inferred from Sequence Orthology
more info
PubMed 
DNA dealkylation involved in DNA repair ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA repair ISO
Inferred from Sequence Orthology
more info
PubMed 
DNA repair ISS
Inferred from Sequence or Structural Similarity
more info
 
cell proliferation ISO
Inferred from Sequence Orthology
more info
PubMed 
cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
oxidative single-stranded DNA demethylation ISO
Inferred from Sequence Orthology
more info
PubMed 
oxidative single-stranded DNA demethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
oxidative single-stranded RNA demethylation IEA
Inferred from Electronic Annotation
more info
 
oxidative single-stranded RNA demethylation ISO
Inferred from Sequence Orthology
more info
PubMed 
Component Evidence Code Pubs
cytosol IEA
Inferred from Electronic Annotation
more info
 
cytosol ISO
Inferred from Sequence Orthology
more info
 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
mitochondrion ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
Names
alkB, alkylation repair homolog 3
alkylated DNA repair protein alkB homolog 3
alkylation repair-like protein 3
NP_001014202.1
XP_006234647.1

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001014180.1NP_001014202.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3

    See identical proteins and their annotated locations for NP_001014202.1

    Status: PROVISIONAL

    Source sequence(s)
    BC083756
    UniProtKB/Swiss-Prot
    Q5XIC8
    Related
    ENSRNOP00000030278.4, ENSRNOT00000030784.5
    Conserved Domains (1) summary
    pfam13532
    Location:90275
    2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005102.4 Reference Rnor_6.0 Primary Assembly

    Range
    82874242..82907467 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006234585.3XP_006234647.1  alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 isoform X1

    See identical proteins and their annotated locations for XP_006234647.1

    UniProtKB/Swiss-Prot
    Q5XIC8
    Conserved Domains (1) summary
    pfam13532
    Location:90275
    2OG-FeII_Oxy_2; 2OG-Fe(II) oxygenase superfamily

Alternate Rn_Celera

Genomic

  1. AC_000071.1 Alternate Rn_Celera

    Range
    79141033..79172722 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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