Human Gene ALKBH1 (uc001xuc.1) Description and Page Index
  Description: Homo sapiens alkB, alkylation repair homolog 1 (E. coli) (ALKBH1), mRNA.
RefSeq Summary (NM_006020): This gene encodes a homolog to the E. coli alkB gene product. The E. coli alkB protein is part of the adaptive response mechanism of DNA alkylation damage repair. It is involved in damage reversal by oxidative demethylation of 1-methyladenine and 3-methylcytosine. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1803616.180648.1, SRR1660805.27277.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2467144, SAMN03267755 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000216489.8/ ENSP00000216489.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr14:78,138,749-78,174,356 Size: 35,608 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr14:78,140,155-78,174,347 Size: 34,193 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:78,138,749-78,174,356)mRNA (may differ from genome)Protein (389 aa)
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OMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: ALKB1_HUMAN
DESCRIPTION: RecName: Full=Alkylated DNA repair protein alkB homolog 1; EC=1.14.11.33; AltName: Full=Alpha-ketoglutarate-dependent dioxygenase ABH1; AltName: Full=DNA lyase ABH1; EC=4.2.99.18; AltName: Full=DNA oxidative demethylase ALKBH1;
FUNCTION: Dioxygenase that repairs alkylated single-stranded DNA and RNA containing 3-methylcytosine by oxidative demethylation. Requires molecular oxygen, alpha-ketoglutarate and iron. May have a role in placental trophoblast lineage differentiation (By similarity). Has DNA lyase activity and introduces double-stranded breaks at abasic sites. Cleaves both single-stranded DNA and double-stranded DNA at abasic sites, with the greatest activity towards double-stranded DNA with two abasic sites. DNA lyase activity does not require alpha-ketoglutarate and iron.
CATALYTIC ACTIVITY: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
CATALYTIC ACTIVITY: DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA- base + formaldehyde + succinate + CO(2).
COFACTOR: Binds 1 Fe(2+) ion per subunit.
SUBUNIT: Monomer. Interacts with DNAJB6 (By similarity).
SUBCELLULAR LOCATION: Mitochondrion. Nucleus (By similarity). Note=Mainly localizes in euchromatin, largely excluded from heterochromatin and nucleoli (By similarity).
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the alkB family.
SIMILARITY: Contains 1 Fe2OG dioxygenase domain.
CAUTION: Detected in cytoplasm and nucleus When expressed as fusion protein with an N-terminal tag, or when the first 26 N- terminal residues are removed (PubMed:17979886 and PubMed:18603530). The endogenous, unmodified protein localizes to mitochondria (PubMed:18603530).
SEQUENCE CAUTION: Sequence=CAA63047.1; Type=Frameshift; Positions=Several;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.90 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 185.89 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -357.981406-0.255 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004574 - Alkb
IPR005123 - Oxoglu/Fe-dep_dioxygenase

Pfam Domains:
PF13532 - 2OG-Fe(II) oxygenase superfamily

ModBase Predicted Comparative 3D Structure on Q13686
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
   Protein SequenceProtein Sequence 
   AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0003824 catalytic activity
GO:0003906 DNA-(apurinic or apyrimidinic site) lyase activity
GO:0008198 ferrous iron binding
GO:0016491 oxidoreductase activity
GO:0016706 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
GO:0016829 lyase activity
GO:0042056 chemoattractant activity
GO:0043734 DNA-N1-methyladenine dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0070579 methylcytosine dioxygenase activity
GO:0103053 1-ethyladenine demethylase activity
GO:1990984 tRNA demethylase activity

Biological Process:
GO:0001701 in utero embryonic development
GO:0001764 neuron migration
GO:0001890 placenta development
GO:0002101 tRNA wobble cytosine modification
GO:0006281 DNA repair
GO:0006307 DNA dealkylation involved in DNA repair
GO:0006417 regulation of translation
GO:0006446 regulation of translational initiation
GO:0006448 regulation of translational elongation
GO:0006974 cellular response to DNA damage stimulus
GO:0008152 metabolic process
GO:0010468 regulation of gene expression
GO:0030154 cell differentiation
GO:0031175 neuron projection development
GO:0035552 oxidative single-stranded DNA demethylation
GO:0042245 RNA repair
GO:0043524 negative regulation of neuron apoptotic process
GO:0048589 developmental growth
GO:0050918 positive chemotaxis
GO:0055114 oxidation-reduction process
GO:0070129 regulation of mitochondrial translation
GO:0070989 oxidative demethylation
GO:0080111 DNA demethylation
GO:1990983 tRNA demethylation

Cellular Component:
GO:0005634 nucleus
GO:0005719 nuclear euchromatin
GO:0005739 mitochondrion


-  Descriptions from all associated GenBank mRNAs
  BC015024 - Homo sapiens alkB, alkylation repair homolog 1 (E. coli), mRNA (cDNA clone IMAGE:3910971), partial cds.
BC025787 - Homo sapiens alkB, alkylation repair homolog 1 (E. coli), mRNA (cDNA clone MGC:34444 IMAGE:5229152), complete cds.
X91992 - H.sapiens mRNA for alkB protein homolog.
JD409507 - Sequence 390531 from Patent EP1572962.
JD298105 - Sequence 279129 from Patent EP1572962.
JD315478 - Sequence 296502 from Patent EP1572962.
JD292034 - Sequence 273058 from Patent EP1572962.
JD094501 - Sequence 75525 from Patent EP1572962.
JD243413 - Sequence 224437 from Patent EP1572962.
JD414377 - Sequence 395401 from Patent EP1572962.
JD265780 - Sequence 246804 from Patent EP1572962.
JD062806 - Sequence 43830 from Patent EP1572962.
JD468381 - Sequence 449405 from Patent EP1572962.
JD334086 - Sequence 315110 from Patent EP1572962.
JD049620 - Sequence 30644 from Patent EP1572962.
JD103027 - Sequence 84051 from Patent EP1572962.
JD293723 - Sequence 274747 from Patent EP1572962.
JD074544 - Sequence 55568 from Patent EP1572962.
JD147540 - Sequence 128564 from Patent EP1572962.
KJ897918 - Synthetic construct Homo sapiens clone ccsbBroadEn_07312 ALKBH1 gene, encodes complete protein.
DQ890543 - Synthetic construct clone IMAGE:100003173; FLH163898.01X; RZPDo839A07162D alkB, alkylation repair homolog 1 (E. coli) (ALKBH1) gene, encodes complete protein.
DQ893703 - Synthetic construct Homo sapiens clone IMAGE:100008163; FLH163894.01L; RZPDo839A07161D alkB, alkylation repair homolog 1 (E. coli) (ALKBH1) gene, encodes complete protein.
CU693074 - Synthetic construct Homo sapiens gateway clone IMAGE:100019201 5' read ALKBH1 mRNA.
BX537699 - Homo sapiens mRNA; cDNA DKFZp686E22171 (from clone DKFZp686E22171).
JD171874 - Sequence 152898 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ABH, ABH1, ALKB1_HUMAN, ALKBH, NM_006020, NP_006011, Q13686, Q8TAU1, Q9ULA7
UCSC ID: uc001xuc.1
RefSeq Accession: NM_006020
Protein: Q13686 (aka ALKB1_HUMAN)
CCDS: CCDS32127.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006020.2
exon count: 6CDS single in 3' UTR: no RNA size: 2585
ORF size: 1170CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2431.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.