Human Gene ALKBH8 (uc009yxp.3) Description and Page Index
  Description: Homo sapiens alkB, alkylation repair homolog 8 (E. coli) (ALKBH8), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr11:107,373,453-107,436,461 Size: 63,009 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr11:107,375,384-107,431,619 Size: 56,236 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:107,373,453-107,436,461)mRNA (may differ from genome)Protein (664 aa)
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neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: ALKB8_HUMAN
DESCRIPTION: RecName: Full=Alkylated DNA repair protein alkB homolog 8; EC=1.14.11.-; AltName: Full=Probable alpha-ketoglutarate-dependent dioxygenase ABH8; AltName: Full=S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8; AltName: Full=tRNA (carboxymethyluridine(34)-5-O)-methyltransferase ABH8; EC=2.1.1.229;
FUNCTION: Catalyzes the methylation of 5-carboxymethyl uridine to 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in tRNA. Catalyzes the last step in the formation of 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in target tRNA. Has a preference for tRNA(Arg) and tRNA(Glu), and does not bind tRNA(Lys). Required for normal survival after DNA damage. May inhibit apoptosis and promote cell survival and angiogenesis.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + carboxymethyluridine(34) in tRNA = S-adenosyl-L-homocysteine + 5- (2-methoxy-2-oxoethyl)uridine(34) in tRNA.
SUBUNIT: Interacts with TRMT112.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Predominantly cytoplasmic.
TISSUE SPECIFICITY: Widely expressed, with highest expression in spleen, followed by pancreas and lung.
INDUCTION: Up-regulated after DNA damage. Induction is mediated via ATM.
SIMILARITY: Belongs to the alkB family.
SIMILARITY: Contains 1 Fe2OG dioxygenase domain.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ALKBH8
CDC HuGE Published Literature: ALKBH8

-  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: 3.02 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 99.78 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
5' UTR -50.60141-0.359 Picture PostScript Text
3' UTR -491.701931-0.255 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
IPR015095 - AlkB_hom8_N
IPR013216 - Methyltransf_11
IPR012677 - Nucleotide-bd_a/b_plait
IPR005123 - Oxoglu/Fe-dep_dioxygenase

Pfam Domains:
PF05148 - Hypothetical methyltransferase
PF08241 - Methyltransferase domain
PF09004 - Domain of unknown function (DUF1891)
PF13489 - Methyltransferase domain
PF13532 - 2OG-Fe(II) oxygenase superfamily
PF13649 - Methyltransferase domain

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2CQ2
- NMR MuPIT

3THP
- X-ray MuPIT

3THT
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96BT7
FrontTopSide
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003824 catalytic activity
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008198 ferrous iron binding
GO:0008270 zinc ion binding
GO:0016300 tRNA (uracil) methyltransferase activity
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:0016740 transferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0002098 tRNA wobble uridine modification
GO:0006974 cellular response to DNA damage stimulus
GO:0008152 metabolic process
GO:0030488 tRNA methylation
GO:0032259 methylation
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  BX649085 - Homo sapiens mRNA; cDNA DKFZp779J1257 (from clone DKFZp779J1257).
LF384506 - JP 2014500723-A/192009: Polycomb-Associated Non-Coding RNAs.
AK095523 - Homo sapiens cDNA FLJ38204 fis, clone FCBBF1000412.
LF375528 - JP 2014500723-A/183031: Polycomb-Associated Non-Coding RNAs.
AK304413 - Homo sapiens cDNA FLJ61557 complete cds.
LF375527 - JP 2014500723-A/183030: Polycomb-Associated Non-Coding RNAs.
AF086489 - Homo sapiens full length insert cDNA clone ZD94D04.
BC015183 - Homo sapiens alkB, alkylation repair homolog 8 (E. coli), mRNA (cDNA clone MGC:10235 IMAGE:3913134), complete cds.
AK298800 - Homo sapiens cDNA FLJ54646 complete cds.
AK293603 - Homo sapiens cDNA FLJ55535 complete cds.
AB218768 - Homo sapiens ABH8 mRNA for AlkB homologue 8, complete cds.
AB590790 - Synthetic construct DNA, clone: pFN21AE2046, Homo sapiens ALKBH8 gene for alkB, alkylation repair homolog 8, without stop codon, in Flexi system.
JD424847 - Sequence 405871 from Patent EP1572962.
JD412371 - Sequence 393395 from Patent EP1572962.
LF375526 - JP 2014500723-A/183029: Polycomb-Associated Non-Coding RNAs.
JD083778 - Sequence 64802 from Patent EP1572962.
LF375525 - JP 2014500723-A/183028: Polycomb-Associated Non-Coding RNAs.
LF375521 - JP 2014500723-A/183024: Polycomb-Associated Non-Coding RNAs.
JD563151 - Sequence 544175 from Patent EP1572962.
JD469642 - Sequence 450666 from Patent EP1572962.
JD286945 - Sequence 267969 from Patent EP1572962.
JD449013 - Sequence 430037 from Patent EP1572962.
JD550416 - Sequence 531440 from Patent EP1572962.
JD299499 - Sequence 280523 from Patent EP1572962.
JD359271 - Sequence 340295 from Patent EP1572962.
HQ447168 - Synthetic construct Homo sapiens clone IMAGE:100070456; CCSB000767_01 alkB, alkylation repair homolog 8 (E. coli) (ALKBH8) gene, encodes complete protein.
CU677231 - Synthetic construct Homo sapiens gateway clone IMAGE:100016853 5' read ALKBH8 mRNA.
KJ904946 - Synthetic construct Homo sapiens clone ccsbBroadEn_14340 ALKBH8 gene, encodes complete protein.
LF375516 - JP 2014500723-A/183019: Polycomb-Associated Non-Coding RNAs.
MA620083 - JP 2018138019-A/192009: Polycomb-Associated Non-Coding RNAs.
MA611105 - JP 2018138019-A/183031: Polycomb-Associated Non-Coding RNAs.
MA611104 - JP 2018138019-A/183030: Polycomb-Associated Non-Coding RNAs.
MA611103 - JP 2018138019-A/183029: Polycomb-Associated Non-Coding RNAs.
MA611102 - JP 2018138019-A/183028: Polycomb-Associated Non-Coding RNAs.
MA611098 - JP 2018138019-A/183024: Polycomb-Associated Non-Coding RNAs.
MA611093 - JP 2018138019-A/183019: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96BT7 (Reactome details) participates in the following event(s):

R-HSA-6786500 ALKBH8 methylates 5-carboxymethyluridine-34 in tRNA(Arg) and tRNA(Glu) yielding 5-methoxycarbonylmethyluridine-34
R-HSA-6782315 tRNA modification in the nucleus and cytosol
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ABH8, ALKB8_HUMAN, B1Q2M0, B4DEF6, NM_138775, NP_620130, Q8N989, Q96BT7
UCSC ID: uc009yxp.3
RefSeq Accession: NM_138775
Protein: Q96BT7 (aka ALKB8_HUMAN)
CCDS: CCDS8337.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138775.2
exon count: 12CDS single in 3' UTR: no RNA size: 4085
ORF size: 1995CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4062.00frame shift in genome: no % Coverage: 99.56
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.