Human Gene ALKBH4 (uc003uzl.3)
  Description: Homo sapiens alkB, alkylation repair homolog 4 (E. coli) (ALKBH4), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:102,096,667-102,105,321 Size: 8,655 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr7:102,097,841-102,105,283 Size: 7,443 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:102,096,667-102,105,321)mRNA (may differ from genome)Protein (302 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ALKB4_HUMAN
DESCRIPTION: RecName: Full=Probable alpha-ketoglutarate-dependent dioxygenase ABH4; EC=1.14.11.-; AltName: Full=Alkylated DNA repair protein alkB homolog 4;
FUNCTION: Probable dioxygenase that requires molecular oxygen, alpha-ketoglutarate and iron (By similarity).
COFACTOR: Binds 1 Fe(2+) ion per subunit (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Widely expressed, with highest expression in pancreas, ovary and spleen.
SIMILARITY: Belongs to the alkB family.
SEQUENCE CAUTION: Sequence=BAB15358.1; Type=Erroneous translation; Note=Wrong choice of CDS;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.48 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 227.41 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.4038-0.405 Picture PostScript Text
3' UTR -440.881174-0.376 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
IPR005123 - Oxoglu/Fe-dep_dioxygenase

ModBase Predicted Comparative 3D Structure on Q9NXW9
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005515 protein 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:0032451 demethylase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006482 protein demethylation
GO:0031032 actomyosin structure organization
GO:0036090 cleavage furrow ingression
GO:0055114 oxidation-reduction process
GO:0070988 demethylation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0030496 midbody
GO:0070938 contractile ring


-  Descriptions from all associated GenBank mRNAs
  LF384052 - JP 2014500723-A/191555: Polycomb-Associated Non-Coding RNAs.
BC017096 - Homo sapiens alkB, alkylation repair homolog 4 (E. coli), mRNA (cDNA clone MGC:12618 IMAGE:2820440), complete cds.
AK222689 - Homo sapiens mRNA for hypothetical protein FLJ20013 variant, clone: CBR05887.
BC002820 - Homo sapiens alkB, alkylation repair homolog 4 (E. coli), mRNA (cDNA clone MGC:3464 IMAGE:3636984), complete cds.
AK000020 - Homo sapiens cDNA FLJ20013 fis, clone ADKA03455.
AK026097 - Homo sapiens cDNA: FLJ22444 fis, clone HRC09425.
HQ447345 - Synthetic construct Homo sapiens clone IMAGE:100070666; CCSB004187_02 alkB, alkylation repair homolog 4 (E. coli) (ALKBH4) gene, encodes complete protein.
KJ894064 - Synthetic construct Homo sapiens clone ccsbBroadEn_03458 ALKBH4 gene, encodes complete protein.
CU678220 - Synthetic construct Homo sapiens gateway clone IMAGE:100018774 5' read ALKBH4 mRNA.
MA619629 - JP 2018138019-A/191555: Polycomb-Associated Non-Coding RNAs.
JD327126 - Sequence 308150 from Patent EP1572962.
JD083667 - Sequence 64691 from Patent EP1572962.
JD110204 - Sequence 91228 from Patent EP1572962.
JD516191 - Sequence 497215 from Patent EP1572962.
JD084884 - Sequence 65908 from Patent EP1572962.
JD267373 - Sequence 248397 from Patent EP1572962.
JD080916 - Sequence 61940 from Patent EP1572962.
JD442739 - Sequence 423763 from Patent EP1572962.
JD444216 - Sequence 425240 from Patent EP1572962.
JD200057 - Sequence 181081 from Patent EP1572962.
JD045163 - Sequence 26187 from Patent EP1572962.
JD511953 - Sequence 492977 from Patent EP1572962.
JD079523 - Sequence 60547 from Patent EP1572962.
JD243196 - Sequence 224220 from Patent EP1572962.
JD136156 - Sequence 117180 from Patent EP1572962.
JD457015 - Sequence 438039 from Patent EP1572962.
JD356997 - Sequence 338021 from Patent EP1572962.
JD512776 - Sequence 493800 from Patent EP1572962.
JD412803 - Sequence 393827 from Patent EP1572962.
JD324181 - Sequence 305205 from Patent EP1572962.
JD173961 - Sequence 154985 from Patent EP1572962.
JD512775 - Sequence 493799 from Patent EP1572962.
JD140064 - Sequence 121088 from Patent EP1572962.
JD409556 - Sequence 390580 from Patent EP1572962.
JD196060 - Sequence 177084 from Patent EP1572962.
JD140062 - Sequence 121086 from Patent EP1572962.
DQ571271 - Homo sapiens piRNA piR-31383, complete sequence.
JD481826 - Sequence 462850 from Patent EP1572962.
JD265249 - Sequence 246273 from Patent EP1572962.
JD071850 - Sequence 52874 from Patent EP1572962.
JD038100 - Sequence 19124 from Patent EP1572962.
JD235300 - Sequence 216324 from Patent EP1572962.
JD309326 - Sequence 290350 from Patent EP1572962.
JD554916 - Sequence 535940 from Patent EP1572962.
JD517228 - Sequence 498252 from Patent EP1572962.
JD366202 - Sequence 347226 from Patent EP1572962.
JD366201 - Sequence 347225 from Patent EP1572962.
JD189767 - Sequence 170791 from Patent EP1572962.
JD405182 - Sequence 386206 from Patent EP1572962.
JD461273 - Sequence 442297 from Patent EP1572962.
JD057123 - Sequence 38147 from Patent EP1572962.
JD406681 - Sequence 387705 from Patent EP1572962.
JD100390 - Sequence 81414 from Patent EP1572962.
JD523352 - Sequence 504376 from Patent EP1572962.
JD246666 - Sequence 227690 from Patent EP1572962.
JD084151 - Sequence 65175 from Patent EP1572962.
JD182624 - Sequence 163648 from Patent EP1572962.
JD331838 - Sequence 312862 from Patent EP1572962.
JD472196 - Sequence 453220 from Patent EP1572962.
JD472195 - Sequence 453219 from Patent EP1572962.
JD180083 - Sequence 161107 from Patent EP1572962.
JD196848 - Sequence 177872 from Patent EP1572962.
JD470843 - Sequence 451867 from Patent EP1572962.
JD472194 - Sequence 453218 from Patent EP1572962.
JD047644 - Sequence 28668 from Patent EP1572962.
JD459213 - Sequence 440237 from Patent EP1572962.
JD513007 - Sequence 494031 from Patent EP1572962.
JD173969 - Sequence 154993 from Patent EP1572962.
JD283239 - Sequence 264263 from Patent EP1572962.
JD265163 - Sequence 246187 from Patent EP1572962.
JD495575 - Sequence 476599 from Patent EP1572962.
JD220773 - Sequence 201797 from Patent EP1572962.
JD411052 - Sequence 392076 from Patent EP1572962.
JD258179 - Sequence 239203 from Patent EP1572962.
JD417453 - Sequence 398477 from Patent EP1572962.
JD143423 - Sequence 124447 from Patent EP1572962.
JD259011 - Sequence 240035 from Patent EP1572962.
JD275610 - Sequence 256634 from Patent EP1572962.
JD522305 - Sequence 503329 from Patent EP1572962.
JD556367 - Sequence 537391 from Patent EP1572962.
JD431358 - Sequence 412382 from Patent EP1572962.
JD431357 - Sequence 412381 from Patent EP1572962.
JD266549 - Sequence 247573 from Patent EP1572962.
JD512780 - Sequence 493804 from Patent EP1572962.
JD412806 - Sequence 393830 from Patent EP1572962.
JD197816 - Sequence 178840 from Patent EP1572962.
JD212425 - Sequence 193449 from Patent EP1572962.
JD512779 - Sequence 493803 from Patent EP1572962.
JD512777 - Sequence 493801 from Patent EP1572962.
JD412804 - Sequence 393828 from Patent EP1572962.
JD283351 - Sequence 264375 from Patent EP1572962.
JD098826 - Sequence 79850 from Patent EP1572962.
JD172781 - Sequence 153805 from Patent EP1572962.
JD391235 - Sequence 372259 from Patent EP1572962.
LF359898 - JP 2014500723-A/167401: Polycomb-Associated Non-Coding RNAs.
LF359897 - JP 2014500723-A/167400: Polycomb-Associated Non-Coding RNAs.
MA595475 - JP 2018138019-A/167401: Polycomb-Associated Non-Coding RNAs.
MA595474 - JP 2018138019-A/167400: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ABH4, ALKB4_HUMAN, NM_017621, NP_060091, Q53H92, Q9H6A4, Q9NXW9
UCSC ID: uc003uzl.3
RefSeq Accession: NM_017621
Protein: Q9NXW9 (aka ALKB4_HUMAN)
CCDS: CCDS5723.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017621.3
exon count: 3CDS single in 3' UTR: no RNA size: 2138
ORF size: 909CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2018.00frame shift in genome: no % Coverage: 99.20
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.