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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ALKBH4 Gene

protein-coding   GIFtS: 41
GCID: GC07M102096

alkB, alkylation repair homolog 4 (E. coli)
  Search for ALKBH4
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 Human Malady Compendium 
Biological research products
for ALKBH4    

Aliases
for ALKBH4 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
AlkB, Alkylation Repair Homolog 4 (E. Coli)1 2     Alpha-Ketoglutarate-Dependent Dioxygenase AlkB Homolog 42
ABH42 3 5     Probable Alpha-Ketoglutarate-Dependent Dioxygenase ABH42
Alkylated DNA Repair Protein AlkB Homolog 42 3     EC 1.14.11.-3
FLJ200131     

External Ids:    HGNC: 219001   Entrez Gene: 547842   Ensembl: ENSG000001609937   OMIM: 6133025   UniProtKB: Q9NXW93   

Export aliases for ALKBH4 gene to outside databases

Previous GC identifers: GC07M101883 GC07M096686


Summaries
for ALKBH4 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: ALKB4_HUMAN, Q9NXW9
Function: Probable dioxygenase that requires molecular oxygen, alpha-ketoglutarate and iron (By similarity)




Genomic Views
for ALKBH4 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.1  NT_007933.15  NT_079596.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ALKBH4 gene promoter:
         SRF   AML1a   SRF (504 AA)   GCNF   Lmo2   GATA-2   HEN1   FAC1   GCNF-1   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: ALKBH4 promoter sequence
   Search SABiosciences Chromatin IP Primers for ALKBH4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ALKBH4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 7q22.1   Ensembl cytogenetic band:  7q22.1   HGNC cytogenetic band: 7q22.1

ALKBH4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ALKBH4 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M102096:  view genomic region     (about GC identifiers)

Start:
 102,096,667 bp from pter      End:
 102,105,323 bp from pter
Size:
 8,657 bases      Orientation:
 minus strand

1 alternative location:
Chr7-,CRA_TCAG 101,456,968-101,465,622     

Proteins
for ALKBH4 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: ALKB4_HUMAN, Q9NXW9 (See protein sequence)
Recommended Name: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 4  
Size: 302 amino acids; 33838 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subcellular location: Cytoplasm. Nucleus
Sequence caution: Sequence=BAB15358.1; Type=Erroneous translation; Note=Wrong choice of CDS;
Secondary accessions: Q53H92 Q9H6A4
Alternative splicing: 2 isoforms:  Q9NXW9-1   Q9NXW9-2   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ALKBH4: NX_Q9NXW9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NXW9

    • ALKBH4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_060091.1  
    ENSEMBL proteins: 
     ENSP00000292566   ENSP00000420362  

    Human Recombinant Protein Products: 
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    Uscn Proteins for ALKBH4

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm ----
    GO:0005739mitochondrion IDA--


    ALKBH4 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for ALKBH4

    Protein Domains /
    Families
    for ALKBH4 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    ALKBH4 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR005123 Oxoglu/Fe-dep_dioxygenase

    Graphical View of Domain Structure for InterPro Entry Q9NXW9

    ProtoNet protein and cluster: Q9NXW9

    UniProtKB/Swiss-Prot: ALKB4_HUMAN, Q9NXW9
    Similarity: Belongs to the alkB family


    Function
    for ALKBH4 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: ALKB4_HUMAN, Q9NXW9
    Function: Probable dioxygenase that requires molecular oxygen, alpha-ketoglutarate and iron (By similarity)

    Enzyme Number (IUBMB): EC 1.14.11.-1

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate ALKBH4:
    hsa-miR-942
    SwitchGear 3'UTR luciferase reporter plasmid: ALKBH4 3' UTR sequence
    Inhib. RNA
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    OriGene shRNA RFP: ALKBH4
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen IEA--
    GO:0016706oxidoreductase 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 IEA--
    GO:0046872metal ion binding IEA--


    ALKBH4 for ontologies           About GeneDecksing



    Pathways & Interactions
    for ALKBH4 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ALKBH4

    2 Interacting proteins for ALKBH4 (Q9NXW93) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DNAJA3Q96EY13I2D: score=4 
    DTX2Q86UW93I2D: score=1 
    About this table

    Drugs & Compounds
    for ALKBH4 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ALKBH4
    Search CenterWatch for drugs/clinical trials and news about ALKBH4 / ALKB4 

    Transcripts
    for ALKBH4 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for ALKBH4 gene: 
    NM_017621.3  

    Unigene Cluster for ALKBH4:

    AlkB, alkylation repair homolog 4 (E. coli)
    Hs.658598  [show with all ESTs]
    Unigene Representative Sequence: NM_017621
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000292566(uc003uzl.3 uc003uzm.3) ENST00000490528 ENST00000498283


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    1 QIAGEN miScript miRNA Assays for microRNA that regulate ALKBH4:
    hsa-miR-942
    SwitchGear 3'UTR luciferase reporter plasmid: ALKBH4 3' UTR sequence
    Inhib. RNA
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    OriGene shRNA RFP: ALKBH4
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    Clone
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    Primer
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    Additional cDNA sequence: 

    AK000020.1 AK026097.1 AK222689.1 BC002820.2 BC017096.1 

    5 DOTS entries:

    DT.422481  DT.95163030  DT.121040393  DT.40260315  DT.101973380 

    24/52 AceView cDNA sequences (see all 52):

    BC002820 BM764940 AK026097 BC017096 BQ425330 AA579919 NM_017621 BU526881 
    CA420615 BP375717 BM457449 BF725596 BG499127 BM752761 BM766100 BE384853 
    BG748277 BM770478 BI818567 BM083633 BF316159 BP381675 BQ082221 BU541234 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for ALKBH4    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c · 3d
    SP1:                          -                           
    SP2:                          -                           
    SP3:              -           -                           
    SP4:                                                      
    SP5:              -     -     -                           


    ECgene alternative splicing isoforms for ALKBH4

    Expression
    for ALKBH4 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ALKBH4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATCATACCAC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image
    See ALKBH4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ALKBH4

    SOURCE GeneReport for Unigene cluster: Hs.658598

    UniProtKB/Swiss-Prot: ALKB4_HUMAN, Q9NXW9
    Tissue specificity: Widely expressed, with highest expression in pancreas, ovary and spleen

        SABiosciences Custom PCR Arrays for ALKBH4
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    In Situ
    Assay Products:     
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    Orthologs
    for ALKBH4 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for ALKBH4 gene from 6/21 species (see all 21)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Alkbh41 , 5 alkB, alkylation repair homolog 4 (E. coli)1, 5 81.55(n)1
    83.26(a)1    		   5 (75.82 cM)5
    720411  NM_028070.11  NP_082346.11 
     1361361465 
    chicken
    (Gallus gallus)    		 Aves ALKBH41 alkB, alkylation repair homolog 4 (E. coli) 64.32(n)
    64.44(a)    		   417510  XM_415758.3  XP_415758.3 
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.39792 Xenopus laevis transcribed sequence with weak similarity more 75.12(n)    CA791123.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii alkbh41 alkB, alkylation repair homolog 4 (E. coli) 57.92(n)
    58.17(a)    		   553475  XM_681983.2  XP_687075.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG40361 CG4036 50.83(n)
    40.23(a)    		   34302  NM_135470.2  NP_609314.1 
    worm
    (Caenorhabditis elegans)    		 Secernentea F09F7.71 Protein F09F7.7 47.39(n)
    39.36(a)    		   175765  NM_171124.3  NP_741141.1 


    ENSEMBL Gene Tree for ALKBH4 (if available)
    TreeFam Gene Tree for ALKBH4 (if available) 

    Paralogs
    for ALKBH4 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for ALKBH4 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/229 NCBI SNPs in ALKBH4 are shown (see all 229)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 7 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1459701011,2
    		--102096168(+) GGGGCC/TGTGAT 3 -- int1 ut310--------
    rs1128367611,2
    		C,--102096210(+) CCAAGT/-TGAGT 3 -- int1 ut312Minor allele frequency- -:0.25CSA 4
    rs102823741,2
    		C,F,--102096223(+) ACCAGG/TGAGCC 3 -- ut31 int11Minor allele frequency- T:0.12WA 118
    rs1397971711,2
    		--102096242(+) GGTGGA/CCTGGG 3 -- ut31 int10--------
    rs1927407351,2
    		--102096269(+) CTAGCA/GGCTGG 3 -- ut31 int10--------
    rs1432034941,2
    		--102096322(+) CTATGC/TGGGGC 3 -- ut31 int10--------
    rs47297891,2
    		C,F,H,--102096361(+) TGGGAC/TGCTGC 3 -- ut31 int119Minor allele frequency- T:0.05NS EA NA WA CSA 1141
    rs1456067731,2
    		--102096470(+) TGGATG/TTAGTT 3 -- ut31 int10--------
    rs102557821,2
    		C,--102096472(+) GATTTA/GGTTCC 3 -- int1 ut312Minor allele frequency- G:0.13WA 120
    rs132232881,2
    		C,H--102096495(+) AGGAAC/TTGAAC 3 -- ut31 int14Minor allele frequency- T:0.00NS EA 416

    HapMap Linkage Disequilibrium report for ALKBH4 (102096667 - 102105323 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for ALKBH4
         3 CNVs: 36585 4553 31385

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    Disorders / Diseases
    for ALKBH4 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    ALKBH4 for disorders           About MalaCards

    ALKBH4 for disorders           About GeneDecksing

    OMIM gene information: 613302    OMIM disorders: --


    Export disorders for ALKBH4 gene to outside databases

    Publications
    for ALKBH4 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for ALKBH4 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with ALKBH4)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Expression and sub-cellular localization of human ABH family molecules. (PubMed id 17979886)1, 2 Tsujikawa K....Yamamoto H. (2007)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Spectroscopic and magnetic studies of wild-type and m utant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4. (PubMed id 21166655)1 BjA...Andersson K.K. (2011)
    5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    7. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    9. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. (PubMed id 8125298)1 Maruyama K. and Sugano S. (1994)

    External Searches for ALKBH4 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
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    Genome Databases showing ALKBH4 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 54784 HGNC: 21900 AceView: FLJ20013 Ensembl:ENSG00000160993 euGenes: HUgn54784
    ECgene: ALKBH4 H-InvDB: ALKBH4

    Other Databases showing ALKBH4 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing ALKBH4 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ALKBH4 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for ALKBH4 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for ALKBH4 gene:
    Search GeneIP for patents involving ALKBH4

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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