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Aliases for XYLB Gene

Aliases for XYLB Gene

  • Xylulokinase 2 3 4 5
  • Xylulokinase Homolog (H. Influenzae) 2 3
  • Xylulose Kinase 2 3
  • D-Xylulokinase 2 3
  • EC 4 56

External Ids for XYLB Gene

Previous GeneCards Identifiers for XYLB Gene

  • GC03P037677
  • GC03P038201
  • GC03P038348

Summaries for XYLB Gene

Entrez Gene Summary for XYLB Gene

  • The protein encoded by this gene shares 22% sequence identity with Hemophilus influenzae xylulokinase, and even higher identity to other gene products in C.elegans (45%) and yeast (31-35%), which are thought to belong to a family of enzymes that include fucokinase, gluconokinase, glycerokinase and xylulokinase. These proteins play important roles in energy metabolism. [provided by RefSeq, Aug 2009]

GeneCards Summary for XYLB Gene

XYLB (Xylulokinase) is a Protein Coding gene. Among its related pathways are Glycosaminoglycan metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include phosphotransferase activity, alcohol group as acceptor and xylulokinase activity.

UniProtKB/Swiss-Prot for XYLB Gene

  • Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.

Additional gene information for XYLB Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XYLB Gene

Genomics for XYLB Gene

GeneHancer (GH) Regulatory Elements for XYLB Gene

Promoters and enhancers for XYLB Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I038346 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 555.9 +0.4 382 2 HDGF PKNOX1 CLOCK FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 XYLB OXSR1 GORASP1 WDR48 SCN11A PIR42930
GH03I038267 Enhancer 0.4 Ensembl ENCODE 11 -79.1 -79063 0.7 SLC22A13 RNU6-235P XYLB MYD88 ACAA1 VILL GC03M038270 LOC101409262
GH03I038268 Enhancer 0.3 Ensembl 11 -78.2 -78159 0.8 SPI1 RNU6-235P XYLB ACAA1 MYD88 VILL DLEC1 GC03M038270 LOC101409262 SLC22A13
GH03I038452 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 0.1 +108.0 108013 4 PKNOX1 CLOCK FOXA2 ARID4B SIN3A FEZF1 YY1 E2F8 PAF1 SP3 ACVR2B-AS1 ACVR2B EXOG XYLB
GH03I038426 Enhancer 0.6 ENCODE dbSUPER 0.2 +80.3 80335 1.3 CBFA2T3 NFE2 CUX1 EXOG ACVR2B PIR42930 XYLB
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around XYLB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the XYLB gene promoter:

Genomic Locations for XYLB Gene

Genomic Locations for XYLB Gene
106,282 bases
Plus strand

Genomic View for XYLB Gene

Genes around XYLB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XYLB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XYLB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XYLB Gene

Proteins for XYLB Gene

  • Protein details for XYLB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Xylulose kinase
    Protein Accession:
    Secondary Accessions:
    • B2RAW4
    • B4DDT2
    • B9EH64

    Protein attributes for XYLB Gene

    536 amino acids
    Molecular mass:
    58382 Da
    Quaternary structure:
    • Monomer.
    • Sequence=BAA31527.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for XYLB Gene

    Alternative splice isoforms for XYLB Gene


neXtProt entry for XYLB Gene

Selected DME Specific Peptides for XYLB Gene


Post-translational modifications for XYLB Gene

  • Ubiquitination at isoforms=2178 and isoforms=2494
  • Modification sites at PhosphoSitePlus

Domains & Families for XYLB Gene

Gene Families for XYLB Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for XYLB Gene

Suggested Antigen Peptide Sequences for XYLB Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the FGGY kinase family.
  • Belongs to the FGGY kinase family.
genes like me logo Genes that share domains with XYLB: view

Function for XYLB Gene

Molecular function for XYLB Gene

GENATLAS Biochemistry:
xylulokinase-like,homolog to xylulokinase of H influenzae
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=24 uM for D-xylulose {ECO:0000269 PubMed:23179721};
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + D-xylulose = ADP + D-xylulose 5-phosphate.
UniProtKB/Swiss-Prot Function:
Phosphorylates D-xylulose to produce D-xylulose 5-phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis.

Enzyme Numbers (IUBMB) for XYLB Gene

Phenotypes From GWAS Catalog for XYLB Gene

Gene Ontology (GO) - Molecular Function for XYLB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004856 xylulokinase activity TAS,IDA 23179721
GO:0005524 ATP binding IEA --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016773 phosphotransferase activity, alcohol group as acceptor IEA --
genes like me logo Genes that share ontologies with XYLB: view
genes like me logo Genes that share phenotypes with XYLB: view

Animal Models for XYLB Gene

MGI Knock Outs for XYLB:
  • Xylb tm1a(EUCOMM)Hmgu

Animal Model Products

  • Taconic Biosciences Mouse Models for XYLB

miRNA for XYLB Gene

Clone Products

  • Addgene plasmids for XYLB

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for XYLB Gene

Localization for XYLB Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for XYLB gene
Compartment Confidence
extracellular 5
cytosol 5
nucleus 2
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for XYLB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA,HDA 23376485
genes like me logo Genes that share ontologies with XYLB: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for XYLB Gene

Pathways & Interactions for XYLB Gene

genes like me logo Genes that share pathways with XYLB: view

Pathways by source for XYLB Gene

Gene Ontology (GO) - Biological Process for XYLB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process TAS 9763671
GO:0005997 xylulose metabolic process IDA 23179721
GO:0005998 xylulose catabolic process TAS 9763671
GO:0006091 generation of precursor metabolites and energy TAS 9763671
GO:0016310 phosphorylation IEA --
genes like me logo Genes that share ontologies with XYLB: view

No data available for SIGNOR curated interactions for XYLB Gene

Drugs & Compounds for XYLB Gene

(2) Drugs for XYLB Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
D-Xylulose Experimental Pharma 0
ATP Investigational Nutra Agonist 0

(2) Additional Compounds for XYLB Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
Xylulose 5-phosphate
  • D-Xylulose 5-phosphate
  • D-Xylulose 5-PO4
  • D-Xylulose-5-P
  • D-Xylulose-5-phosphate
  • Xu-5-P
genes like me logo Genes that share compounds with XYLB: view

Transcripts for XYLB Gene

Unigene Clusters for XYLB Gene

Xylulokinase homolog (H. influenzae):
Representative Sequences:

Clone Products

  • Addgene plasmids for XYLB

Alternative Splicing Database (ASD) splice patterns (SP) for XYLB Gene

No ASD Table

Relevant External Links for XYLB Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for XYLB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for XYLB Gene

mRNA differential expression in normal tissues according to GTEx for XYLB Gene

This gene is overexpressed in Liver (x14.5).

Protein differential expression in normal tissues from HIPED for XYLB Gene

This gene is overexpressed in Liver (20.7), Gallbladder (20.2), and Skin (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for XYLB Gene

Protein tissue co-expression partners for XYLB Gene

NURSA nuclear receptor signaling pathways regulating expression of XYLB Gene:


SOURCE GeneReport for Unigene cluster for XYLB Gene:


Evidence on tissue expression from TISSUES for XYLB Gene

  • Liver(4.4)
  • Kidney(4.3)
  • Lung(4)
genes like me logo Genes that share expression patterns with XYLB: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for XYLB Gene

Orthologs for XYLB Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for XYLB Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia XYLB 33 34
  • 99.11 (n)
(Canis familiaris)
Mammalia XYLB 33 34
  • 89.05 (n)
(Bos Taurus)
Mammalia XYLB 33 34
  • 88.19 (n)
(Mus musculus)
Mammalia Xylb 33 16 34
  • 85.45 (n)
(Rattus norvegicus)
Mammalia Xylb 33
  • 84.83 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 74 (a)
-- 34
  • 70 (a)
-- 34
  • 68 (a)
-- 34
  • 66 (a)
-- 34
  • 62 (a)
(Monodelphis domestica)
Mammalia XYLB 34
  • 72 (a)
(Gallus gallus)
Aves XYLB 33 34
  • 71.69 (n)
(Anolis carolinensis)
Reptilia XYLB 34
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia xylb 33
  • 67.56 (n)
(Danio rerio)
Actinopterygii xylb 33 34
  • 64.26 (n)
zgc64119 33
fruit fly
(Drosophila melanogaster)
Insecta CG3534 35 33 34
  • 52.58 (n)
CG3544 35 34
  • 39 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000220 33
  • 51.29 (n)
(Caenorhabditis elegans)
Secernentea R08D7.7 33 34
  • 47.99 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes XKS1 34 36
  • 30 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons XK-2 33
  • 52.13 (n)
(Oryza sativa)
Liliopsida Os07g0640200 33
  • 51.29 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 60 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13149 33
Species where no ortholog for XYLB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for XYLB Gene

Gene Tree for XYLB (if available)
Gene Tree for XYLB (if available)

Paralogs for XYLB Gene

No data available for Paralogs for XYLB Gene

Variants for XYLB Gene

Sequence variations from dbSNP and Humsavar for XYLB Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000004136 -- 38,380,019(+) C/ genic_downstream_transcript_variant, intron_variant
rs1000026313 -- 38,422,831(+) C/A coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, missense_variant
rs1000039786 -- 38,415,509(+) A/G genic_downstream_transcript_variant, intron_variant
rs1000048689 -- 38,371,838(+) C/G intron_variant
rs1000178304 -- 38,449,263(+) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for XYLB Gene

Variant ID Type Subtype PubMed ID
esv2584185 CNV insertion 19546169
esv3568701 CNV loss 25503493
nsv1114371 CNV deletion 24896259
nsv1129411 OTHER inversion 24896259
nsv237015 CNV deletion 16902084
nsv238024 CNV deletion 16902084
nsv473449 CNV novel sequence insertion 20440878

Variation tolerance for XYLB Gene

Residual Variation Intolerance Score: 86.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.80; 89.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for XYLB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XYLB Gene

Disorders for XYLB Gene

Additional Disease Information for XYLB

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for XYLB Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for XYLB Gene

Publications for XYLB Gene

  1. Genomic structure of a novel human gene (XYLB) on chromosome 3p22-->p21.3 encoding a xylulokinase-like protein. (PMID: 9763671) Tamari M … Nakamura Y (Cytogenetics and cell genetics 1998) 2 3 4 22 58
  2. Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism. (PMID: 23179721) Bunker RD … Baker EN (The Journal of biological chemistry 2013) 2 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae. (PMID: 19389651) Smith JG … Newton-Cheh C (Heart rhythm 2009) 3 44 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for XYLB Gene

  • Addgene plasmids for XYLB

Sources for XYLB Gene

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