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... See more...

Aliases for XYLB Gene

Aliases for XYLB Gene

  • Xylulokinase 2 3 4 5
  • Xylulose Kinase 2 3 4
  • Xylulokinase Homolog (H. Influenzae) 2 3
  • D-Xylulokinase 2 3
  • EC 2.7.1.17 4 50
  • FLJ10343 2
  • FLJ12539 2
  • XYLB 5

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. Diseases associated with XYLB include Pentosuria and Galactosemia I. 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. An important paralog of this gene is GK.

UniProtKB/Swiss-Prot Summary 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.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for XYLB Gene

Genomics for XYLB Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for XYLB Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J038346 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 255.8 +0.4 416 2.1 BCLAF1 SP1 ZNF600 IKZF1 MYC ZNF592 KLF9 CEBPA ATF3 POLR2A XYLB HSALNG0025224 piR-32214-487 WDR48 GORASP1 C3orf35 SCN11A HSALNG0025225 ACVR2B
GH03J038347 Enhancer 0.3 Ensembl 250.7 -1.1 -1059 0.2 HLF HSALNG0025224 XYLB piR-32214-487 SLC22A14
GH03J038345 Enhancer 0.2 Ensembl 250.7 -1.7 -1659 0.2 HSALNG0025224 XYLB piR-32214-487 SCN11A MN309174-468 SLC22A14
GH03J038471 Enhancer 0.7 Ensembl 12.5 +126.2 126241 3.2 CEBPA ATF3 NFIC ZIC2 YY1 FOXA2 RXRA SAP130 JUND FOXP1 EXOG XYLB HSALNG0025233 ACVR2B ACVR2B-AS1
GH03J038468 Enhancer 0.5 Ensembl 12.5 +122.1 122141 0.2 FOXA2 RXRA TCF7L2 HNF4A FOXA1 RAD21 MAX SP1 EXOG XYLB ACVR2B-AS1 ACVR2B HSALNG0025233
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around XYLB on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for XYLB

Top Transcription factor binding sites by QIAGEN in the XYLB gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • GR
  • GR-alpha
  • LCR-F1
  • Pax-4a
  • POU2F1
  • POU2F1a

Genomic Locations for XYLB Gene

Latest Assembly
chr3:38,346,760-38,453,041
(GRCh38/hg38)
Size:
106,282 bases
Orientation:
Plus strand

Previous Assembly
chr3:38,388,276-38,468,677
(GRCh37/hg19 by Entrez Gene)
Size:
80,402 bases
Orientation:
Plus strand

chr3:38,388,251-38,462,839
(GRCh37/hg19 by Ensembl)
Size:
74,589 bases
Orientation:
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:
    O75191-XYLB_HUMAN
    Recommended name:
    Xylulose kinase
    Protein Accession:
    O75191
    Secondary Accessions:
    • B2RAW4
    • B4DDT2
    • B9EH64

    Protein attributes for XYLB Gene

    Size:
    536 amino acids
    Molecular mass:
    58382 Da
    Quaternary structure:
    • Monomer.
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for XYLB Gene

Selected DME Specific Peptides for XYLB Gene

O75191:
  • GNLGFYFDVMEITPEIIG
  • KVWSQACL
  • EGQFMAKRIHAEGLGYR
  • ISSYYVQRYGFPPGCKVVAF
  • LTVTSPVLMWVQALD
  • SLGTSDT
  • DGSGMNL
  • ILQVLADVF
  • ERISLVSSFAASLFLG
  • CFKNGSL
  • PALEGHIFCNPVD
  • CCLGWDFSTQQVKVVAVDAEL

Post-translational modifications for XYLB Gene

  • Ubiquitination at Lys178 and Lys494
  • Modification sites at PhosphoSitePlus

Domains & Families for XYLB Gene

Gene Families for XYLB Gene

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

Suggested Antigen Peptide Sequences for XYLB Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ53504, highly similar to Xylulose kinase (EC 2.7.1.17) (B4DDT2_HUMAN)
  • XYLB protein (Q6PIS3_HUMAN)
  • Xylulose kinase (XYLB_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75191

UniProtKB/Swiss-Prot:

XYLB_HUMAN :
  • Belongs to the FGGY kinase family.
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

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + D-xylulose = ADP + D-xylulose 5-phosphate + H(+); Xref=Rhea:RHEA:10964, ChEBI:CHEBI:15378, ChEBI:CHEBI:17140, ChEBI:CHEBI:30616, ChEBI:CHEBI:57737, ChEBI:CHEBI:456216; EC=2.7.1.17; Evidence={ECO:0000269|PubMed:23179721};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=24 uM for D-xylulose {ECO:0000269|PubMed:23179721};
GENATLAS Biochemistry:
xylulokinase-like,homolog to xylulokinase of H influenzae

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:0000166 nucleotide binding IEA --
GO:0004856 xylulokinase activity IEA,IDA 23179721
GO:0005524 ATP binding IEA --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity 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 Xylb<tm1a(EUCOMM)Hmgu>

Animal Models for research

  • Taconic Biosciences Mouse Models for XYLB

miRNA for XYLB Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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

COMPARTMENTS
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
cytosol 4
extracellular 2
mitochondrion 2
nucleus 2
plasma membrane 1
cytoskeleton 1
peroxisome 1
golgi apparatus 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:0005829 cytosol TAS --
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 IEA,TAS 9763671
GO:0005997 xylulose metabolic process IEA,IDA 23179721
GO:0005998 xylulose catabolic process TAS 9763671
GO:0006091 generation of precursor metabolites and energy TAS 9763671
GO:0016310 phosphorylation IEA,IBA 21873635
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 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
58-64-0
Xylulose 5-phosphate
  • 5-O-Phosphono-D-threo-pentos-2-ulose
  • 5-O-Phosphono-D-xylulose
  • D-Xylulose-5-phosphate
  • D-Xylulose-5-phosphoric acid
  • Xylulose 5-phosphoric acid
4212-65-1
genes like me logo Genes that share compounds with XYLB: view

Transcripts for XYLB Gene

mRNA/cDNA for XYLB Gene

4 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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
XYLB

Expression for XYLB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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, MaxQB, and MOPED for XYLB Gene



Protein tissue co-expression partners for XYLB Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for XYLB

SOURCE GeneReport for Unigene cluster for XYLB Gene:

Hs.659985

Evidence on tissue expression from TISSUES for XYLB Gene

  • Liver(4.5)
  • Kidney(4.4)
  • Lung(4.1)
genes like me logo Genes that share expression patterns with XYLB: view

Primer products for research

No data available for 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
Chimpanzee
(Pan troglodytes)
Mammalia XYLB 29 30
  • 99.11 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia XYLB 29 30
  • 89.05 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia XYLB 29 30
  • 88.19 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Xylb 29 16 30
  • 85.45 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Xylb 29
  • 84.83 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 74 (a)
OneToMany
-- 30
  • 70 (a)
OneToMany
-- 30
  • 68 (a)
OneToMany
-- 30
  • 66 (a)
OneToMany
-- 30
  • 62 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia XYLB 30
  • 72 (a)
OneToOne
Chicken
(Gallus gallus)
Aves XYLB 29 30
  • 71.69 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia XYLB 30
  • 71 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia xylb 29
  • 67.56 (n)
Zebrafish
(Danio rerio)
Actinopterygii xylb 29 30
  • 64.26 (n)
OneToOne
zgc64119 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG3534 29 30 31
  • 52.58 (n)
OneToMany
CG3544 30 31
  • 37 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000220 29
  • 51.29 (n)
Worm
(Caenorhabditis elegans)
Secernentea R08D7.7 29 30
  • 47.99 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes XKS1 30 32
  • 30 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons XK-2 29
  • 52.13 (n)
Rice
(Oryza sativa)
Liliopsida Os07g0640200 29
  • 51.29 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 60 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.13149 29
Species where no ortholog for XYLB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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

ENSEMBL:
Gene Tree for XYLB (if available)
TreeFam:
Gene Tree for XYLB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for XYLB: view image
Alliance of Genome Resources:
Additional Orthologs for XYLB

Paralogs for XYLB Gene

Paralogs for XYLB Gene

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

Variants for XYLB Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for XYLB Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs2234610 Benign: not provided 38,365,626(+) G/Ap.Asp133Asn
NM_005108.4(XYLB):c.397G>A (p.Asp133Asn)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR
rs2234622 Benign: not provided 38,376,154(+) A/Gp.Asn348Asp
NM_005108.4(XYLB):c.1042A>G (p.Asn348Asp)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs151611 -- p.Asp139Glu
rs17118 -- p.Asp85Glu
rs196380 -- p.Tyr262Asn

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for XYLB Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
XYLB
Leiden Open Variation Database (LOVD)
XYLB

SNP Genotyping and Copy Number Assays for research

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

Disorders for XYLB Gene

MalaCards: The human disease database

(3) MalaCards diseases for XYLB Gene - From: COP

Disorder Aliases PubMed IDs
pentosuria
  • pntsu
galactosemia i
  • galac1
transient global amnesia
  • amnesia, transient global
- elite association - COSMIC cancer census association via MalaCards
Search XYLB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for XYLB

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with XYLB: view

No data available for 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
  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
  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 40
  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 40
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for XYLB Gene

Sources for XYLB Gene