Human Gene XYLB (uc011ayp.1)
  Description: Homo sapiens xylulokinase homolog (H. influenzae) (XYLB), mRNA.
RefSeq Summary (NM_005108): 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].
Transcript (Including UTRs)
   Position: hg19 chr3:38,388,251-38,456,467 Size: 68,217 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr3:38,407,132-38,454,504 Size: 47,373 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:38,388,251-38,456,467)mRNA (may differ from genome)Protein (399 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedReactomeTreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: XYLB_HUMAN
DESCRIPTION: RecName: Full=Xylulose kinase; Short=Xylulokinase; EC=2.7.1.17;
CATALYTIC ACTIVITY: ATP + D-xylulose = ADP + D-xylulose 5- phosphate.
SIMILARITY: Belongs to the FGGY kinase family.
SEQUENCE CAUTION: Sequence=BAA31527.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): XYLB
CDC HuGE Published Literature: XYLB
Positive Disease Associations: Electrocardiography
Related Studies:
  1. Electrocardiography
    J Gustav Smith et al. Heart rhythm 2009, Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae., Heart rhythm : the official journal of the Heart Rhythm Society. [PubMed 19389651]
    The PR interval and its subcomponents showed substantial heritability in a South Pacific islander population and were associated with common genetic variation in SCN5A.

-  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: 5.97 RPKM in Liver
Total median expression: 33.01 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 -151.40369-0.410 Picture PostScript Text
3' UTR -499.461963-0.254 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
IPR018485 - Carb_kinase_FGGY_C
IPR018484 - Carb_kinase_FGGY_N

Pfam Domains:
PF00370 - FGGY family of carbohydrate kinases, N-terminal domain
PF02782 - FGGY family of carbohydrate kinases, C-terminal domain

SCOP Domains:
53067 - Actin-like ATPase domain

ModBase Predicted Comparative 3D Structure on O75191
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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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004856 xylulokinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor

Biological Process:
GO:0005975 carbohydrate metabolic process
GO:0005997 xylulose metabolic process
GO:0005998 xylulose catabolic process
GO:0006091 generation of precursor metabolites and energy
GO:0016310 phosphorylation
GO:0019640 glucuronate catabolic process to xylulose 5-phosphate
GO:0042732 D-xylose metabolic process
GO:0046835 carbohydrate phosphorylation

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AB015046 - Homo sapiens XYLB mRNA for xylulokinase, complete cds.
BC052984 - Homo sapiens cDNA clone IMAGE:6166461, containing frame-shift errors.
AK025728 - Homo sapiens cDNA: FLJ22075 fis, clone HEP12302, highly similar to AB015046 Homo sapiens XYLB mRNA for xylulokinase.
AK314386 - Homo sapiens cDNA, FLJ95159, highly similar to Homo sapiens xylulokinase homolog (H. influenzae) (XYLB), mRNA.
BC030231 - Homo sapiens xylulokinase homolog (H. influenzae), mRNA (cDNA clone IMAGE:5309777), partial cds.
BC137076 - Homo sapiens xylulokinase homolog (H. influenzae), mRNA (cDNA clone MGC:168696 IMAGE:9021073), complete cds.
BC137080 - Homo sapiens xylulokinase homolog (H. influenzae), mRNA (cDNA clone MGC:168700 IMAGE:9021077), complete cds.
AK293325 - Homo sapiens cDNA FLJ53504 complete cds, highly similar to Xylulose kinase (EC 2.7.1.17).
KJ905384 - Synthetic construct Homo sapiens clone ccsbBroadEn_14948 XYLB gene, encodes complete protein.
BC039712 - Homo sapiens xylulokinase homolog (H. influenzae), mRNA (cDNA clone IMAGE:5249044), with apparent retained intron.
JD210504 - Sequence 191528 from Patent EP1572962.
AK001205 - Homo sapiens cDNA FLJ10343 fis, clone NT2RM2000951, highly similar to Xylulose kinase (EC 2.7.1.17).
AK022601 - Homo sapiens cDNA FLJ12539 fis, clone NT2RM4000414.
JD368579 - Sequence 349603 from Patent EP1572962.
JD226766 - Sequence 207790 from Patent EP1572962.
JD519933 - Sequence 500957 from Patent EP1572962.
JD270976 - Sequence 252000 from Patent EP1572962.
JD299625 - Sequence 280649 from Patent EP1572962.
JD388206 - Sequence 369230 from Patent EP1572962.
JD118347 - Sequence 99371 from Patent EP1572962.
JD038522 - Sequence 19546 from Patent EP1572962.
JD069257 - Sequence 50281 from Patent EP1572962.
JD254438 - Sequence 235462 from Patent EP1572962.
JD375393 - Sequence 356417 from Patent EP1572962.
JD259234 - Sequence 240258 from Patent EP1572962.
JD222114 - Sequence 203138 from Patent EP1572962.
JD119553 - Sequence 100577 from Patent EP1572962.
JD467062 - Sequence 448086 from Patent EP1572962.
JD253198 - Sequence 234222 from Patent EP1572962.
JD259315 - Sequence 240339 from Patent EP1572962.
JD151536 - Sequence 132560 from Patent EP1572962.
JD259293 - Sequence 240317 from Patent EP1572962.
JD150579 - Sequence 131603 from Patent EP1572962.
JD402138 - Sequence 383162 from Patent EP1572962.
JD398163 - Sequence 379187 from Patent EP1572962.
JD506926 - Sequence 487950 from Patent EP1572962.
JD525661 - Sequence 506685 from Patent EP1572962.
JD560270 - Sequence 541294 from Patent EP1572962.
JD501481 - Sequence 482505 from Patent EP1572962.
JD297981 - Sequence 279005 from Patent EP1572962.
JD556040 - Sequence 537064 from Patent EP1572962.
JD281639 - Sequence 262663 from Patent EP1572962.
JD267662 - Sequence 248686 from Patent EP1572962.
JD172499 - Sequence 153523 from Patent EP1572962.
JD241269 - Sequence 222293 from Patent EP1572962.
JD557210 - Sequence 538234 from Patent EP1572962.
JD223570 - Sequence 204594 from Patent EP1572962.
JD507679 - Sequence 488703 from Patent EP1572962.
JD349607 - Sequence 330631 from Patent EP1572962.
JD545669 - Sequence 526693 from Patent EP1572962.
JD452402 - Sequence 433426 from Patent EP1572962.
JD449217 - Sequence 430241 from Patent EP1572962.
JD044073 - Sequence 25097 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00040 - Pentose and glucuronate interconversions
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein O75191 (Reactome details) participates in the following event(s):

R-HSA-5662466 XYLB phosphorylates D-xylulose
R-HSA-5661270 Catabolism of glucuronate to xylulose-5-phosphate
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: AK293325, B2RAW4, B9EH64, O75191, XYLB_HUMAN
UCSC ID: uc011ayp.1
RefSeq Accession: NM_005108
Protein: O75191 (aka XYLB_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK293325.1
exon count: 17CDS single in 3' UTR: no RNA size: 1737
ORF size: 1200CDS single in intron: no Alignment % ID: 99.88
txCdsPredict score: 1927.00frame shift in genome: no % Coverage: 100.00
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.