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XYLB Gene

protein-coding GIFtS: 54

GC03P038363

xylulokinase homolog (H. influenzae)
(Previous name: xylulokinase (H. influenzae) homolog )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases
EC 2.7.1.17 ^³
FLJ10343 ^¹, ²
FLJ12539 ^¹, ²
FLJ22075 ^²
Xylulokinase ^³
xylulokinase ^²

Descriptions
xylulokinase (H. influenzae) homolog ^¹
xylulokinase homolog (H. influenzae) ^²

External Ids
HGNC: 12839¹
Entrez Gene: 9942²
UniProtKB: O75191³
Ensembl: ENSG00000093217⁷

Search outside databases for aliases for XYLB gene

Previous GC identifers: GC03P037677 GC03P038201 GC03P038348

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for XYLB:

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. Multiple transcripts resulting from use of alternate polyadenylation sites have been

noted for this gene. [provided by RefSeq]

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the XYLB gene

Entrez Gene cytogenetic band: 3p22-p21.3 Ensembl cytogenetic band: 3p22.2 HGNC cytogenetic band: 3p22-p21.3

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

GeneLoc gene densities for chromosome 3 GeneLoc Exon Structure

GeneLoc location for GC03P038363: (about GC identifiers)

Start:	38,363,244 bp from pter
End:	38,431,471 bp from pter
Size:	68,228 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000003.10 NT_022517.17

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: XYLB_HUMAN, O75191 (See protein sequence)

Recommended Name: Xylulose kinase

Size: 536 amino acids; 58382 Da

Sequence caution: Sequence=BAA31527.1; Type=Miscellaneous discrepancy; Note=Probable cloning

artifact;

Secondary accessions: B2RAW4 B9EH64

REFSEQ proteins: NP_005099.2

ENSEMBL proteins:

ENSP00000207870

Human Recombinant Proteins

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	Recombinant Proteins from Abcam (XYLB)
	Human Recombinant Proteins from Abnova (XYLB)

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

Antibodies for XYLB:

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	Antibodies from Abcam (XYLB), each with their Abpromise^SM
	Monoclonal and Polyclonal Antibodies from Abnova (XYLB)
	Novus Biologicals Antibodies for XYLB

Assays for XYLB:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Graphical View of Domain Structure for InterPro Entry O75191

ProtoNet protein and cluster: O75191

UniProtKB/Swiss-Prot: XYLB_HUMAN, O75191

Similarity: Belongs to the FGGY kinase family

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (XYLB)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (XYLB)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_005108

Applied Biosystems Silencer® siRNAs for XYLB

Sigma-Aldrich siRNA and siRNA Panels for XYLB

Sigma-Aldrich shRNA Panels and shRNA for XYLB

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Browse Clone Ranger at Invitrogen for clones
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_005108
Myc/DDK tagged cDNA clone in CMV expression vector: NM_005108
untagged cDNA clone in CMV expression vector: NM_005108

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_005108

UniProtKB/Swiss-Prot: XYLB_HUMAN, O75191

Catalytic activity: ATP + D-xylulose = ADP + D-xylulose 5-phosphate

Enzyme Number (IUBMB): EC 2.7.1.17

Genatlas biochemistry entry for XYLB:

xylulokinase-like,homolog to xylulokinase of H influenzae

1 MGI phenotypic allele

for Xylb (no phenotypes)

3 Gene Ontology (GO) molecular function terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004856	xylulokinase activity	TAS	9763671
GO:0016301	kinase activity	IEA	--
GO:0016740	transferase activity	IEA	--

About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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1 Sigma-Aldrich "Your Favorite Gene" Pathway for XYLB (Your Favorite Gene powered by Ingenuity)

Pentose and Glucuronate Interconversions

GeneDecks XYLB for the pathways selected above

About GeneDecksing

5/6 Interacting proteins for XYLB (ENSP00000207870³) via UniProtKB, MINT, and/or STRING (see all 6 )

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
SLC22A14	ENSP00000273173³	STRING (score=.945)
SLC22A13	ENSP00000310241³	STRING (score=.924)
EEF2	ENSP00000307940³	STRING (score=.877)
HSP90AA2	ENSP00000335153³	STRING (score=.778)
CALM3	ENSP00000291295³	STRING (score=.744)

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3 Gene Ontology (GO) biological process terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005975	carbohydrate metabolic process	TAS	9763671
GO:0006091	generation of precursor metabolites and energy	TAS	9763671
GO:0042732	D-xylose metabolic process	IEA	--

About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for XYLB

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (XYLB)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (XYLB)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_005108

Sigma-Aldrich siRNA and siRNA Panels for XYLB

Sigma-Aldrich shRNA Panels and shRNA for XYLB

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_005108

REFSEQ mRNAs for XYLB gene:

NM_005108.2

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_005108

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_005108
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_005108
                                 untagged cDNA clone in CMV expression vector: NM_005108

Additional cDNA sequence:

AK001205.1 AK022601.1 AK025728.1 AK293325.1 AK314386.1 BC030231.2 BC039712.1 BC052984.1

BC137076.1 BC137080.1 CR603420.1

4 DOTS entries:

DT.92068857 DT.97809611 DT.100640731 DT.91814738

24/48 AceView cDNA sequences (see all 48 ):

AK022601 BX485668 NM_005108 BU733607 BM823852 BM709607 BU194672 CR603420

BM013957 AU123748 AK001205 AB015046 BU155907 BV197903 AA360549 BC039712

BI917458 AK025728 AW771907 AL556887 BU932999 AL579011 AU124699 BG761093

highest scoring ESTs for XYLB:

AK001205 AK022601 AK025728 AU124699 AW754059 AW771907 BC052984 BE782125 BF593198 BG031172

Unigene Cluster for XYLB:

Xylulokinase homolog (H. influenzae)

Hs.659985 [show with all ESTs]

Unigene Representative Sequence: NM_005108

GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:

ENST00000207870

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

XYLB expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for XYLB

¹ / ² / ³

7 probe-sets matching XYLB gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
31767_at²^{, 3}	U95-A	1	1.00	1.00	1.00	1.00	AB015046	0.40	1.00	0.76	1
208318_s_at²^{, 3}	U133-A	1	1.00	1.00	--	--	NM_005108	0.60	1.00	0.82	1
208317_at²^{, 3}	U133-A	1	1.00	1.00	--	--	NM_005108	0.60	1.00	0.82	1
214776_x_at²^{, 3}	U133-A	1	0.82	1.00	--	--	AA777793	0.40	1.00	0.76	1
208318_s_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
208317_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
214776_x_at²	U133Plus2	1	0.82	1.00	--	--	--	--	--	--	--

About this table

Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.659985
Expression variation in blood from EXPOLDB for XYLB

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for XYLB gene from 5/15 species (see all 15 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	XYLB¹	--	xylulokinase homolog (H. influenzae)	89.05(n) 91.98(a)	609126 XM_846334.1 XP_851427.1
chimpanzee (Pan troglodytes)	XYLB¹	--	xylulokinase homolog (H. influenzae)	97.06(n) 96.44(a)	470793 XM_526176.2 XP_526176.2
cow (Bos taurus)	XYLB¹	--	xylulokinase homolog (H. influenzae)	88.26(n) 91.04(a)	515146 NM_001034483.1 NP_001029655.1
rat (Rattus norvegicus)	Xylb¹	--	xylulokinase homolog (H. influenzae)	84.83(n) 87.87(a)	316067 NM_001033704.1 NP_001028876.1
mouse (Mus musculus)	Xylb^{1, 5}	9⁵	xylulokinase homolog (H. influenzae)^{1, 5}	85.39(n)¹ 87.69(a)¹	102448¹ NM_001033209.2¹ NP_001028381.1¹ AI132223⁵ AI327421⁵ (see all 20)

About this table Species with no ortholog for XYLB

ENSEMBL Gene Tree for XYLB

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/572 NCBI SNPs in XYLB are shown (see all 572 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 196)

AB	SNP ID	Valid	Chr 3 pos	Sequence	Recs	AA Chg	Type	More	Recs	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--			--
	rs2234600^1,2	A,C,F,H	38363018(+)	`AAGCCT/GGCTTA`	1	--	ng5¹		4	EU EA WA	412
	rs580454^1,2	A,C,F,H	38361520(-)	`cagaaC/Tatttc`	1	--	ng5¹		4	EU EA WA	412
	rs4147025^1,2	A,C,F,H	38431535(-)	`ttctgG/Attcaa`	1	--	ng3¹		4	EU EA WA	414
	rs7373930^1,2	A,C,F,H	38429935(+)	`CCTCCG/ACAAAC`	1	--	ut3¹ ese³		9	NA EU EA WA	736
	rs17118^1,2	A,C,F,H	38379476(+)	`TTCGAC/ATTCTC`	1	E/D	mis¹		17	MN EA NA EU WA	2804
	rs4147024^1,2	A,C,F,H	38431668(-)	`gctttG/Attgag`	1	--	ng3¹		4	EU EA WA	410
	rs7373805^1,2	A,C,F,H	38430443(+)	`ATTCTC/TACTTT`	1	--	ut3¹ ese³		4	EU EA WA	410
	rs13074025^1,2	A,C,F,H	38430708(+)	`AGTGGC/ATCAGA`	1	--	ut3¹		7	NA EU EA WA	552
	rs2234597^1,2	C,F,H	38362625(+)	`GGGACG/AGGAAG`	1	--	ng5¹		4	EU EA WA	418
	rs13074160^1,2	A,C,F	38430654(+)	`AATACG/TCATGT`	1	--	ut3¹ ese³		3	NA	140

About this table

HapMap Linkage Disequilibrium images for XYLB (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 604049

(Possibly Related Articles in Doctor's Guide)
About This Section

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

9 PubMed articles for XYLB gene:

Genomic structure of a novel human gene (XYLB) on chromosome 3p22-->p21.3 encoding a xylulokinase-like protein. (PubMed id 9763671)^{1, 2, 3, 4} Tamari M.... Nakamura Y. (1998)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{3, 4} Ota T....Sugano S. (2004)
The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)⁴ Muzny D.M....Gibbs R.A. (2006)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)⁴ Gerhard D.S....Malek J. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)³ Strausberg R.L....Marra M.A. (2002)
Characterization of a 1200-kb genomic segment of chromosome 3p22- p21.3. (PubMed id 10231028)³ Daigo Y.... Nakamura Y. (1999)
Molecular and industrial aspects of glucose isomerase. (PubMed id 8801434)¹ Bhosale S.H....Deshpande V.V. (1996)
ntn genes determining the early steps in the divergent catabolism of 4-nitrotoluene and toluene in Pseudomonas sp. strain TW3. (PubMed id 9555884)¹ James K.D. and Williams P.A. (1998)
Identification of new members of a carbohydrate kinase-encoding gene family. (PubMed id 8521274)¹ Worley K.C....Smith R.F. (1995)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
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Entrez Gene: 9942	HGNC: 12839	AceView: XYLB	Ensembl:ENSG00000093217	euGenes: HUgn9942
ECgene: XYLB	H-InvDB: XYLB

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Licensable Technologies for XYLB
(Available from WIS Yeda, Salk, Tufts)

About This Section

(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section

Products for XYLB:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for XYLB-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for XYLB		Browse antibodies at Sigma-Aldrich
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for XYLB		Browse small molecules at Sigma-Aldrich
	"Your Favorite Gene" Pathways		feedback

	Antibodies		Primer Pairs
	Cell Culture Products		ELISAs
	Flow Cytometry Kits		Protease Activity Assays & Reagents
	Cell Selection/Detection Kits & Reagents		ELISA/Assay Development Kits & Reagents
	Multiplex/Array Assay Kits & Reagents		ELISpot Kits & Development Modules
	Recombinant & Natural Proteins

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	Custom Service for Rabbit Pab from Full-length Protein

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Antibodies for XYLB

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XYLB Gene at Home site.
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XYLB Gene

protein-coding GIFtS: 54

Aliases &
Descriptions
for XYLB

Summaries
for XYLB

Genomic Location
for XYLB

Proteins
for XYLB

Protein Domains/
Families
for XYLB

Gene Function
for XYLB

Pathways & Interactions
for XYLB

Drugs & Compounds
for XYLB

Transcripts
for XYLB

Expression
for XYLB

Orthologs
for XYLB

Paralogs
for XYLB

SNPs/Variants
for XYLB

Disorders & Mutations
for XYLB

Medical News
for XYLB

Publications
for XYLB

Search for XYLB

Genome Databases showing XYLB

Other Databases showing XYLB

Specialized Databases showing XYLB

Licensable Technologies
for XYLB

Services
for XYLB

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

XYLB Gene

protein-coding GIFtS: 54

Aliases & Descriptionsfor XYLB

Summariesfor XYLB

Genomic Locationfor XYLB

Proteinsfor XYLB

Protein Domains/Familiesfor XYLB

Gene Functionfor XYLB

Pathways & Interactionsfor XYLB

Drugs & Compoundsfor XYLB

Transcriptsfor XYLB

Expression for XYLB

Orthologsfor XYLB

Paralogsfor XYLB

SNPs/Variantsfor XYLB

Disorders & Mutationsfor XYLB

Medical Newsfor XYLB

Publicationsfor XYLB

Search for XYLB

Genome Databases showing XYLB

Other Databases showing XYLB

Specialized Databases showing XYLB

Licensable Technologiesfor XYLB

Servicesfor XYLB

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for XYLB

Summaries
for XYLB

Genomic Location
for XYLB

Proteins
for XYLB

Protein Domains/
Families
for XYLB

Gene Function
for XYLB

Pathways & Interactions
for XYLB

Drugs & Compounds
for XYLB

Transcripts
for XYLB

Expression
for XYLB

Orthologs
for XYLB

Paralogs
for XYLB

SNPs/Variants
for XYLB

Disorders & Mutations
for XYLB

Medical News
for XYLB

Publications
for XYLB

Licensable Technologies
for XYLB

Services
for XYLB