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    XYLB xylulokinase [ Homo sapiens (human) ]

    Gene ID: 9942, updated on 3-Dec-2024

    Summary

    Official Symbol
    XYLBprovided by HGNC
    Official Full Name
    xylulokinaseprovided by HGNC
    Primary source
    HGNC:HGNC:12839
    See related
    Ensembl:ENSG00000093217 MIM:604049; AllianceGenome:HGNC:12839
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    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]
    Expression
    Broad expression in liver (RPKM 5.0), kidney (RPKM 3.6) and 18 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See XYLB in Genome Data Viewer
    Location:
    3p22.2
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38346785..38453041)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38352536..38459118)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38388276..38468677)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 22 member 14 Neighboring gene RNA, U6 small nuclear 235, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38358039-38358575 Neighboring gene DLEC1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38388053-38388884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38388885-38389716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38415461-38415962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38447285-38447785 Neighboring gene MPRA-validated peak4613 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38494963-38495462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14212 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38496067-38496650 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:38496651-38497235 Neighboring gene ACVR2B antisense RNA 1 Neighboring gene activin A receptor type 2B Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:38518043-38518542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19686 Neighboring gene exo/endonuclease G Neighboring gene DDT pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genetic determinants of P wave duration and PR segment.
    EBI GWAS Catalog
    Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10343, FLJ12539, FLJ22075

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables D-xylulokinase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables D-xylulokinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables D-xylulokinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    xylulose kinase
    Names
    D-xylulokinase
    xylulokinase homolog (H. influenzae)
    NP_001336107.1
    NP_001336108.1
    NP_001336109.1
    NP_005099.2
    XP_011532627.1
    XP_011532629.1
    XP_011532630.1
    XP_011532631.1
    XP_011532632.1
    XP_016863085.1
    XP_016863086.1
    XP_024309618.1
    XP_047305337.1
    XP_047305338.1
    XP_047305339.1
    XP_047305340.1
    XP_054204638.1
    XP_054204639.1
    XP_054204640.1
    XP_054204641.1
    XP_054204642.1
    XP_054204643.1
    XP_054204644.1
    XP_054204645.1
    XP_054204646.1
    XP_054204647.1
    XP_054204648.1
    XP_054204649.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001349178.2NP_001336107.1  xylulose kinase isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AP006191, AP006193
      UniProtKB/TrEMBL
      A0A3B3IRM4
      Conserved Domains (1) summary
      cd07776
      Location:9479
      FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
    2. NM_001349179.2NP_001336108.1  xylulose kinase isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate 5' exons and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus and has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AP006191, AP006193
      Conserved Domains (1) summary
      cl17037
      Location:1342
      NBD_sugar-kinase_HSP70_actin; Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily
    3. NM_001349180.2NP_001336109.1  xylulose kinase isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an alternate exon in place of most of the 3' exons compared to variant 1. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AP006193
      Consensus CDS
      CCDS87062.1
      UniProtKB/TrEMBL
      C9J0N9
      Related
      ENSP00000412282.1, ENST00000427323.5
      Conserved Domains (1) summary
      cl17037
      Location:962
      NBD_sugar-kinase_HSP70_actin; Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily
    4. NM_005108.4NP_005099.2  xylulose kinase isoform 2

      See identical proteins and their annotated locations for NP_005099.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AP006191, AP006193
      Consensus CDS
      CCDS2678.1
      UniProtKB/Swiss-Prot
      B2RAW4, B4DDT2, B9EH64, O75191
      UniProtKB/TrEMBL
      A0A3B3IRM4
      Related
      ENSP00000207870.3, ENST00000207870.8
      Conserved Domains (2) summary
      PLN02669
      Location:11535
      PLN02669; xylulokinase
      cd07776
      Location:9479
      FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases

    RNA

    1. NR_146068.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two alternate 5' exons compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AP006191, AP006193

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      38346785..38453041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534327.3XP_011532629.1  xylulose kinase isoform X5

      UniProtKB/TrEMBL
      A0A3B3IRM4
      Conserved Domains (2) summary
      cd07776
      Location:9479
      FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
      COG1070
      Location:10504
      XylB; Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]
    2. XM_011534329.3XP_011532631.1  xylulose kinase isoform X7

      UniProtKB/TrEMBL
      A0A3B3IRM4
      Conserved Domains (2) summary
      cd07776
      Location:9479
      FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
      COG1070
      Location:10520
      XylB; Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]
    3. XM_011534328.4XP_011532630.1  xylulose kinase isoform X6

      UniProtKB/TrEMBL
      A0A3B3IRM4
      Conserved Domains (2) summary
      cd07776
      Location:9479
      FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
      COG1070
      Location:10504
      XylB; Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]
    4. XM_011534330.4XP_011532632.1  xylulose kinase isoform X8

      UniProtKB/TrEMBL
      A0A3B3IRM4
      Conserved Domains (2) summary
      PLN02669
      Location:11516
      PLN02669; xylulokinase
      cd07776
      Location:9479
      FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
    5. XM_011534325.4XP_011532627.1  xylulose kinase isoform X1

      Conserved Domains (5) summary
      cd05482
      Location:678764
      HIV_retropepsin_like; Retropepsins, pepsin-like aspartate proteases
      smart00443
      Location:789822
      G_patch; glycine rich nucleic binding domain
      cd07776
      Location:9479
      FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
      COG1070
      Location:10504
      XylB; Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]
      cl00493
      Location:582658
      trimeric_dUTPase; Trimeric dUTP diphosphatases
    6. XM_047449383.1XP_047305339.1  xylulose kinase isoform X9

      UniProtKB/TrEMBL
      A0A3B3IRM4
      Related
      ENSP00000496840.1, ENST00000650590.1
    7. XM_047449384.1XP_047305340.1  xylulose kinase isoform X11

    8. XM_024453850.2XP_024309618.1  xylulose kinase isoform X10

      Conserved Domains (1) summary
      cd07776
      Location:1413
      FGGY_D-XK_euk; eukaryotic D-xylulose kinases; a subfamily of the FGGY family of carbohydrate kinases
    9. XM_017007596.2XP_016863085.1  xylulose kinase isoform X2

    10. XM_047449382.1XP_047305338.1  xylulose kinase isoform X3

    11. XM_047449381.1XP_047305337.1  xylulose kinase isoform X2

    12. XM_017007597.2XP_016863086.1  xylulose kinase isoform X4

    RNA

    1. XR_001740394.3 RNA Sequence

    2. XR_001740393.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      38352536..38459118
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348668.1XP_054204643.1  xylulose kinase isoform X5

      UniProtKB/TrEMBL
      A0A3B3IRM4
    2. XM_054348670.1XP_054204645.1  xylulose kinase isoform X7

      UniProtKB/TrEMBL
      A0A3B3IRM4
    3. XM_054348669.1XP_054204644.1  xylulose kinase isoform X6

      UniProtKB/TrEMBL
      A0A3B3IRM4
    4. XM_054348671.1XP_054204646.1  xylulose kinase isoform X8

      UniProtKB/TrEMBL
      A0A3B3IRM4
    5. XM_054348663.1XP_054204638.1  xylulose kinase isoform X1

    6. XM_054348672.1XP_054204647.1  xylulose kinase isoform X9

      UniProtKB/TrEMBL
      A0A3B3IRM4
    7. XM_054348674.1XP_054204649.1  xylulose kinase isoform X11

    8. XM_054348673.1XP_054204648.1  xylulose kinase isoform X10

    9. XM_054348666.1XP_054204641.1  xylulose kinase isoform X2

    10. XM_054348665.1XP_054204640.1  xylulose kinase isoform X3

    11. XM_054348664.1XP_054204639.1  xylulose kinase isoform X2

    12. XM_054348667.1XP_054204642.1  xylulose kinase isoform X4

    RNA

    1. XR_008486878.1 RNA Sequence

    2. XR_008486877.1 RNA Sequence