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    Fam20b FAM20B, glycosaminoglycan xylosylkinase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304885, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Fam20bprovided by RGD
    Official Full Name
    FAM20B, glycosaminoglycan xylosylkinaseprovided by RGD
    Primary source
    RGD:1311162
    See related
    EnsemblRapid:ENSRNOG00000004337 AllianceGenome:RGD:1311162
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1311162
    Summary
    Predicted to enable phosphotransferase activity, alcohol group as acceptor. Predicted to be involved in proteoglycan biosynthetic process. Predicted to be located in cytoplasm and nucleoplasm. Predicted to colocalize with Golgi apparatus. Orthologous to human FAM20B (FAM20B glycosaminoglycan xylosylkinase). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 160.5), Kidney (RPKM 156.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Fam20b in Genome Data Viewer
    Location:
    13q22
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (71351834..71390192, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (68801663..68839979, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (74280173..74333463, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene ABL proto-oncogene 2, non-receptor tyrosine kinase Neighboring gene DNA cross-link repair 1B, pseudogene 1 Neighboring gene torsin family 3, member A Neighboring gene uncharacterized LOC134481574 Neighboring gene uncharacterized LOC134481575 Neighboring gene enolase 1 like 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. FAM20B is a kinase that phosphorylates xylose in the glycosaminoglycan-protein linkage region. Koike T, et al. Biochem J, 2009 Jun 26. PMID 19473117
    2. The Raine syndrome protein FAM20C is a Golgi kinase that phosphorylates bio-mineralization proteins. Ishikawa HO, et al. PLoS One, 2012. PMID 22900076, Free PMC Article
    3. FAM20: an evolutionarily conserved family of secreted proteins expressed in hematopoietic cells. Nalbant D, et al. BMC Genomics, 2005 Jan 27. PMID 15676076, Free PMC Article
    4. High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy. Hasson SA, et al. Nature, 2013 Dec 12. PMID 24270810, Free PMC Article
    5. Characterization of the piRNA complex from rat testes. Lau NC, et al. Science, 2006 Jul 21. PMID 16778019

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphotransferase activity, alcohol group as acceptor IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphotransferase activity, alcohol group as acceptor ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in proteoglycan biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    colocalizes_with Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    glycosaminoglycan xylosylkinase
    Names
    family with sequence similarity 20, member B
    NP_001100657.1
    XP_006250120.1
    XP_006250121.1
    XP_008767856.1
    XP_017454300.1
    XP_038946677.1
    XP_038946678.1
    XP_063128401.1

    NCBI Reference Sequences (RefSeq)

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    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_001107187.1 → NP_001100657.1  glycosaminoglycan xylosylkinase

      See identical proteins and their annotated locations for NP_001100657.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473958
      UniProtKB/TrEMBL
      A6ID16, A6ID17, D3ZUZ4
      Related
      ENSRNOP00000006018.3, ENSRNOT00000006018.5
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      71351834..71390192 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006250058.5 → XP_006250120.1  glycosaminoglycan xylosylkinase isoform X1

      See identical proteins and their annotated locations for XP_006250120.1

      UniProtKB/TrEMBL
      A6ID16, A6ID17, D3ZUZ4
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    2. XM_017598811.3 → XP_017454300.1  glycosaminoglycan xylosylkinase isoform X1

      UniProtKB/TrEMBL
      A6ID16, A6ID17, D3ZUZ4
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    3. XM_006250059.5 → XP_006250121.1  glycosaminoglycan xylosylkinase isoform X1

      See identical proteins and their annotated locations for XP_006250121.1

      UniProtKB/TrEMBL
      A6ID16, A6ID17, D3ZUZ4
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    4. XM_008769634.4 → XP_008767856.1  glycosaminoglycan xylosylkinase isoform X1

      See identical proteins and their annotated locations for XP_008767856.1

      UniProtKB/TrEMBL
      A6ID16, A6ID17, D3ZUZ4
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    5. XM_039090749.2 → XP_038946677.1  glycosaminoglycan xylosylkinase isoform X1

      UniProtKB/TrEMBL
      A6ID16, A6ID17, D3ZUZ4
      Conserved Domains (1) summary
      cd10470
      Location:188 → 394
      FAM20B_C; C-terminal putative kinase domain of FAM20B xylose kinase

    6. XM_063272331.1 → XP_063128401.1  glycosaminoglycan xylosylkinase isoform X2

      UniProtKB/TrEMBL
      A6ID17

    7. XM_039090750.2 → XP_038946678.1  glycosaminoglycan xylosylkinase isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version

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