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

Gene ID: 304885, updated on 2-Nov-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, Nov 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

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

Nucleotide Protein Strain
Heading Accession and Version

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