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Aliases for FAM20B Gene

Aliases for FAM20B Gene

  • FAM20B, Glycosaminoglycan Xylosylkinase 2 3 5
  • Family With Sequence Similarity 20, Member B 2 3
  • Xylose Kinase 3 4
  • Glycosaminoglycan Xylosylkinase 3
  • EC 2.7.1.- 4
  • KIAA0475 4
  • Gxk1 3

External Ids for FAM20B Gene

Previous GeneCards Identifiers for FAM20B Gene

  • GC01P175593
  • GC01P176234
  • GC01P175726
  • GC01P177261
  • GC01P178995
  • GC01P150222

Summaries for FAM20B Gene

GeneCards Summary for FAM20B Gene

FAM20B (FAM20B, Glycosaminoglycan Xylosylkinase) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include kinase activity and phosphotransferase activity, alcohol group as acceptor. An important paralog of this gene is FAM20A.

UniProtKB/Swiss-Prot for FAM20B Gene

  • Responsible for the 2-O-phosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature GAG chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG-protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-O-phosphorylation may influence the catalytic activity of B3GAT3 (GlcAT-I) which completes the precursor tetrasaccharide of GAG-protein linkage regions on which the repeating disaccharide region is synthesized.

Gene Wiki entry for FAM20B Gene

Additional gene information for FAM20B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FAM20B Gene

Genomics for FAM20B Gene

GeneHancer (GH) Regulatory Elements for FAM20B Gene

Promoters and enhancers for FAM20B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J179023 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 663.3 +0.1 89 3.9 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 FAM20B TOR3A RALGPS2 CEP350 AXDND1 GC01M179035 GC01P179007
GH01J179016 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 663.3 -8.0 -7971 3.2 PKNOX1 CLOCK SMAD1 ARID4B NEUROD1 SIN3A YY1 FOS DEK SP5 FAM20B TOR3A C1orf220 GC01P179007
GH01J179047 Enhancer 1.2 ENCODE dbSUPER 15.8 +21.7 21744 1.3 PKNOX1 SMAD1 ARNT POLR2B ZNF766 E2F8 FOS REST ZNF592 MEF2D FAM20B TOR3A RPS26P16 GC01M179070
GH01J179060 Enhancer 0.9 dbSUPER 16.6 +35.3 35286 1.8 HDGF PKNOX1 ATF1 ARNT NCOA2 TCF12 ZNF766 ATF7 CAVIN1 NCOA1 FAM20B TOR3A GC01M179070 RPS26P16
GH01J179046 Enhancer 1 ENCODE dbSUPER 14.1 +20.9 20933 0.3 NFRKB TCF12 ZNF766 E2F8 EGR1 SMARCA5 ELF1 ZEB2 ZNF148 ATF4 FAM20B TOR3A RPS26P16 GC01M179070
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FAM20B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FAM20B gene promoter:
  • c-Ets-1
  • GCNF-2
  • GCNF-1
  • GCNF
  • AML1a
  • GATA-3
  • GATA-1
  • GATA-2
  • Evi-1
  • POU3F2 (N-Oct-5a)

Genomic Locations for FAM20B Gene

Genomic Locations for FAM20B Gene
chr1:179,025,804-179,076,567
(GRCh38/hg38)
Size:
50,764 bases
Orientation:
Plus strand
chr1:178,994,939-179,045,702
(GRCh37/hg19)
Size:
50,764 bases
Orientation:
Plus strand

Genomic View for FAM20B Gene

Genes around FAM20B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FAM20B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FAM20B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FAM20B Gene

Proteins for FAM20B Gene

  • Protein details for FAM20B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75063-XYLK_HUMAN
    Recommended name:
    Glycosaminoglycan xylosylkinase
    Protein Accession:
    O75063
    Secondary Accessions:
    • Q5W0C3
    • Q5W0C4

    Protein attributes for FAM20B Gene

    Size:
    409 amino acids
    Molecular mass:
    46432 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA32320.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for FAM20B Gene

Post-translational modifications for FAM20B Gene

  • Glycosylation at isoforms=193
  • Modification sites at PhosphoSitePlus

Other Protein References for FAM20B Gene

No data available for DME Specific Peptides for FAM20B Gene

Domains & Families for FAM20B Gene

Gene Families for FAM20B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for FAM20B Gene

Suggested Antigen Peptide Sequences for FAM20B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O75063

UniProtKB/Swiss-Prot:

XYLK_HUMAN :
  • Belongs to the FAM20 family.
Family:
  • Belongs to the FAM20 family.
genes like me logo Genes that share domains with FAM20B: view

Function for FAM20B Gene

Molecular function for FAM20B Gene

UniProtKB/Swiss-Prot Function:
Responsible for the 2-O-phosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature GAG chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG-protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-O-phosphorylation may influence the catalytic activity of B3GAT3 (GlcAT-I) which completes the precursor tetrasaccharide of GAG-protein linkage regions on which the repeating disaccharide region is synthesized.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + D-xylose = ADP + D-xylose 2-phosphate.

Enzyme Numbers (IUBMB) for FAM20B Gene

Phenotypes From GWAS Catalog for FAM20B Gene

Gene Ontology (GO) - Molecular Function for FAM20B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0005515 protein binding IPI 25331875
GO:0005524 ATP binding IEA --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with FAM20B: view
genes like me logo Genes that share phenotypes with FAM20B: view

Animal Model Products

  • Taconic Biosciences Mouse Models for FAM20B

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for FAM20B Gene

Localization for FAM20B Gene

Subcellular locations from UniProtKB/Swiss-Prot for FAM20B Gene

Golgi apparatus membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FAM20B gene
Compartment Confidence
nucleus 5
golgi apparatus 5
extracellular 4
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FAM20B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005615 extracellular space IEA,IBA --
GO:0005654 nucleoplasm IDA --
GO:0005794 Golgi apparatus IEA,IDA 19473117
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with FAM20B: view

Pathways & Interactions for FAM20B Gene

SuperPathways for FAM20B Gene

No Data Available

Gene Ontology (GO) - Biological Process for FAM20B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 NOT protein phosphorylation IBA --
GO:0016310 phosphorylation IEA --
GO:0030166 proteoglycan biosynthetic process IBA --
GO:1903955 positive regulation of protein targeting to mitochondrion IMP --
genes like me logo Genes that share ontologies with FAM20B: view

No data available for Pathways by source and SIGNOR curated interactions for FAM20B Gene

Drugs & Compounds for FAM20B Gene

(2) Drugs for FAM20B Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
xylose Approved Pharma 0
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(1) Additional Compounds for FAM20B Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with FAM20B: view

Transcripts for FAM20B Gene

mRNA/cDNA for FAM20B Gene

Unigene Clusters for FAM20B Gene

Family with sequence similarity 20, member B:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FAM20B Gene

No ASD Table

Relevant External Links for FAM20B Gene

GeneLoc Exon Structure for
FAM20B
ECgene alternative splicing isoforms for
FAM20B

Expression for FAM20B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FAM20B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FAM20B Gene

This gene is overexpressed in Breast (22.8), Peripheral blood mononuclear cells (15.3), Testis (7.7), and Placenta (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for FAM20B Gene



Protein tissue co-expression partners for FAM20B Gene

NURSA nuclear receptor signaling pathways regulating expression of FAM20B Gene:

FAM20B

SOURCE GeneReport for Unigene cluster for FAM20B Gene:

Hs.5737

mRNA Expression by UniProt/SwissProt for FAM20B Gene:

O75063-XYLK_HUMAN
Tissue specificity: Widely expressed. Strongly expressed in pancreas, spleen and fetal liver.

Evidence on tissue expression from TISSUES for FAM20B Gene

  • Nervous system(4.4)
  • Eye(4.2)
genes like me logo Genes that share expression patterns with FAM20B: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for FAM20B Gene

Orthologs for FAM20B Gene

This gene was present in the common ancestor of animals.

Orthologs for FAM20B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FAM20B 34 33
  • 99.51 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia FAM20B 34
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia FAM20B 34 33
  • 94.55 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia FAM20B 34
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia FAM20B 34 33
  • 92.83 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Fam20b 16 34 33
  • 90.79 (n)
rat
(Rattus norvegicus)
Mammalia Fam20b 33
  • 89.81 (n)
chicken
(Gallus gallus)
Aves FAM20B 34 33
  • 83.78 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FAM20B 34
  • 94 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia fam20b 33
  • 73.11 (n)
MGC75786 33
zebrafish
(Danio rerio)
Actinopterygii fam20b 34 33
  • 70.1 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG3631 34 33
  • 50.36 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001051 33
  • 47.65 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9012 34
  • 47 (a)
OneToOne
Cin.6706 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6706 33
Species where no ortholog for FAM20B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for FAM20B Gene

ENSEMBL:
Gene Tree for FAM20B (if available)
TreeFam:
Gene Tree for FAM20B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FAM20B: view image

Paralogs for FAM20B Gene

Paralogs for FAM20B Gene

(3) SIMAP similar genes for FAM20B Gene using alignment to 1 proteins:

  • XYLK_HUMAN

Pseudogenes.org Pseudogenes for FAM20B Gene

genes like me logo Genes that share paralogs with FAM20B: view

Variants for FAM20B Gene

Sequence variations from dbSNP and Humsavar for FAM20B Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000005619 -- 179,035,749(+) A/G intron_variant
rs1000094800 -- 179,047,724(+) A/T intron_variant
rs1000102718 -- 179,067,556(+) A/G intron_variant
rs1000146420 -- 179,057,906(+) T/C intron_variant
rs1000257251 -- 179,051,496(+) G/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for FAM20B Gene

Variant ID Type Subtype PubMed ID
nsv3721 CNV insertion 18451855
nsv946520 CNV duplication 23825009

Variation tolerance for FAM20B Gene

Residual Variation Intolerance Score: 16.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.32; 26.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FAM20B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
FAM20B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FAM20B Gene

Disorders for FAM20B Gene

Additional Disease Information for FAM20B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for FAM20B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for FAM20B Gene

Publications for FAM20B Gene

  1. FAM20B is a kinase that phosphorylates xylose in the glycosaminoglycan-protein linkage region. (PMID: 19473117) Koike T … Kitagawa H (The Biochemical journal 2009) 2 3 4 58
  2. FAM20: an evolutionarily conserved family of secreted proteins expressed in hematopoietic cells. (PMID: 15676076) Nalbant D … Williams SC (BMC genomics 2005) 3 4 22 58
  3. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PMID: 9455484) Seki N … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for FAM20B Gene

Sources for FAM20B Gene

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