Aliases for FAM98B Gene

Aliases for FAM98B Gene

  • Family With Sequence Similarity 98 Member B 2 3 5
  • Protein FAM98B 3 4
  • Family With Sequence Similarity 98, Member B 2
  • FLJ38426 2
  • FAM98B 5

External Ids for FAM98B Gene

Previous GeneCards Identifiers for FAM98B Gene

  • GC15P036534
  • GC15P038746
  • GC15P015591

Summaries for FAM98B Gene

GeneCards Summary for FAM98B Gene

FAM98B (Family With Sequence Similarity 98 Member B) is a Protein Coding gene. Diseases associated with FAM98B include Spastic Paraplegia 11, Autosomal Recessive and Chromosome 22Q11.2 Duplication Syndrome. Among its related pathways are tRNA processing and Gene Expression. An important paralog of this gene is FAM98A.

UniProtKB/Swiss-Prot Summary for FAM98B Gene

  • Positively stimulates PRMT1-induced protein arginine dimethylated arginine methylation (PubMed:28040436). Promotes colorectal cancer cell malignancy (PubMed:28040436).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for FAM98B Gene

Genomics for FAM98B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for FAM98B 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
GH15J038453 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.6 574 2.6 BCLAF1 SP1 ZNF207 NCOR1 MYC ZNF600 SIX5 ZNF580 POLR2A BRCA1 FAM98B LINC02694 RASGRP1 piR-53522-002
GH15J038071 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.5 -381.3 -381269 3.1 ZNF600 SSRP1 ATF2 KLF9 ZNF10 NFIC POLR2A ZIC2 MXD4 CTCF HSALNG0105101 LINC01852 lnc-TMCO5A-7 SPRED1 FAM98B TMCO5A
GH15J038695 Promoter/Enhancer 1.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.6 +243.4 243374 6.2 BCLAF1 ZNF654 CTCF REST TARDBP TRIM22 RAD21 IRF4 SMC3 ZNF316 RASGRP1 FAM98B LINC02694 SPRED1 5MWI_A-048 HQ292120 THBS1
GH15J038531 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 10.4 +85.1 85073 18.8 MYC ZNF600 JUND ZNF592 ATF2 REST CEBPB BHLHE40 FEZF1 MNT RASGRP1 LINC02694 FAM98B RF00019-048 HSALNG0105126 ENSG00000259598
GH15J038682 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 10.5 +231.9 231874 10.4 ZNF654 CTCF REST TRIM22 ZNF513 MAFF RAD21 SMC3 ZNF316 EBF1 RASGRP1 FAM98B LINC02694 HSALNG0105129-001 piR-50443-126 LOC105370775 THBS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FAM98B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for FAM98B

Top Transcription factor binding sites by QIAGEN in the FAM98B gene promoter:
  • CREB
  • deltaCREB
  • E2F
  • E2F-1
  • E47
  • En-1
  • HEN1
  • ITF-2
  • Tal-1
  • Tal-1beta

Genomic Locations for FAM98B Gene

Latest Assembly
chr15:38,454,127-38,487,710
(GRCh38/hg38)
Size:
33,584 bases
Orientation:
Plus strand

Previous Assembly
chr15:38,746,328-38,779,911
(GRCh37/hg19 by Entrez Gene)
Size:
33,584 bases
Orientation:
Plus strand

chr15:38,746,328-38,779,911
(GRCh37/hg19 by Ensembl)
Size:
33,584 bases
Orientation:
Plus strand

Genomic View for FAM98B Gene

Genes around FAM98B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FAM98B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FAM98B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FAM98B Gene

Proteins for FAM98B Gene

  • Protein details for FAM98B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q52LJ0-FA98B_HUMAN
    Recommended name:
    Protein FAM98B
    Protein Accession:
    Q52LJ0
    Secondary Accessions:
    • A8MUW5
    • Q8N935

    Protein attributes for FAM98B Gene

    Size:
    433 amino acids
    Molecular mass:
    45547 Da
    Quaternary structure:
    • Homodimer (PubMed:28040436). Component of the tRNA-splicing ligase complex (PubMed:21311021, PubMed:24870230). Interacts with FAM98A (PubMed:28040436).
    Miscellaneous:
    • [Isoform 1]: Dubious isoform due to intron retention.

    Alternative splice isoforms for FAM98B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FAM98B Gene

Post-translational modifications for FAM98B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FAM98B Gene

No data available for DME Specific Peptides for FAM98B Gene

Domains & Families for FAM98B Gene

Gene Families for FAM98B Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for FAM98B Gene

InterPro:

Suggested Antigen Peptide Sequences for FAM98B Gene

GenScript: Design optimal peptide antigens:
  • Protein FAM98B (FA98B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q52LJ0

UniProtKB/Swiss-Prot:

FA98B_HUMAN :
  • Belongs to the FAM98 family.
Family:
  • Belongs to the FAM98 family.
genes like me logo Genes that share domains with FAM98B: view

Function for FAM98B Gene

Molecular function for FAM98B Gene

UniProtKB/Swiss-Prot Function:
Positively stimulates PRMT1-induced protein arginine dimethylated arginine methylation (PubMed:28040436). Promotes colorectal cancer cell malignancy (PubMed:28040436).

Phenotypes From GWAS Catalog for FAM98B Gene

Gene Ontology (GO) - Molecular Function for FAM98B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 28040436
GO:0008276 protein methyltransferase activity IMP 28040436
GO:0042802 identical protein binding IDA 28040436
genes like me logo Genes that share ontologies with FAM98B: view
genes like me logo Genes that share phenotypes with FAM98B: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FAM98B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for FAM98B Gene

Localization for FAM98B Gene

Subcellular locations from UniProtKB/Swiss-Prot for FAM98B Gene

Nucleus. Cytoplasm.

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 FAM98B gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FAM98B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 24608264
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 18445686
GO:0043231 intracellular membrane-bounded organelle IDA --
GO:0072669 tRNA-splicing ligase complex IDA 21311021
genes like me logo Genes that share ontologies with FAM98B: view

Pathways & Interactions for FAM98B Gene

PathCards logo

SuperPathways for FAM98B Gene

genes like me logo Genes that share pathways with FAM98B: view

Pathways by source for FAM98B Gene

3 Reactome pathways for FAM98B Gene

Gene Ontology (GO) - Biological Process for FAM98B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation TAS --
GO:0006479 protein methylation IMP 28040436
GO:0008284 positive regulation of cell proliferation IMP 28040436
GO:0010628 positive regulation of gene expression IMP 28040436
genes like me logo Genes that share ontologies with FAM98B: view

No data available for SIGNOR curated interactions for FAM98B Gene

Drugs & Compounds for FAM98B Gene

No Compound Related Data Available

Transcripts for FAM98B Gene

mRNA/cDNA for FAM98B Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FAM98B

Alternative Splicing Database (ASD) splice patterns (SP) for FAM98B Gene

No ASD Table

Relevant External Links for FAM98B Gene

GeneLoc Exon Structure for
FAM98B

Expression for FAM98B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for FAM98B Gene

Protein differential expression in normal tissues from HIPED for FAM98B Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for FAM98B Gene



Protein tissue co-expression partners for FAM98B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for FAM98B

SOURCE GeneReport for Unigene cluster for FAM98B Gene:

Hs.744003

mRNA Expression by UniProt/SwissProt for FAM98B Gene:

Q52LJ0-FA98B_HUMAN
Tissue specificity: Expressed strongly in colorectal cancer tissues compared to wild-type colon samples (at protein level) (PubMed:28040436). Expressed strongly in colorectal cancer tissues compared to wild-type colon samples (PubMed:28040436).

Evidence on tissue expression from TISSUES for FAM98B Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with FAM98B: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for FAM98B Gene

Orthologs for FAM98B Gene

This gene was present in the common ancestor of animals.

Orthologs for FAM98B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia FAM98B 29 30
  • 99.67 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia FAM98B 29 30
  • 92.12 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia FAM98B 29 30
  • 91.78 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Fam98b 29 16 30
  • 86.26 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia FAM98B 30
  • 85 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Fam98b 29
  • 84.78 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia FAM98B 30
  • 54 (a)
OneToOne
Chicken
(Gallus gallus)
Aves FAM98B 29 30
  • 76.52 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia FAM98B 30
  • 67 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia fam98b 29
  • 64.87 (n)
Zebrafish
(Danio rerio)
Actinopterygii fam98b 30
  • 46 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG5913 30
  • 32 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea tag-322 30
  • 26 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 43 (a)
OneToMany
Species where no ortholog for FAM98B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 Vase (Ciona intestinalis)
  • 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)

Evolution for FAM98B Gene

ENSEMBL:
Gene Tree for FAM98B (if available)
TreeFam:
Gene Tree for FAM98B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FAM98B: view image
Alliance of Genome Resources:
Additional Orthologs for FAM98B

Paralogs for FAM98B Gene

Paralogs for FAM98B Gene

(2) SIMAP similar genes for FAM98B Gene using alignment to 2 proteins:

  • FA98B_HUMAN
  • H0YNA1_HUMAN

Pseudogenes.org Pseudogenes for FAM98B Gene

genes like me logo Genes that share paralogs with FAM98B: view

Variants for FAM98B Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for FAM98B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for FAM98B Gene

Variant ID Type Subtype PubMed ID
nsv1500 CNV deletion 18451855

Variation tolerance for FAM98B Gene

Residual Variation Intolerance Score: 39.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.68; 32.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FAM98B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
FAM98B
Leiden Open Variation Database (LOVD)
FAM98B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for FAM98B Gene

Disorders for FAM98B Gene

MalaCards: The human disease database

(2) MalaCards diseases for FAM98B Gene - From: COP

Disorder Aliases PubMed IDs
spastic paraplegia 11, autosomal recessive
  • spg11
chromosome 22q11.2 duplication syndrome
  • chromosome 22q11.2 microduplication syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for FAM98B

genes like me logo Genes that share disorders with FAM98B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FAM98B Gene

Publications for FAM98B Gene

  1. hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex. (PMID: 24608264) Pérez-González A … Nieto A (PloS one 2014) 2 3 4
  2. FAM98A associates with DDX1-C14orf166-FAM98B in a novel complex involved in colorectal cancer progression. (PMID: 28040436) Akter KA … Senga T (The international journal of biochemistry & cell biology 2017) 3 4
  3. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. (PMID: 24870230) Popow J … Martinez J (Nature 2014) 3 4
  4. HSPC117 is the essential subunit of a human tRNA splicing ligase complex. (PMID: 21311021) Popow J … Martinez J (Science (New York, N.Y.) 2011) 3 4
  5. EML3 is a nuclear microtubule-binding protein required for the correct alignment of chromosomes in metaphase. (PMID: 18445686) Tegha-Dunghu J … Gruss OJ (Journal of cell science 2008) 3 4

Products for FAM98B Gene

Sources for FAM98B Gene