Human Gene FAM98B (ENST00000397609.6_6) from GENCODE V47lift37
  Description: family with sequence similarity 98 member B (from RefSeq NM_173611.4)
Gencode Transcript: ENST00000397609.6_6
Gencode Gene: ENSG00000171262.11_8
Transcript (Including UTRs)
   Position: hg19 chr15:38,746,328-38,779,911 Size: 33,584 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr15:38,746,363-38,776,860 Size: 30,498 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:38,746,328-38,779,911)mRNA (may differ from genome)Protein (433 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FA98B_HUMAN
DESCRIPTION: RecName: Full=Protein FAM98B;
SUBUNIT: Component of the tRNA-splicing ligase complex.
INTERACTION: O14874:BCKDK; NbExp=1; IntAct=EBI-1043130, EBI-1046765;
SIMILARITY: Belongs to the FAM98 family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: FAM98B
Diseases sorted by gene-association score: spastic paraplegia 11, autosomal recessive (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.17 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 213.85 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -11.5035-0.329 Picture PostScript Text
3' UTR -713.703051-0.234 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018797 - Uncharacterised_FAM98

Pfam Domains:
PF10239 - Protein of unknown function (DUF2465)

ModBase Predicted Comparative 3D Structure on Q52LJ0
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGD  WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008276 protein methyltransferase activity
GO:0042802 identical protein binding

Biological Process:
GO:0006479 protein methylation
GO:0008284 positive regulation of cell proliferation
GO:0010628 positive regulation of gene expression

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0043231 intracellular membrane-bounded organelle
GO:0072669 tRNA-splicing ligase complex


-  Descriptions from all associated GenBank mRNAs
  AK095745 - Homo sapiens cDNA FLJ38426 fis, clone FEBRA2012507.
BC093898 - Homo sapiens family with sequence similarity 98, member B, mRNA (cDNA clone MGC:120933 IMAGE:7939743), complete cds.
BC035600 - Homo sapiens family with sequence similarity 98, member B, mRNA (cDNA clone IMAGE:4430622).
BC045690 - Homo sapiens cDNA clone IMAGE:5301489.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY-7803 - tRNA splicing II

Reactome (by CSHL, EBI, and GO)

Protein Q52LJ0 (Reactome details) participates in the following event(s):

R-HSA-5696816 tRNA ligase complex ligates tRNA exons
R-HSA-6784531 tRNA processing in the nucleus
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8MUW5, ENST00000397609.1, ENST00000397609.2, ENST00000397609.3, ENST00000397609.4, ENST00000397609.5, FA98B_HUMAN, NM_173611, Q52LJ0, Q8N935, uc318zdn.1, uc318zdn.2
UCSC ID: ENST00000397609.6_6
RefSeq Accession: NM_173611.4
Protein: Q52LJ0 (aka FA98B_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.