Gene explorer

Glossary

• Isoform

  One of several transcripts produced from a single gene by alternative transcription start sites, alternative 3' ends or alternative splicing. Isoforms of a gene share some exons and differ in others.

• MANE Select

  The single transcript of a human gene that RefSeq and Ensembl jointly designate as the reference, with an identical sequence in both annotation sets. It is the default transcript for display in genome browsers and key genomic resources. MANE Select is defined for human only. Mouse and rat have RefSeq Select and Ensembl canonical transcripts instead, and the two may differ.

• Spliced length

  The length of the mature transcript after the introns are removed. It is typically much shorter than the genomic span of the gene, which includes the introns.

• TPM

  Transcripts per million, a unit of RNA abundance: the number of transcripts of a gene per million transcripts in a sample, normalized for transcript length. TPM compares genes within one sample. Comparing one gene's TPM between samples, datasets or methods is not direct, because the value depends on the mix of RNA in each sample.

• pLDDT

  Predicted local distance difference test, the per-residue confidence score of an AlphaFold model. Regions of high pLDDT typically correspond to well-ordered domains, and regions of low pLDDT typically correspond to flexible or disordered regions. pLDDT describes confidence in the predicted structure.

• Post-translational modification

  A modification made to a protein after translation, such as phosphorylation, acetylation, ubiquitination, glycosylation, lipidation or disulfide bond formation.

• Resolution

  A measure of the level of detail in an experimental structure, in angstroms (Å). A lower value indicates finer detail. X-ray and electron microscopy structures have a resolution. Solution NMR structures do not.

• LOEUF

  Loss-of-function observed/expected upper bound fraction, a gene constraint metric from gnomAD. It is the upper bound of the confidence interval for the ratio of observed to expected loss-of-function variants in a gene. A low value indicates fewer loss-of-function variants than expected, consistent with selection against the loss of one copy of the gene. A high value indicates that the gene tolerates such variants. LOEUF is a measure of selection in human populations.

• Ortholog

  A gene in another species that descends from the same ancestral gene, typically with the same function. Ortholog assignments can differ between databases.

• Strand

  The orientation of a gene on the chromosome, plus or minus. A gene on the minus strand is transcribed from higher to lower genomic coordinates, so exon 1 has the highest genomic position.

• Gapmer

  An antisense oligonucleotide with a central region of DNA-like nucleotides flanked on both sides by modified nucleotides. When a gapmer hybridizes to its target RNA, the central region allows RNase H1 to cleave the RNA. The flanking regions increase binding affinity and protect the oligonucleotide from nucleases. Gapmers are used for transcript knockdown, which is assessed at the RNA level. The protein level can also be measured.

• Steric block

  An oligonucleotide that hybridizes to its target RNA without recruiting RNase H, so the transcript is not cleaved. Hybridization blocks the process that would occur at the target site, such as translation initiation, splice-site recognition, or the binding of a microRNA or a protein. Because the transcript is not cleaved, the effect is assessed by the protein level, the splice product or a downstream functional readout.