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Glossary

Original terms

  • AS affecting protein function: Alternative splicing which cause functional annotation changes such as protein motif, GO, subceller localization signal and transmembrane domain.
  • Bridged: One of the complex AS patterns. Two transcripts were arrayed tandemly without sharing any exons and another transcript 'bridged' them, sharing at least some of its exons with both of them and also sharing the same reading frame to their ORFs. See Complex AS pattern.
  • Complex AS pattern: Phenomenon which produces totally different proteins by alternative splicing from same locus. We identified three patterns such as bridged, nested and multiple CDS. See Complex AS pattern.
  • Conserved AS: Alternative splicing conserved between human and other species by transcript level. In concrete terms, it means that two or more different ESV pairs (or clusters) exist in the human locus. See Scheme of genomic comparison.
  • Equally-spliced variant (ESV): Human and other species' RASV pair which consists of only transcript-conserved exons. See Scheme of genomic comparison.
  • Genome-conserved: In exon, the full-length or ORF of human exon is mapped on human-other species genome alignment with over threshold (Coverange=70% and Identity=60%) but not mapped or mapped with under the threshold on the other species counterpart exon. In transcript, non-conserved exons are nothing and at least one genome-conserved exon exists. See Scheme of genomic comparison.
  • H-Invitational: The human full-length cDNA annotation meeting. The aims were collecting information regarding human full-lengh cDNAs and annotating them by biologists invited from all over the world. It held two times in Tokyo, Japan in 2002 and 2003.
  • HIT: Transcript ID used by H-InvDB. Same HIT ID with different suffix indicates same sequences mapped on different genomic location.
  • HIX: Locus ID used by H-InvDB.
  • Multiple CDS: One of the complex AS patterns. Different ORFs >200 bp in length were annotated independently for different transcripts sharing at least some of the exons but not sharing any reading frame. See Complex AS pattern.
  • Nested: One of the complex AS patterns. ORF region of one transcript was not shared with another transcript. See Complex AS pattern.
  • Non-conserved: In exon, the full-length or ORF of human exon is not mapped on human-other species genome alignment or mapped on it with under threshold (Coverange=70% and Identity=60%). In transcript, at least one non-conserved exon exists. See Scheme of genomic comparison.
  • Other ASV: AS variants which are not representatives (RASVs).
  • Representative AS variant (RASV): A representative among AS variants whose exon structures are same. See Flowchart of RASV decision.
  • Transcript-conserved: In exon, the full-length or ORF of human exon is mapped on human-other species genome alignment with over threshold (Coverange=70% and Identity=60%) and mapped on the other species counterpart exon with over the same threshold. In transcript, all exons are transcript-conserved ones. See Scheme of genomic comparison.
  • Truncated transcript: Transcripts which do not seem to be full-length. See Scheme of truncated transcript decision.

General terms

  • Alternative splicing (AS): Phenomenon in which different combinations of exons are spliced to produce distinct transcripts.
  • Alternative 3' splice: One of basic AS patterns. See Scheme of RASV decision.
  • Alternative 5' splice: One of basic AS patterns. See Scheme of RASV decision.
  • Alternative first exon: AS pattern relating transcription initiation. See Scheme of RASV decision.
  • Alternative last exon: AS pattern relating transcription termination. See Scheme of RASV decision.
  • Cassette exon: One of basic AS patterns. See Scheme of RASV decision.
  • CDS: Abbreviation of coding sequence.
  • ESE: Abbreviation of exonic splicing enhancer.
  • ESS: Abbreviation of exonic splicing silencer.
  • Full-length cDNA: Transcript whose 5' end was validated by Oligo-capping, CAP-trapper and so on.
  • GO: Abbreviation of Gene ontology.
  • ISE: Abbreviation of intronic splicing enhancer.
  • ISS: Abbreviation of intronic splicing silencer.
  • Mutually exclusive exon: One of basic AS patterns. See Scheme of RASV decision.
  • NAGNAG: 3' splice-sites of exon. Although N indicates any nucleotides, the appearance frequency is biased. There are E and I types. See NAGNAG acceptor.
  • ncRNA: Abbreviation of non-coding RNA.
  • NMD: Abbreviation of nonsense-mediated mRNA decay. Phenomenon that mRNA whose termination codon (pre-mature termination codon, PTC) was located at more than 55 bp upstream of the last exon-exon junction was degraded.
  • ORF: Abbreviation of open reading frame.
  • Protein motif: Functional amino acid sequences within protein.
  • PTC: Abbreviation of premature termination codon.
  • Retained intron: One of basic AS patterns. See Scheme of RASV decision.
  • Retrotransposon: Genomic elements which can duplicate themselves by reverse-transcription. There are two types such as LTR and Non-LTR (LINE and SINE). Alu is one of the SINE.
  • SNP: Abbreviation of single nucleotide polymorphism.
  • Splice-site sequences: GT-AG is dominant splice-site sequences of intron in metazoan. There are two minor types of splice-site sequences such as GC-AG and AT-AC. All three types are recognized by U2-type spliceosomes containing U1, U2, U4, U5 and U6 snRNPs. AT-AC and GT-AG are recognized by U12-type spliceosomes containing U11, U12, U4atac, U5 and U6atac snRNPs.
  • Subcellular localization signal (Subcell): Distinguishing amino acid sequences of protein located in specified cellular fraction.
  • Transmembrane domain (TMD): The helix structure part of the transmembrane protein.
  • UTR: Abbreviation of untranslated region.